5,599 results match your criteria Acta Crystallographica Section D-Biological Crystallography[Journal]


Structural insights into the synthesis of FMN in prokaryotic organisms.

Acta Crystallogr D Biol Crystallogr 2015 Dec 27;71(Pt 12):2526-42. Epub 2015 Nov 27.

Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, and Instituto de Biocomputación y Física de Sistemas Complejos (Joint Unit BIFI-IQFR), Universidad de Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain.

Riboflavin kinases (RFKs) catalyse the phosphorylation of riboflavin to produce FMN. In most bacteria this activity is catalysed by the C-terminal module of a bifunctional enzyme, FAD synthetase (FADS), which also catalyses the transformation of FMN into FAD through its N-terminal FMN adenylyltransferase (FMNAT) module. The RFK module of FADS is a homologue of eukaryotic monofunctional RFKs, while the FMNAT module lacks homologyto eukaryotic enzymes involved in FAD production. Read More

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December 2015

Native sulfur/chlorine SAD phasing for serial femtosecond crystallography.

Acta Crystallogr D Biol Crystallogr 2015 Dec 27;71(Pt 12):2519-25. Epub 2015 Nov 27.

RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.

Serial femtosecond crystallography (SFX) allows structures to be determined with minimal radiation damage. However, phasing native crystals in SFX is not very common. Here, the structure determination of native lysozyme from single-wavelength anomalous diffraction (SAD) by utilizing the anomalous signal of sulfur and chlorine at a wavelength of 1. Read More

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December 2015

Serial crystallographic analysis of protein isomorphous replacement data from a mixture of native and derivative microcrystals.

Acta Crystallogr D Biol Crystallogr 2015 Dec 27;71(Pt 12):2513-8. Epub 2015 Nov 27.

Institute of Physics, Chinese Academy of Sciences, Beijing 100190, People's Republic of China.

A post-experimental identification/purification procedure similar to that described in Zhang et al. [(2015), IUCrJ, 2, 322-326] has been proposed for use in the treatment of multiphase protein serial crystallography (SX) diffraction snapshots. As a proof of concept, the procedure was tested using theoretical serial femtosecond crystallography (SFX) data from a mixture containing native and derivatized crystals of a protein. Read More

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December 2015

The first crystal structure of the peptidase domain of the U32 peptidase family.

Acta Crystallogr D Biol Crystallogr 2015 Dec 27;71(Pt 12):2505-12. Epub 2015 Nov 27.

Department of Chemistry, Institute of Biochemistry, University of Cologne, Otto-Fischer-Strasse 12-14, D-50674 Cologne, Germany.

The U32 family is a collection of over 2500 annotated peptidases in the MEROPS database with unknown catalytic mechanism. They mainly occur in bacteria and archaea, but a few representatives have also been identified in eukarya. Many of the U32 members have been linked to pathogenicity, such as proteins from Helicobacter and Salmonella. Read More

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December 2015

Atomic resolution crystal structure of Sapp2p, a secreted aspartic protease from Candida parapsilosis.

Acta Crystallogr D Biol Crystallogr 2015 Dec 27;71(Pt 12):2494-504. Epub 2015 Nov 27.

Institute of Organic Chemistry and Biochemistry (IOCB), Academy of Sciences of the Czech Republic, Flemingovo náměstí 2, 166 10 Prague 6, Czech Republic.

The virulence of the Candida pathogens is enhanced by the production of secreted aspartic proteases, which therefore represent possible targets for drug design. Here, the crystal structure of the secreted aspartic protease Sapp2p from Candida parapsilosis was determined. Sapp2p was isolated from its natural source and crystallized in complex with pepstatin A, a classical aspartic protease inhibitor. Read More

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December 2015

Structural characterization of a mitochondrial 3-ketoacyl-CoA (T1)-like thiolase from Mycobacterium smegmatis.

Acta Crystallogr D Biol Crystallogr 2015 Dec 27;71(Pt 12):2479-93. Epub 2015 Nov 27.

Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka 560 012, India.

Thiolases catalyze the degradation and synthesis of 3-ketoacyl-CoA molecules. Here, the crystal structures of a T1-like thiolase (MSM-13 thiolase) from Mycobacterium smegmatis in apo and liganded forms are described. Systematic comparisons of six crystallographically independent unliganded MSM-13 thiolase tetramers (dimers of tight dimers) from three different crystal forms revealed that the two tight dimers are connected to a rigid tetramerization domain via flexible hinge regions, generating an asymmetric tetramer. Read More

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December 2015

Sequence-dependent structural changes in a self-assembling DNA oligonucleotide.

Acta Crystallogr D Biol Crystallogr 2015 Dec 26;71(Pt 12):2471-8. Epub 2015 Nov 26.

Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA.

DNA has proved to be a remarkable molecule for the construction of sophisticated two-dimensional and three-dimensional architectures because of its programmability and structural predictability provided by complementary Watson-Crick base pairing. DNA oligonucleotides can, however, exhibit a great deal of local structural diversity. DNA conformation is strongly linked to both environmental conditions and the nucleobase identities inherent in the oligonucleotide sequence, but the exact relationship between sequence and local structure is not completely understood. Read More

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December 2015

Octameric structure of Staphylococcus aureus enolase in complex with phosphoenolpyruvate.

Acta Crystallogr D Biol Crystallogr 2015 Dec 26;71(Pt 12):2457-70. Epub 2015 Nov 26.

Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, Collaborative Innovation Center of Chemistry for Life Science, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, People's Republic of China.

Staphylococcus aureus is a Gram-positive bacterium with strong pathogenicity that causes a wide range of infections and diseases. Enolase is an evolutionarily conserved enzyme that plays a key role in energy production through glycolysis. Additionally, enolase is located on the surface of S. Read More

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December 2015

Crystal structure and kinetic studies of a tetrameric type II β-carbonic anhydrase from the pathogenic bacterium Vibrio cholerae.

Acta Crystallogr D Biol Crystallogr 2015 Dec 26;71(Pt 12):2449-56. Epub 2015 Nov 26.

Dipartimento di Chimica `Ugo Shiff', Polo Scientifico, Università degli Studi di Firenze, Via della Lastruccia 3, Sesto Fiorentino, Firenze, 50019, Italy.

Carbonic anhydrase (CA) is a zinc enzyme that catalyzes the reversible conversion of carbon dioxide to bicarbonate (hydrogen carbonate) and a proton. CAs have been extensively investigated owing to their involvement in numerous physiological and pathological processes. Currently, CA inhibitors are widely used as antiglaucoma, anticancer and anti-obesity drugs and for the treatment of neurological disorders. Read More

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December 2015

Structure-function relationships in Gan42B, an intracellular GH42 β-galactosidase from Geobacillus stearothermophilus.

Acta Crystallogr D Biol Crystallogr 2015 Dec 26;71(Pt 12):2433-48. Epub 2015 Nov 26.

Institute of Chemistry and the Laboratory for Structural Chemistry and Biology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.

Geobacillus stearothermophilus T-6 is a Gram-positive thermophilic soil bacterium that contains a battery of degrading enzymes for the utilization of plant cell-wall polysaccharides, including xylan, arabinan and galactan. A 9.4 kb gene cluster has recently been characterized in G. Read More

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December 2015

An enzyme captured in two conformational states: crystal structure of S-adenosyl-L-homocysteine hydrolase from Bradyrhizobium elkanii.

Acta Crystallogr D Biol Crystallogr 2015 Dec 26;71(Pt 12):2422-32. Epub 2015 Nov 26.

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

S-Adenosyl-L-homocysteine hydrolase (SAHase) is involved in the enzymatic regulation of S-adenosyl-L-methionine (SAM)-dependent methylation reactions. After methyl-group transfer from SAM, S-adenosyl-L-homocysteine (SAH) is formed as a byproduct, which in turn is hydrolyzed to adenosine (Ado) and homocysteine (Hcy) by SAHase. The crystal structure of BeSAHase, an SAHase from Bradyrhizobium elkanii, which is a nitrogen-fixing bacterial symbiont of legume plants, was determined at 1. Read More

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December 2015

Small-angle scattering determination of the shape and localization of human cytochrome P450 embedded in a phospholipid nanodisc environment.

Acta Crystallogr D Biol Crystallogr 2015 Dec 26;71(Pt 12):2412-21. Epub 2015 Nov 26.

Structural Biophysics, Niels Bohr Institute, Faculty of Science, University of Copenhagen, Copenhagen, Denmark.

Membrane proteins reconstituted into phospholipid nanodiscs comprise a soluble entity accessible to solution small-angle X-ray scattering (SAXS) studies. It is demonstrated that using SAXS data it is possible to determine both the shape and localization of the membrane protein cytochrome P450 3A4 (CYP3A4) while it is embedded in the phospholipid bilayer of a nanodisc. In order to accomplish this, a hybrid approach to analysis of small-angle scattering data was developed which combines an analytical approach to describe the multi-contrast nanodisc with a free-form bead-model description of the embedded protein. Read More

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December 2015

X-ray-induced catalytic active-site reduction of a multicopper oxidase: structural insights into the proton-relay mechanism and O2-reduction states.

Acta Crystallogr D Biol Crystallogr 2015 Dec 26;71(Pt 12):2396-411. Epub 2015 Nov 26.

Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, 62210 Cuernavaca, MOR, Mexico.

During X-ray data collection from a multicopper oxidase (MCO) crystal, electrons and protons are mainly released into the system by the radiolysis of water molecules, leading to the X-ray-induced reduction of O2 to 2H2O at the trinuclear copper cluster (TNC) of the enzyme. In this work, 12 crystallographic structures of Thermus thermophilus HB27 multicopper oxidase (Tth-MCO) in holo, apo and Hg-bound forms and with different X-ray absorbed doses have been determined. In holo Tth-MCO structures with four Cu atoms, the proton-donor residue Glu451 involved in O2 reduction was found in a double conformation: Glu451a (∼7 Å from the TNC) and Glu451b (∼4. Read More

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December 2015

Sent packing: protein engineering generates a new crystal form of Pseudomonas aeruginosa DsbA1 with increased catalytic surface accessibility.

Acta Crystallogr D Biol Crystallogr 2015 Dec 26;71(Pt 12):2386-95. Epub 2015 Nov 26.

Institute for Molecular Bioscience, Division of Chemistry and Structural Biology, University of Queensland, 306 Carmody Road, Brisbane, Queensland 4072, Australia.

Pseudomonas aeruginosa is an opportunistic human pathogen for which new antimicrobial drug options are urgently sought. P. aeruginosa disulfide-bond protein A1 (PaDsbA1) plays a pivotal role in catalyzing the oxidative folding of multiple virulence proteins and as such holds great promise as a drug target. Read More

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December 2015

Unravelling the shape and structural assembly of the photosynthetic GAPDH-CP12-PRK complex from Arabidopsis thaliana by small-angle X-ray scattering analysis.

Acta Crystallogr D Biol Crystallogr 2015 Dec 26;71(Pt 12):2372-85. Epub 2015 Nov 26.

Department of Pharmacy and Biotechnology - FaBiT, University of Bologna, Bologna, Italy.

Oxygenic photosynthetic organisms produce sugars through the Calvin-Benson cycle, a metabolism that is tightly linked to the light reactions of photosynthesis and is regulated by different mechanisms, including the formation of protein complexes. Two enzymes of the cycle, glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and phosphoribulokinase (PRK), form a supramolecular complex with the regulatory protein CP12 with the formula (GAPDH-CP122-PRK)2, in which both enzyme activities are transiently inhibited during the night. Small-angle X-ray scattering analysis performed on both the GAPDH-CP12-PRK complex and its components, GAPDH-CP12 and PRK, from Arabidopsis thaliana showed that (i) PRK has an elongated, bent and screwed shape, (ii) the oxidized N-terminal region of CP12 that is not embedded in the GAPDH-CP12 complex prefers a compact conformation and (iii) the interaction of PRK with the N-terminal region of CP12 favours the approach of two GAPDH tetramers. Read More

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December 2015

A structural view of the dissociation of Escherichia coli tryptophanase.

Acta Crystallogr D Biol Crystallogr 2015 Dec 26;71(Pt 12):2364-71. Epub 2015 Nov 26.

Department of Clinical Biochemistry and Pharmacology, Ben-Gurion University of the Negev, PO Box 105, Beer Sheva 84105, Israel.

Tryptophanase (Trpase) is a pyridoxal 5'-phosphate (PLP)-dependent homotetrameric enzyme which catalyzes the degradation of L-tryptophan. Trpase is also known for its cold lability, which is a reversible loss of activity at low temperature (2°C) that is associated with the dissociation of the tetramer. Escherichia coli Trpase dissociates into dimers, while Proteus vulgaris Trpase dissociates into monomers. Read More

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December 2015

Structural insights into the interaction of human IgG1 with FcγRI: no direct role of glycans in binding.

Acta Crystallogr D Biol Crystallogr 2015 Nov 31;71(Pt 11):2354-61. Epub 2015 Oct 31.

Department of Antibody Discovery and Protein Engineering, MedImmune LLC, 1 MedImmune Way, Gaithersburg, MD 20878, USA.

The three-dimensional structure of a human IgG1 Fc fragment bound to wild-type human FcγRI is reported. The structure of the corresponding complex was solved at a resolution of 2.4 Å using molecular replacement; this is the highest resolution achieved for an unmutated FcγRI molecule. Read More

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November 2015

The oxygenating constituent of 3,6-diketocamphane monooxygenase from the CAM plasmid of Pseudomonas putida: the first crystal structure of a type II Baeyer-Villiger monooxygenase.

Acta Crystallogr D Biol Crystallogr 2015 Nov 31;71(Pt 11):2344-53. Epub 2015 Oct 31.

The Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, England.

The three-dimensional structures of the native enzyme and the FMN complex of the overexpressed form of the oxygenating component of the type II Baeyer-Villiger 3,6-diketocamphane monooxygenase have been determined to 1.9 Å resolution. The structure of this dimeric FMN-dependent enzyme, which is encoded on the large CAM plasmid of Pseudomonas putida, has been solved by a combination of multiple anomalous dispersion from a bromine crystal soak and molecular replacement using a bacterial luciferase model. Read More

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November 2015

MeshAndCollect: an automated multi-crystal data-collection workflow for synchrotron macromolecular crystallography beamlines.

Acta Crystallogr D Biol Crystallogr 2015 Nov 31;71(Pt 11):2328-43. Epub 2015 Oct 31.

Structural Biology Group, European Synchrotron Radiation Facility, CS 40220, 38043 Grenoble, France.

Here, an automated procedure is described to identify the positions of many cryocooled crystals mounted on the same sample holder, to rapidly predict and rank their relative diffraction strengths and to collect partial X-ray diffraction data sets from as many of the crystals as desired. Subsequent hierarchical cluster analysis then allows the best combination of partial data sets, optimizing the quality of the final data set obtained. The results of applying the method developed to various systems and scenarios including the compilation of a complete data set from tiny crystals of the membrane protein bacteriorhodopsin and the collection of data sets for successful structure determination using the single-wavelength anomalous dispersion technique are also presented. Read More

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November 2015

Structural insight and flexible features of NS5 proteins from all four serotypes of Dengue virus in solution.

Acta Crystallogr D Biol Crystallogr 2015 Nov 31;71(Pt 11):2309-27. Epub 2015 Oct 31.

School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.

Infection by the four serotypes of Dengue virus (DENV-1 to DENV-4) causes an important arthropod-borne viral disease in humans. The multifunctional DENV nonstructural protein 5 (NS5) is essential for capping and replication of the viral RNA and harbours a methyltransferase (MTase) domain and an RNA-dependent RNA polymerase (RdRp) domain. In this study, insights into the overall structure and flexibility of the entire NS5 of all four Dengue virus serotypes in solution are presented for the first time. Read More

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November 2015

Structure and inhibition of subunit I of the anthranilate synthase complex of Mycobacterium tuberculosis and expression of the active complex.

Acta Crystallogr D Biol Crystallogr 2015 Nov 31;71(Pt 11):2297-308. Epub 2015 Oct 31.

School of Biological Sciences, University of Auckland, 3a Symonds Steet, Private Bag 90210, Auckland 1142, New Zealand.

The tryptophan-biosynthesis pathway is essential for Mycobacterium tuberculosis (Mtb) to cause disease, but not all of the enzymes that catalyse this pathway in this organism have been identified. The structure and function of the enzyme complex that catalyses the first committed step in the pathway, the anthranilate synthase (AS) complex, have been analysed. It is shown that the open reading frames Rv1609 (trpE) and Rv0013 (trpG) encode the chorismate-utilizing (AS-I) and glutamine amidotransferase (AS-II) subunits of the AS complex, respectively. Read More

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November 2015

Crystallographic study of a MATE transporter presents a difficult case in structure determination with low-resolution, anisotropic data and crystal twinning.

Acta Crystallogr D Biol Crystallogr 2015 Nov 31;71(Pt 11):2287-96. Epub 2015 Oct 31.

Department of Biochemistry and Molecular Biology, Rosalind Franklin University of Medicine and Science, North Chicago, Illinois, USA.

NorM from Neisseria gonorrhoeae (NorM-NG) belongs to the multidrug and toxic compound extrusion (MATE) family of membrane-transport proteins, which can extrude cytotoxic chemicals across cell membranes and confer multidrug resistance. Here, the structure determination of NorM-NG is described, which had been hampered by low resolution (∼ 4 Å), data anisotropy and pseudo-merohedral twinning. The crystal structure was solved using molecular replacement and was corroborated by conducting a difference Fourier analysis. Read More

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November 2015

The structure of the GemC1 coiled coil and its interaction with the Geminin family of coiled-coil proteins.

Acta Crystallogr D Biol Crystallogr 2015 Nov 31;71(Pt 11):2278-86. Epub 2015 Oct 31.

Department of Biochemistry, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands.

GemC1, together with Idas and Geminin, an important regulator of DNA-replication licensing and differentiation decisions, constitute a superfamily sharing a homologous central coiled-coil domain. To better understand this family of proteins, the crystal structure of a GemC1 coiled-coil domain variant engineered for better solubility was determined to 2.2 Å resolution. Read More

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November 2015

Structure of AadA from Salmonella enterica: a monomeric aminoglycoside (3'')(9) adenyltransferase.

Acta Crystallogr D Biol Crystallogr 2015 Nov 31;71(Pt 11):2267-77. Epub 2015 Oct 31.

Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden.

Aminoglycoside resistance is commonly conferred by enzymatic modification of drugs by aminoglycoside-modifying enzymes such as aminoglycoside nucleotidyltransferases (ANTs). Here, the first crystal structure of an ANT(3'')(9) adenyltransferase, AadA from Salmonella enterica, is presented. AadA catalyses the magnesium-dependent transfer of adenosine monophosphate from ATP to the two chemically dissimilar drugs streptomycin and spectinomycin. Read More

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November 2015

The putative role of some conserved water molecules in the structure and function of human transthyretin.

Acta Crystallogr D Biol Crystallogr 2015 Nov 31;71(Pt 11):2248-66. Epub 2015 Oct 31.

Supercomputer Education and Research Centre, Indian Institute of Science, Bangalore 560 012, India.

Human transthyretin (hTTR) is a multifunctional protein that is involved in several neurodegenerative diseases. Besides the transportation of thyroxin and vitamin A, it is also involved in the proteolysis of apolipoprotein A1 and Aβ peptide. Extensive analyses of 32 high-resolution X-ray and neutron diffraction structures of hTTR followed by molecular-dynamics simulation studies using a set of 15 selected structures affirmed the presence of 44 conserved water molecules in its dimeric structure. Read More

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November 2015

Superoxide reductase from Giardia intestinalis: structural characterization of the first SOR from a eukaryotic organism shows an iron centre that is highly sensitive to photoreduction.

Acta Crystallogr D Biol Crystallogr 2015 Nov 31;71(Pt 11):2236-47. Epub 2015 Oct 31.

Instituto de Tecnologia Química e Biológica, António Xavier Universidade Nova de Lisboa, Avenida da República, 2780-157 Oeiras, Portugal.

Superoxide reductase (SOR), which is commonly found in prokaryotic organisms, affords protection from oxidative stress by reducing the superoxide anion to hydrogen peroxide. The reaction is catalyzed at the iron centre, which is highly conserved among the prokaryotic SORs structurally characterized to date. Reported here is the first structure of an SOR from a eukaryotic organism, the protozoan parasite Giardia intestinalis (GiSOR), which was solved at 2. Read More

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November 2015

Selecting soluble/foldable protein domains through single-gene or genomic ORF filtering: structure of the head domain of Burkholderia pseudomallei antigen BPSL2063.

Acta Crystallogr D Biol Crystallogr 2015 Nov 31;71(Pt 11):2227-35. Epub 2015 Oct 31.

Department of Biosciences, University of Milan, Via Celoria 26, 20133 Milan, Italy.

The 1.8 Å resolution crystal structure of a conserved domain of the potential Burkholderia pseudomallei antigen and trimeric autotransporter BPSL2063 is presented as a structural vaccinology target for melioidosis vaccine development. Since BPSL2063 (1090 amino acids) hosts only one conserved domain, and the expression/purification of the full-length protein proved to be problematic, a domain-filtering library was generated using β-lactamase as a reporter gene to select further BPSL2063 domains. Read More

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November 2015

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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November 2015

Structural basis for the slow photocycle and late proton release in Acetabularia rhodopsin I from the marine plant Acetabularia acetabulum.

Acta Crystallogr D Biol Crystallogr 2015 Nov 27;71(Pt 11):2203-16. Epub 2015 Oct 27.

RIKEN Systems and Structural Biology Center, Yokohama 230-0045, Japan.

Although many crystal structures of microbial rhodopsins have been solved, those with sufficient resolution to identify the functional water molecules are very limited. In this study, the Acetabularia rhodopsin I (ARI) protein derived from the marine alga A. acetabulum was synthesized on a large scale by the Escherichia coli cell-free membrane-protein production method, and crystal structures of ARI were determined at the second highest (1. Read More

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November 2015

Structure of the ordered hydration of amino acids in proteins: analysis of crystal structures.

Acta Crystallogr D Biol Crystallogr 2015 Nov 27;71(Pt 11):2192-202. Epub 2015 Oct 27.

Laboratory of Biomolecular Recognition, Institute of Biotechnology CAS, Videnska 1083, 142 20 Prague, Czech Republic.

Crystallography provides unique information about the arrangement of water molecules near protein surfaces. Using a nonredundant set of 2818 protein crystal structures with a resolution of better than 1.8 Å, the extent and structure of the hydration shell of all 20 standard amino-acid residues were analyzed as function of the residue conformation, secondary structure and solvent accessibility. Read More

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November 2015