95 results match your criteria Acta crystallographica. Section D Biological crystallography[Journal]


On the accuracy of unit-cell parameters in protein crystallography.

Acta Crystallogr D Biol Crystallogr 2015 Nov 31;71(Pt 11):2217-26. Epub 2015 Oct 31.

Protein Structure Section, MCL, National Cancer Institute, Frederick, MD 21702, USA.

The availability in the Protein Data Bank (PDB) of a number of structures that are presented in space group P1 but in reality possess higher symmetry allowed the accuracy and precision of the unit-cell parameters of the crystals of macromolecules to be evaluated. In addition, diffraction images from crystals of several proteins, previously collected as part of in-house projects, were processed independently with three popular software packages. An analysis of the results, augmented by published serial crystallography data, suggests that the apparent precision of the presentation of unit-cell parameters in the PDB to three decimal points is not justified, since these parameters are subject to errors of not less than 0. Read More

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http://dx.doi.org/10.1107/S1399004715015503DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4631477PMC
November 2015
2 Reads

Structure of RC1339/APRc from Rickettsia conorii, a retropepsin-like aspartic protease.

Acta Crystallogr D Biol Crystallogr 2015 Oct 30;71(Pt 10):2109-18. Epub 2015 Sep 30.

Protein Structure Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA.

The crystal structures of two constructs of RC1339/APRc from Rickettsia conorii, consisting of either residues 105-231 or 110-231 followed by a His tag, have been determined in three different crystal forms. As predicted, the fold of a monomer of APRc resembles one-half of the mandatory homodimer of retroviral pepsin-like aspartic proteases (retropepsins), but the quaternary structure of the dimer of APRc differs from that of the canonical retropepsins. The observed dimer is most likely an artifact of the expression and/or crystallization conditions since it cannot support the previously reported enzymatic activity of this bacterial aspartic protease. Read More

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http://dx.doi.org/10.1107/S1399004715013905DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4601372PMC
October 2015
15 Reads

Crystallography and chemistry should always go together: a cautionary tale of protein complexes with cisplatin and carboplatin.

Acta Crystallogr D Biol Crystallogr 2015 Sep 28;71(Pt 9):1965-79. Epub 2015 Aug 28.

Protein Structure Section, MCL, National Cancer Institute, Frederick, MD 21702, USA.

The anticancer activity of platinum-containing drugs such as cisplatin and carboplatin is considered to primarily arise from their interactions with nucleic acids; nevertheless, these drugs, or the products of their hydrolysis, also bind to proteins, potentially leading to the known side effects of the treatments. Here, over 40 crystal structures deposited in the Protein Data Bank (PDB) of cisplatin and carboplatin complexes of several proteins were analysed. Significant problems of either a crystallographic or a chemical nature were found in most of the presented atomic models and they could be traced to less or more serious deficiencies in the data-collection and refinement procedures. Read More

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http://dx.doi.org/10.1107/S139900471500629XDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4556316PMC
September 2015
4 Reads

Structure of the green fluorescent protein NowGFP with an anionic tryptophan-based chromophore.

Acta Crystallogr D Biol Crystallogr 2015 Aug 31;71(Pt 8):1699-707. Epub 2015 Jul 31.

Synchrotron Radiation Research Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Argonne, IL 60439, USA.

A green-emitting fluorescent variant, NowGFP, with a tryptophan-based chromophore (Thr65-Trp66-Gly67) was recently developed from the cyan mCerulean by introducing 18 point mutations. NowGFP is characterized by bright green fluorescence at physiological and higher pH and by weak cyan fluorescence at low pH. Illumination with blue light induces irreversible photoconversion of NowGFP from a green-emitting to a cyan-emitting form. Read More

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http://scripts.iucr.org/cgi-bin/paper?S1399004715010159
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http://dx.doi.org/10.1107/S1399004715010159DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4528802PMC
August 2015
13 Reads

Protonation and geometry of histidine rings.

Acta Crystallogr D Biol Crystallogr 2015 Jul 30;71(Pt 7):1444-54. Epub 2015 Jun 30.

Synchrotron Radiation Research Section, MCL, National Cancer Institute, Argonne National Laboratory, Argonne, IL 60439, USA.

The presence of H atoms connected to either or both of the two N atoms of the imidazole moiety in a histidine residue affects the geometry of the five-membered ring. Analysis of the imidazole moieties found in histidine residues of atomic resolution protein crystal structures in the Protein Data Bank (PDB), and in small-molecule structures retrieved from the Cambridge Structural Database (CSD), identified characteristic patterns of bond lengths and angles related to the protonation state of the imidazole moiety. Using discriminant analysis, two functions could be defined, corresponding to linear combinations of the four most sensitive stereochemical parameters, two bond lengths (ND1-CE1 and CE1-NE2) and two endocyclic angles (-ND1- and -NE2-), that uniquely identify the protonation states of all imidazole moieties in the CSD and can be used to predict which N atom(s) of the histidine side chains in protein structures are protonated. Read More

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http://dx.doi.org/10.1107/S1399004715007816DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4498602PMC
July 2015
2 Reads
4 Citations
7.232 Impact Factor

ANS complex of St John's wort PR-10 protein with 28 copies in the asymmetric unit: a fiendish combination of pseudosymmetry with tetartohedral twinning.

Acta Crystallogr D Biol Crystallogr 2015 Apr 26;71(Pt 4):829-43. Epub 2015 Mar 26.

Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.

Hyp-1, a pathogenesis-related class 10 (PR-10) protein from St John's wort (Hypericum perforatum), was crystallized in complex with the fluorescent probe 8-anilino-1-naphthalene sulfonate (ANS). The highly pseudosymmetric crystal has 28 unique protein molecules arranged in columns with sevenfold translational noncrystallographic symmetry (tNCS) along c and modulated X-ray diffraction with intensity crests at l = 7n and l = 7n ± 3. The translational NCS is combined with pseudotetragonal rotational NCS. Read More

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http://dx.doi.org/10.1107/S1399004715001388DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4388264PMC
April 2015
7 Reads

Novel crystalline phase and first-order phase transitions of human insulin complexed with two distinct phenol derivatives.

Acta Crystallogr D Biol Crystallogr 2015 Apr 26;71(Pt 4):819-28. Epub 2015 Mar 26.

Section of Genetics, Cell Biology and Development, Department of Biology, University of Patras, GR-26500 Patras, Greece.

The primary focus of the present work is the study of the effects that two ligands and the crystallization pH have on the crystalline forms of human insulin. For this purpose, human insulin (HI) was co-crystallized with two distinct phenolic derivatives: the organic ligands meta-cresol (m-cresol) and 4-nitrophenol. The formation of polycrystalline precipitates was then followed by means of structural characterization of the individual specimens in terms of unit-cell symmetry and parameters. Read More

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http://dx.doi.org/10.1107/S1399004715001376DOI Listing
April 2015
2 Reads

Radiation decay of thaumatin crystals at three X-ray energies.

Acta Crystallogr D Biol Crystallogr 2015 Apr 26;71(Pt 4):772-8. Epub 2015 Mar 26.

Synchrotron Radiation Research Section, MCL, National Cancer Institute, Argonne National Laboratory, Argonne, IL 60439, USA.

Radiation damage is an unavoidable obstacle in X-ray crystallographic data collection for macromolecular structure determination, so it is important to know how much radiation a sample can endure before being degraded beyond an acceptable limit. In the literature, the threshold at which the average intensity of all recorded reflections decreases to a certain fraction of the initial value is called the `dose limit'. The first estimated D50 dose-limit value, at which the average diffracted intensity was reduced to 50%, was 20 MGy and was derived from observing sample decay in electron-diffraction experiments. Read More

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http://dx.doi.org/10.1107/S1399004715001030DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4388262PMC
April 2015
12 Reads

Combining biophysical methods for the analysis of protein complex stoichiometry and affinity in SEDPHAT.

Acta Crystallogr D Biol Crystallogr 2015 Jan 1;71(Pt 1):3-14. Epub 2015 Jan 1.

Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA.

Reversible macromolecular interactions are ubiquitous in signal transduction pathways, often forming dynamic multi-protein complexes with three or more components. Multivalent binding and cooperativity in these complexes are often key motifs of their biological mechanisms. Traditional solution biophysical techniques for characterizing the binding and cooperativity are very limited in the number of states that can be resolved. Read More

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http://dx.doi.org/10.1107/S1399004714010372DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4304681PMC
January 2015
1 Read

ACHESYM: an algorithm and server for standardized placement of macromolecular models in the unit cell.

Acta Crystallogr D Biol Crystallogr 2014 Dec 28;70(Pt 12):3290-8. Epub 2014 Nov 28.

Synchrotron Radiation Research Section, Macromolecular Crystallography Laboratory, NCI, Argonne National Laboratory, Argonne, USA.

Despite the existence of numerous useful conventions in structural crystallography, for example for the choice of the asymmetric part of the unit cell or of reciprocal space, surprisingly no standards are in use for the placement of the molecular model in the unit cell, often leading to inconsistencies or confusion. A conceptual solution for this problem has been proposed for macromolecular crystal structures based on the idea of the anti-Cheshire unit cell. Here, a program and server (called ACHESYM; http://achesym. Read More

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http://dx.doi.org/10.1107/S1399004714024572DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4257622PMC
December 2014
5 Reads

Structural insights into interactions of C/EBP transcriptional activators with the Taz2 domain of p300.

Acta Crystallogr D Biol Crystallogr 2014 Jul 29;70(Pt 7):1914-21. Epub 2014 Jun 29.

Protein Structure Section, Macromolecular Crystallography Laboratory, National Cancer Institute at Frederick, Frederick, MD 21702, USA.

Members of the C/EBP family of transcription factors bind to the Taz2 domain of p300/CBP and mediate its phosphorylation through the recruitment of specific kinases. Short sequence motifs termed homology boxes A and B, which comprise their minimal transactivation domains (TADs), are conserved between C/EBP activators and are necessary for specific p300/CBP binding. A possible mode of interaction between C/EBP TADs and the p300 Taz2 domain was implied by the crystal structure of a chimeric protein composed of residues 1723-1818 of p300 Taz2 and residues 37-61 of C/EBPℇ. Read More

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http://scripts.iucr.org/cgi-bin/paper?S1399004714009262
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http://dx.doi.org/10.1107/S1399004714009262DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4089485PMC
July 2014
5 Reads

Phosphates in the Z-DNA dodecamer are flexible, but their P-SAD signal is sufficient for structure solution.

Acta Crystallogr D Biol Crystallogr 2014 Jul 24;70(Pt 7):1790-800. Epub 2014 Jun 24.

Synchrotron Radiation Research Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Argonne National Laboratory, Argonne, IL 60439, USA.

A large number of Z-DNA hexamer duplex structures and a few oligomers of different lengths are available, but here the first crystal structure of the d(CGCGCGCGCGCG)2 dodecameric duplex is presented. Two synchrotron data sets were collected; one was used to solve the structure by the single-wavelength anomalous dispersion (SAD) approach based on the anomalous signal of P atoms, the other set, extending to an ultrahigh resolution of 0.75 Å, served to refine the atomic model to an R factor of 12. Read More

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http://dx.doi.org/10.1107/S1399004714004684DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4089481PMC
July 2014
15 Reads

Structure of the oligogalacturonate-specific KdgM porin.

Acta Crystallogr D Biol Crystallogr 2014 Jun 30;70(Pt 6):1770-8. Epub 2014 May 30.

Focal Area of Structural Biology and Biophysics, Biozentrum, University of Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland.

The phytopathogenic Gram-negative bacterium Dickeya dadantii (Erwinia chrysanthemi) feeds on plant cell walls by secreting pectinases and utilizing the oligogalacturanate products. An outer membrane porin, KdgM, is indispensable for the uptake of these acidic oligosaccharides. Here, the crystal structure of KdgM determined to 1. Read More

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http://dx.doi.org/10.1107/S1399004714007147DOI Listing

Likelihood-based molecular-replacement solution for a highly pathological crystal with tetartohedral twinning and sevenfold translational noncrystallographic symmetry.

Acta Crystallogr D Biol Crystallogr 2014 Feb 29;70(Pt 2):471-80. Epub 2014 Jan 29.

Department of Haematology, University of Cambridge, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 0XY, England.

Translational noncrystallographic symmetry (tNCS) is a pathology of protein crystals in which multiple copies of a molecule or assembly are found in similar orientations. Structure solution is problematic because this breaks the assumptions used in current likelihood-based methods. To cope with such cases, new likelihood approaches have been developed and implemented in Phaser to account for the statistical effects of tNCS in molecular replacement. Read More

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http://dx.doi.org/10.1107/S1399004713030319DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3940205PMC
February 2014
3 Reads

Weak data do not make a free lunch, only a cheap meal.

Acta Crystallogr D Biol Crystallogr 2014 Feb 17;70(Pt 2):253-60. Epub 2014 Jan 17.

Synchrotron Radiation Research Section, MCL, National Cancer Institute, Argonne National Laboratory, Argonne, IL 90439, USA.

Four data sets were processed at resolutions significantly exceeding the criteria traditionally used for estimating the diffraction data resolution limit. The analysis of these data and the corresponding model-quality indicators suggests that the criteria of resolution limits widely adopted in the past may be somewhat conservative. Various parameters, such as Rmerge and I/σ(I), optical resolution and the correlation coefficients CC1/2 and CC*, can be used for judging the internal data quality, whereas the reliability factors R and Rfree as well as the maximum-likelihood target values and real-space map correlation coefficients can be used to estimate the agreement between the data and the refined model. Read More

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http://dx.doi.org/10.1107/S1399004713026680DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3940200PMC
February 2014
6 Reads

On the reproducibility of protein crystal structures: five atomic resolution structures of trypsin.

Acta Crystallogr D Biol Crystallogr 2013 Aug 17;69(Pt 8):1447-62. Epub 2013 Jul 17.

Synchrotron Radiation Research Section, MCL, National Cancer Institute, Argonne National Laboratory, Argonne, IL 60439, USA.

Structural studies of proteins usually rely on a model obtained from one crystal. By investigating the details of this model, crystallographers seek to obtain insight into the function of the macromolecule. It is therefore important to know which details of a protein structure are reproducible or to what extent they might differ. Read More

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https://journals.iucr.org/d/issues/2013/08/00/rr5036/rr5036.
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http://scripts.iucr.org/cgi-bin/paper?S0907444913009050
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http://dx.doi.org/10.1107/S0907444913009050DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3727327PMC
August 2013
2 Reads

High-resolution powder X-ray data reveal the T(6) hexameric form of bovine insulin.

Acta Crystallogr D Biol Crystallogr 2013 Jun 11;69(Pt 6):978-90. Epub 2013 May 11.

Department of Biology, Section of Genetics, Cell Biology and Development, University of Patras, GR-26500 Patras, Greece.

A series of bovine insulin samples were obtained as 14 polycrystalline precipitates at room temperature in the pH range 5.0-7.6. Read More

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http://dx.doi.org/10.1107/S0907444913003867DOI Listing
June 2013
3 Reads

On optimal placement of molecules in the unit cell.

Authors:
Zbigniew Dauter

Acta Crystallogr D Biol Crystallogr 2013 May 19;69(Pt 5):872-8. Epub 2013 Apr 19.

Synchrotron Radiation Research Section, MCL, National Cancer Institute, Argonne National Laboratory, Argonne, IL 60439, USA.

There are currently no rules for a unified, standard way of placing macromolecular structures in the crystal lattice. An analysis of all possible symmetry-equivalent representations of molecular structures in various space groups leads to the concept of the anti-Cheshire symmetry and suggests that the center of a unique structural motif can always be placed within the selected asymmetric unit of the anti-Cheshire cell. The placement of structures according to this suggestion will ensure uniformity of presentation of all structurally equivalent Protein Data Bank models and will therefore diminish the possibility of confusing less crystallographically knowledgeable users of the PDB. Read More

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http://dx.doi.org/10.1107/S0907444913002722DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4005360PMC
May 2013
3 Reads

On the usefulness of ion-mobility mass spectrometry and SAXS data in scoring docking decoys.

Acta Crystallogr D Biol Crystallogr 2013 May 19;69(Pt 5):683-94. Epub 2013 Apr 19.

Faculty of Science, Padualaan 8, Bijvoet Center for Biomolecular Research, 3548 CH Utrecht, The Netherlands.

Scoring, the process of selecting the biologically relevant solution from a pool of generated conformations, is one of the major challenges in the field of biomolecular docking. A prominent way to cope with this challenge is to incorporate information-based terms into the scoring function. Within this context, low-resolution shape data obtained from either ion-mobility mass spectrometry (IM-MS) or SAXS experiments have been integrated into the conventional scoring function of the information-driven docking program HADDOCK. Read More

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http://dx.doi.org/10.1107/S0907444913007063DOI Listing
May 2013
6 Reads

Placement of molecules in (not out of) the cell.

Authors:
Zbigniew Dauter

Acta Crystallogr D Biol Crystallogr 2013 Jan 20;69(Pt 1):2-4. Epub 2012 Dec 20.

Synchrotron Radiation Research Section, National Cancer Institute, Argonne National Laboratory, Argonne, IL 60439, USA.

To uniquely describe a crystal structure, it is sufficient to specify the crystal unit cell and symmetry, and describe the unique structural motif which is repeated by the space-group symmetry throughout the whole crystal. It is somewhat arbitrary how such a unique motif can be defined and positioned with respect to the unit-cell origin. As a result of such freedom, some isomorphous structures are presented in the Protein Data Bank in different locations and appear as if they have different atomic coordinates, despite being completely equivalent structurally. Read More

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http://dx.doi.org/10.1107/S0907444912044794DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4004389PMC
January 2013
2 Reads

Dimeric structure of the N-terminal domain of PriB protein from Thermoanaerobacter tengcongensis solved ab initio.

Acta Crystallogr D Biol Crystallogr 2012 Dec 9;68(Pt 12):1680-9. Epub 2012 Nov 9.

Synchrotron Radiation Research Section, MCL, National Cancer Institute, Argonne National Laboratory, Argonne, IL 60439, USA.

PriB is one of the components of the bacterial primosome, which catalyzes the reactivation of stalled replication forks at sites of DNA damage. The N-terminal domain of the PriB protein from the thermophilic bacterium Thermoanaerobacter tengcongensis (TtePriB) was expressed and its crystal structure was solved at the atomic resolution of 1.09 Å by direct methods. Read More

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http://dx.doi.org/10.1107/S0907444912041637DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3498933PMC
December 2012
3 Reads

Structural studies of human insulin cocrystallized with phenol or resorcinol via powder diffraction.

Acta Crystallogr D Biol Crystallogr 2012 Dec 9;68(Pt 12):1632-41. Epub 2012 Nov 9.

Department of Biology, Section of Genetics, Cell Biology and Development, University of Patras, Patras, Greece.

The effects of the ligands phenol and resorcinol on the crystallization of human insulin have been investigated as a function of pH. Powder diffraction data were used to characterize several distinct polymorphic forms. A previously unknown polymorph with monoclinic symmetry (P2(1)) was identified for both types of ligand with similar characteristics [the unit-cell parameters for the insulin-resorcinol complex were a = 114. Read More

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http://dx.doi.org/10.1107/S0907444912039339DOI Listing
December 2012
2 Reads

How good can our beamlines be?

Acta Crystallogr D Biol Crystallogr 2012 Oct 18;68(Pt 10):1430-6. Epub 2012 Sep 18.

Synchrotron Radiation Research Section, MCL, National Cancer Institute, Argonne National Laboratory, Argonne, IL 60439, USA.

The accuracy of X-ray diffraction data depends on the properties of the crystalline sample and on the performance of the data-collection facility (synchrotron beamline elements, goniostat, detector etc.). However, it is difficult to evaluate the level of performance of the experimental setup from the quality of data sets collected in rotation mode, as various crystal properties such as mosaicity, non-uniformity and radiation damage affect the measured intensities. Read More

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http://dx.doi.org/10.1107/S0907444912034658DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3447404PMC
October 2012
3 Reads

Structural basis for bathochromic shift of fluorescence in far-red fluorescent proteins eqFP650 and eqFP670.

Acta Crystallogr D Biol Crystallogr 2012 Sep 18;68(Pt 9):1088-97. Epub 2012 Aug 18.

Synchrotron Radiation Research Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Argonne, IL 60439, USA.

The crystal structures of the far-red fluorescent proteins (FPs) eqFP650 (λ(ex)(max)/λ(em)(max) 592/650 nm) and eqFP670 (λ(ex)(max)/λ(em)(max) 605/670 nm), the successors of the far-red FP Katushka (λ(ex)(max)/λ(em)(max) 588/635 nm), have been determined at 1.8 and 1.6 Å resolution, respectively. Read More

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http://dx.doi.org/10.1107/S0907444912020598DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3489099PMC
September 2012
5 Reads

Structures of NodZ α1,6-fucosyltransferase in complex with GDP and GDP-fucose.

Acta Crystallogr D Biol Crystallogr 2012 Feb 6;68(Pt 2):160-8. Epub 2012 Jan 6.

Synchrotron Radiation Research Section, MCL, National Cancer Institute, Argonne National Laboratory, Argonne, IL 60439, USA.

Rhizobial NodZ α1,6-fucosyltransferase (α1,6-FucT) catalyzes the transfer of the fucose (Fuc) moiety from guanosine 5'-diphosphate-β-L-fucose to the reducing end of the chitin oligosaccharide core during Nod-factor (NF) biosynthesis. NF is a key signalling molecule required for successful symbiosis with a legume host for atmospheric nitrogen fixation. To date, only two α1,6-FucT structures have been determined, both without any donor or acceptor molecule that could highlight the structural background of the catalytic mechanism. Read More

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http://scripts.iucr.org/cgi-bin/paper?S0907444911053157
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http://dx.doi.org/10.1107/S0907444911053157DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3266854PMC
February 2012
3 Reads

Human Suv3 protein reveals unique features among SF2 helicases.

Acta Crystallogr D Biol Crystallogr 2011 Nov 19;67(Pt 11):988-96. Epub 2011 Oct 19.

Synchrotron Radiation Research Section, National Cancer Institute, Argonne National Laboratory, Argonne, IL 60439, USA.

Suv3 is a helicase that is involved in efficient turnover and surveillance of RNA in eukaryotes. In vitro studies show that human Suv3 (hSuv3) in complex with human polynucleotide phosphorylase has RNA degradosome activity. The enzyme is mainly localized in mitochondria, but small fractions are found in cell nuclei. Read More

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http://dx.doi.org/10.1107/S0907444911040248DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3211972PMC
November 2011
1 Read

Spatial dependence and mitigation of radiation damage by a line-focus mini-beam.

Acta Crystallogr D Biol Crystallogr 2010 Dec 16;66(Pt 12):1287-94. Epub 2010 Nov 16.

Physics Department, University of Washington, Seattle, Washington 98195-1560, USA.

Recently, strategies to reduce primary radiation damage have been proposed which depend on focusing X-rays to dimensions smaller than the penetration depth of excited photoelectrons. For a line focus as used here the penetration depth is the maximum distance from the irradiated region along the X-ray polarization direction that the photoelectrons penetrate. Reported here are measurements of the penetration depth and distribution of photoelectron damage excited by 18. Read More

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http://dx.doi.org/10.1107/S0907444910036875DOI Listing
December 2010
3 Reads

Structure of the N-terminal fragment of Escherichia coli Lon protease.

Acta Crystallogr D Biol Crystallogr 2010 Aug 9;66(Pt 8):865-73. Epub 2010 Jul 9.

Protein Structure Section, Macromolecular Crystallography Laboratory, National Cancer Institute at Frederick, Frederick, MD 21702-1201, USA.

The structure of a recombinant construct consisting of residues 1-245 of Escherichia coli Lon protease, the prototypical member of the A-type Lon family, is reported. This construct encompasses all or most of the N-terminal domain of the enzyme. The structure was solved by SeMet SAD to 2. Read More

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http://dx.doi.org/10.1107/S0907444910019554DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2917273PMC
August 2010
6 Reads

Carrying out an optimal experiment.

Authors:
Zbigniew Dauter

Acta Crystallogr D Biol Crystallogr 2010 Apr 24;66(Pt 4):389-92. Epub 2010 Mar 24.

Synchrotron Radiation Research Section, MCL, National Cancer Institute, Argonne National Laboratory, Argonne, IL 60439, USA.

Diffraction data collection is the last experimental stage in structural crystallography. It has several technical and theoretical aspects and a compromise usually has to be found between various parameters in order to achieve optimal data quality. The influence and importance of various experimental parameters and their consequences are discussed in the context of different data applications, such as molecular replacement, anomalous phasing, high-resolution refinement or searching for ligands. Read More

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http://dx.doi.org/10.1107/S0907444909038578DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2852303PMC
April 2010
2 Reads

Know your dose: RADDOSE.

Acta Crystallogr D Biol Crystallogr 2010 Apr 24;66(Pt 4):381-8. Epub 2010 Mar 24.

Department of Biochemistry, Laboratory of Molecular Biophysics, University of Oxford, South Parks Road, Oxford OX1 3QU, England.

The program RADDOSE is widely used to compute the dose absorbed by a macromolecular crystal during an X-ray diffraction experiment. A number of factors affect the absorbed dose, including the incident X-ray flux density, the photon energy and the composition of the macromolecule and of the buffer in the crystal. An experimental dose limit for macromolecular crystallography (MX) of 30 MGy at 100 K has been reported, beyond which the biological information obtained may be compromised. Read More

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http://dx.doi.org/10.1107/S0907444910006724DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2852302PMC

A rational approach to heavy-atom derivative screening.

Acta Crystallogr D Biol Crystallogr 2010 Apr 24;66(Pt 4):358-65. Epub 2010 Mar 24.

Structural Immunology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 12441 Parklawn Drive, Rockville, Maryland 20852, USA.

Despite the development in recent times of a range of techniques for phasing macromolecules, the conventional heavy-atom derivatization method still plays a significant role in protein structure determination. However, this method has become less popular in modern high-throughput oriented crystallography, mostly owing to its trial-and-error nature, which often results in lengthy empirical searches requiring large numbers of well diffracting crystals. In addition, the phasing power of heavy-atom derivatives is often compromised by lack of isomorphism or even loss of diffraction. Read More

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http://journals.iucr.org/d/issues/2010/04/00/ba5135/ba5135.p
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http://scripts.iucr.org/cgi-bin/paper?S0907444909053074
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http://dx.doi.org/10.1107/S0907444909053074DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2852299PMC
April 2010
23 Reads

A toolkit for the characterization of CCD cameras for transmission electron microscopy.

Acta Crystallogr D Biol Crystallogr 2010 Jan 21;66(Pt 1):97-109. Epub 2009 Dec 21.

Section Electron Microscopy, Department of Molecular Cell Biology, Leiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands.

Charge-coupled devices (CCD) are nowadays commonly utilized in transmission electron microscopy (TEM) for applications in life sciences. Direct access to digitized images has revolutionized the use of electron microscopy, sparking developments such as automated collection of tomographic data, focal series, random conical tilt pairs and ultralarge single-particle data sets. Nevertheless, for ultrahigh-resolution work photographic plates are often still preferred. Read More

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http://journals.iucr.org/d/issues/2010/01/00/ic5061/ic5061.p
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http://scripts.iucr.org/cgi-bin/paper?S0907444909031205
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http://dx.doi.org/10.1107/S0907444909031205DOI Listing
January 2010
1 Read

A case of structure determination using pseudosymmetry.

Acta Crystallogr D Biol Crystallogr 2009 Dec 17;65(Pt 12):1334-40. Epub 2009 Nov 17.

Structural Immunology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland 20852, USA.

Here, a case is presented of an unusual structure determination which was facilitated by the use of pseudosymmetry. Group A streptococcus uses cysteine protease Mac-1 (also known as IdeS) to evade the host immune system. Native Mac-1 was crystallized in the orthorhombic space group P2(1)2(1)2. Read More

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http://scripts.iucr.org/cgi-bin/paper?S0907444909039912
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http://dx.doi.org/10.1107/S0907444909039912DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2789005PMC
December 2009
3 Reads

Structure of the Taz2 domain of p300: insights into ligand binding.

Acta Crystallogr D Biol Crystallogr 2009 Dec 17;65(Pt 12):1301-8. Epub 2009 Nov 17.

Protein Structure Section, Macromolecular Crystallography Laboratory, NCI-Frederick, Frederick, Maryland 21702-1201, USA.

CBP and its paralog p300 are histone acetyl transferases that regulate gene expression by interacting with multiple transcription factors via specialized domains. The structure of a segment of human p300 protein (residues 1723-1836) corresponding to the extended zinc-binding Taz2 domain has been investigated. The crystal structure was solved by the SAD approach utilizing the anomalous diffraction signal of the bound Zn ions. Read More

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http://dx.doi.org/10.1107/S0907444909040153DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2789004PMC
December 2009
1 Read

To scavenge or not to scavenge: that is the question.

Acta Crystallogr D Biol Crystallogr 2009 Sep 14;65(Pt 9):1004-6. Epub 2009 Aug 14.

Synchrotron Radiation Research Section, MCL, National Cancer Institute, Argonne National Laboratory, Argonne, IL 60439, USA.

Analysis of a series of diffraction data sets measured from four native as well as four nicotinic acid-soaked crystals of trypsin at 100 K shows a high variability in radiation-sensitivity among individual crystals for both nicotinic acid-soaked and native crystals. The level of radiation-sensitivity and the extent of its variability is statistically indistinguishable between the two conditions. This suggests that this potential scavenger does not have any statistically significant effect on the amount of radiation damage incurred in the crystals on X-ray irradiation. Read More

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http://scripts.iucr.org/cgi-bin/paper?S0907444909026821
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http://dx.doi.org/10.1107/S0907444909026821DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2733885PMC
September 2009
3 Reads

A 7μm mini-beam improves diffraction data from small or imperfect crystals of macromolecules.

Acta Crystallogr D Biol Crystallogr 2008 Apr 19;64(Pt 4):425-35. Epub 2008 Mar 19.

Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA.

A simple apparatus for achieving beam sizes in the range 5-10 μm on a synchrotron beamline was implemented in combination with a small 125 x 25 μm focus. The resulting beam had sufficient flux for crystallographic data collection from samples smaller than 10 x 10 x 10 μm. Sample data were collected representing three different scenarios: (i) a complete 2. Read More

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http://scripts.iucr.org/cgi-bin/paper?S0907444908001741
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http://dx.doi.org/10.1107/S0907444908001741DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2631116PMC
April 2008
5 Reads

Towards a rational approach for heavy-atom derivative screening in protein crystallography.

Acta Crystallogr D Biol Crystallogr 2008 Apr 19;64(Pt 4):354-67. Epub 2008 Mar 19.

Structural Immunology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 12441 Parklawn Drive, Rockville, Maryland 20852, USA.

Heavy-atom derivatization is routinely used in protein structure determination and is thus of critical importance in structural biology. In order to replace the current trial-and-error heavy-atom derivative screening with a knowledge-based rational derivative-selection method, the reactivity of more than 40 heavy-atom compounds over a wide range of buffer and pH values was systematically examined using peptides which contained a single reactive amino-acid residue. Met-, Cys- and His-containing peptides were derivatized against Hg, Au and Pt compounds, while Tyr-, Glu-, Asp-, Asn- and Gln-containing peptides were assessed against Pb compounds. Read More

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http://dx.doi.org/10.1107/S0907444907068849DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2725783PMC
April 2008
7 Reads

Structure of the single-stranded DNA-binding protein SSB from Thermus aquaticus.

Acta Crystallogr D Biol Crystallogr 2006 Nov 18;62(Pt 11):1407-12. Epub 2006 Oct 18.

Synchrotron Radiation Research Section, MCL, National Cancer Institute, Argonne National Laboratory, Argonne, IL 60439, USA.

The crystal structure of the single-stranded DNA-binding protein from Thermus aquaticus has been solved and refined at 1.85 A resolution. Two monomers, each encompassing two oligonucleotide/oligosaccharide-binding (OB) domains and a number of flexible beta-hairpin loops, form an oligomer of approximate D(2) symmetry typical of bacterial SSBs. Read More

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http://dx.doi.org/10.1107/S0907444906036031DOI Listing
November 2006
15 Reads

Quantifying X-ray radiation damage in protein crystals at cryogenic temperatures.

Acta Crystallogr D Biol Crystallogr 2006 Sep 19;62(Pt 9):1030-8. Epub 2006 Aug 19.

Physics Department, Cornell University, Ithaca, NY 14853, USA.

The dependence of radiation damage to protein crystals at cryogenic temperatures upon the X-ray absorption cross-section of the crystal has been examined. Lysozyme crystals containing varying heavy-atom concentrations were irradiated and diffraction patterns were recorded as a function of the total number of incident photons. An experimental protocol and a coefficient of sensitivity to absorbed dose, proportional to the change in relative isotropic B factor, are defined that together yield a sensitive and robust measure of damage. Read More

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http://dx.doi.org/10.1107/S0907444906023869DOI Listing
September 2006
2 Reads

Estimation of anomalous signal in diffraction data.

Authors:
Zbigniew Dauter

Acta Crystallogr D Biol Crystallogr 2006 Aug 18;62(Pt 8):867-76. Epub 2006 Jul 18.

Synchrotron Radiation Research Section, MCL, National Cancer Institute, Argonne National Laboratory, Biosciences Division, Building 202, 9700 South Cass Avenue, Argonne, IL 60439, USA.

It is difficult to judge objectively the amount and resolution limit of the anomalous signal present in diffraction data. While several criteria can be used for this purpose, the usefulness of these indicators varies and depends on factors such as the data redundancy, the accuracy of the estimation of intensities and their uncertainties, and the properties of the anomalously scattering atoms in the crystal. Various indicators give an approximate measure of the anomalous signal, but do not provide a reliable guarantee that the crystal structure will be solved. Read More

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http://dx.doi.org/10.1107/S0907444906023481DOI Listing

A survey of protein-protein complex crystallizations.

Acta Crystallogr D Biol Crystallogr 2006 Jun 12;62(Pt 6):605-12. Epub 2006 May 12.

Structural Immunology Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 12441 Parklawn Drive, Rockville, Maryland 20852, USA.

A survey of crystallization conditions was carried out for 650 published protein-protein complexes in the Protein Data Bank (PDB) of the Research Collaboratory for Structural Bioinformatics (RCSB). This resulted in the establishment of a Protein Complex Crystallization Database (PCCD) and a set of configuration-space boundaries for protein-complex crystallizations. Overall, polyethylene glycol (PEG) based conditions accounted for 70-80% of all crystallizations, with PEG 3000-4000, 5000-6000 and 8000 being the most frequently used. Read More

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http://scripts.iucr.org/cgi-bin/paper?S0907444906011735
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http://dx.doi.org/10.1107/S0907444906011735DOI Listing
June 2006
2 Reads

Structure of DraD invasin from uropathogenic Escherichia coli: a dimer with swapped beta-tails.

Acta Crystallogr D Biol Crystallogr 2006 Feb 18;62(Pt 2):157-64. Epub 2006 Jan 18.

Synchrotron Radiation Research Section, MCL, National Cancer Institute, Argonne National Laboratory, Argonne, IL 60439, USA.

The dra gene cluster of uropathogenic strains of Escherichia coli produces proteins involved in bacterial attachment to and invasion of the eukaryotic host tissues. The crystal structure of a construct of E. coli DraD possessing an additional C-terminal extension of 13 amino acids, including a His6 tag, has been solved at a resolution of 1. Read More

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http://dx.doi.org/10.1107/S0907444905036747DOI Listing
February 2006
13 Reads

Current state and prospects of macromolecular crystallography.

Authors:
Zbigniew Dauter

Acta Crystallogr D Biol Crystallogr 2006 Jan 14;62(Pt 1):1-11. Epub 2005 Dec 14.

Synchrotron Radiation Research Section, MCL, National Cancer Institute, Argonne National Laboratory, Building 202, 9700 South Cass Avenue, Argonne, IL 60439, USA.

The current situation and possible future development of macromolecular crystallography are reviewed. The rapid progress and maturation of this field in recent years have to a large extent been made possible by the inspiration and generous support of several active structural genomics initiatives. Two tendencies can be currently observed: one which treats protein crystallography as a highly automatic tool for investigating various biological problems without the need to engage in the intricacies of the technique and a second approach where this method is applied to crystals of difficult, large and complex biological systems, requiring a deeper knowledge of various aspects of crystallography. Read More

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http://dx.doi.org/10.1107/S0907444905034050DOI Listing
January 2006

Pathological crystallography: case studies of several unusual macromolecular crystals.

Acta Crystallogr D Biol Crystallogr 2005 Jul 24;61(Pt 7):967-75. Epub 2005 Jun 24.

Synchrotron Radiation Research Section, Macromolecular Crystallography Laboratory, National Cancer Institute and Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA.

Although macromolecular crystallography is rapidly becoming largely routine owing to advances in methods of data collection, structure solution and refinement, difficult cases are still common. To remind structural biologists about the kinds of crystallographic difficulties that might be encountered, case studies of several successfully completed structure determinations that utilized less than perfect crystals are discussed here. The structure of the proteolytic domain of Archaeoglobus fulgidus Lon was solved with crystals that contained superimposed orthorhombic and monoclinic lattices, a case not previously described for proteins. Read More

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http://dx.doi.org/10.1107/S0907444905011285DOI Listing
July 2005
6 Reads

Following directed evolution with crystallography: structural changes observed in changing the substrate specificity of dienelactone hydrolase.

Acta Crystallogr D Biol Crystallogr 2005 Jul 24;61(Pt 7):920-31. Epub 2005 Jun 24.

Research School of Chemistry, Australian National University, Building 35, Science Road, Canberra, ACT 0200, Australia.

The enzyme dienelactone hydrolase (DLH) has undergone directed evolution to produce a series of mutant proteins that have enhanced activity towards the non-physiological substrates alpha-naphthyl acetate and p-nitrophenyl acetate. In terms of steady-state kinetics, the mutations caused a drop in the K(m) for the hydrolysis reaction with these two substrates. For the best mutant, there was a 5. Read More

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http://dx.doi.org/10.1107/S0907444905009042DOI Listing
July 2005
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Crystallization of foot-and-mouth disease virus 3C protease: surface mutagenesis and a novel crystal-optimization strategy.

Acta Crystallogr D Biol Crystallogr 2005 May 20;61(Pt 5):646-50. Epub 2005 Apr 20.

Biophysics Section, Department of Biological Sciences, Blackett Laboratory, Imperial College, South Kensington Campus, London SW7 2AZ, England.

Foot-and-mouth disease virus (FMDV) 3C protease (3C(pro)) plays a vital role in virus replication by performing most of the cleavages required to divide the viral polyprotein precursor into its functional component proteins. To date, no structural information has been available for FMDV 3C(pro), which is an attractive target for antiviral drugs. Targeted mutagenesis of surface amino acids identified two Cys residues that were detrimental to solubility and contributed to the time-dependent formation of a proteinaceous skin in samples of purified wild-type protein. Read More

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http://dx.doi.org/10.1107/S0907444905007924DOI Listing

Preparation, crystallization and preliminary X-ray analysis of a complex between the Plasmodium vivax sexual stage 25 kDa protein Pvs25 and a malaria transmission-blocking antibody Fab fragment.

Acta Crystallogr D Biol Crystallogr 2004 Nov 20;60(Pt 11):2054-7. Epub 2004 Oct 20.

Structural Biology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Twinbrook II, 12441 Parklawn Drive, Rockville, Maryland 20852, USA.

The Plasmodium vivax sexual stage 25 kDa protein Pvs25, located on the surface of the ookinete form of the parasite, is a vaccine candidate designed to elicit immunity that blocks the transmission of malaria by mosquitoes. The 2A8 murine monoclonal antibody directed against recombinant Pvs25 prevents the formation of P. vivax oocysts in mosquitoes fed in the laboratory. Read More

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http://scripts.iucr.org/cgi-bin/paper?S0907444904021584
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November 2004
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Crystallization and preliminary X-ray crystallographic analysis of chitinase F1 (ChiF1) from the alkaliphilic Nocardiopsis sp. strain F96.

Acta Crystallogr D Biol Crystallogr 2004 Nov 20;60(Pt 11):2016-8. Epub 2004 Oct 20.

Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan.

Chitinase F1 (ChiF1) isolated from the alkaliphilic Nocardiopsis sp. strain F96 is a family 18 chitinase that hydrolyzes chitin, an insoluble beta-1,4-linked polymer of N-acetylglucosamine. Crystals of recombinant ChiF1 with molecular weight of 33 000 Da were grown to a suitable size for X-ray structure analysis using 18%(w/v) polyethylene glycol 8000, 200 mM zinc acetate dehydrate and 100 mM sodium cacodylate buffer pH 6. Read More

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http://scripts.iucr.org/cgi-bin/paper?S0907444904020475
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http://dx.doi.org/10.1107/S0907444904020475DOI Listing
November 2004
6 Reads

A pivotal role for reductive methylation in the de novo crystallization of a ternary complex composed of Yersinia pestis virulence factors YopN, SycN and YscB.

Acta Crystallogr D Biol Crystallogr 2004 Nov 20;60(Pt 11):1981-6. Epub 2004 Oct 20.

Protein Engineering Section, Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute at Frederick, PO Box B, Frederick, MD 21702-1201, USA.

Structural studies of a ternary complex composed of the Yersina pestis virulence factors YopN, SycN and YscB were initially hampered by poor solubility of the individual proteins. Co-expression of all three proteins in Escherichia coli yielded a well behaved complex, but this sample proved to be recalcitrant to crystallization. As crystallization efforts remained fruitless, even after the proteolysis-guided engineering of a truncated YopN polypeptide, reductive methylation of lysine residues was employed to alter the surface properties of the complex. Read More

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http://dx.doi.org/10.1107/S0907444904023005DOI Listing
November 2004
1 Read

Structure of the Yersinia pestis type III secretion chaperone SycH in complex with a stable fragment of YscM2.

Acta Crystallogr D Biol Crystallogr 2004 Sep 26;60(Pt 9):1591-9. Epub 2004 Aug 26.

Protein Engineering Section, Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute at Frederick, PO Box B, Frederick, MD 21702, USA.

Pathogenic Yersinia species use a type III secretion system to inject cytotoxic effector proteins directly into the cytosol of mammalian cells, where they neutralize the innate immune response by interfering with the signal-transduction pathways that control phagocytosis and inflammation. To be exported efficiently, some effectors must transiently associate with cognate cytoplasmic secretion chaperones. SycH is the chaperone for YopH, a potent eukaryotic-like protein tyrosine phosphatase that is essential for virulence. Read More

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http://dx.doi.org/10.1107/S0907444904017597DOI Listing
September 2004
6 Reads