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Acta Crystallographica. Section D, Structural Biology

Oleg Kovalevskiy, Robert A Nicholls, Garib N Murshudov
Since the ratio of the number of observations to adjustable parameters is small at low resolution, it is necessary to use complementary information for the analysis of such data. ProSMART is a program that can generate restraints for macromolecules using homologous structures, as well as generic restraints for the stabilization of secondary structures. These restraints are used by REFMAC5 to stabilize the refinement of an atomic model. However, the optimal refinement protocol varies from case to case, and it is not always obvious how to select appropriate homologous structure(s), or other sources of prior information, for restraint generation...
October 1, 2016: Acta Crystallographica. Section D, Structural Biology
Guray Kuzu, Ozlem Keskin, Ruth Nussinov, Attila Gursoy
The structures of protein assemblies are important for elucidating cellular processes at the molecular level. Three-dimensional electron microscopy (3DEM) is a powerful method to identify the structures of assemblies, especially those that are challenging to study by crystallography. Here, a new approach, PRISM-EM, is reported to computationally generate plausible structural models using a procedure that combines crystallographic structures and density maps obtained from 3DEM. The predictions are validated against seven available structurally different crystallographic complexes...
October 1, 2016: Acta Crystallographica. Section D, Structural Biology
Janice M Reimer, Martin N Aloise, Harold R Powell, T Martin Schmeing
Nonribosomal peptide synthetases (NRPSs) are multimodular enzymes that synthesize a myriad of diverse molecules. Tailoring domains have been co-opted into NRPSs to introduce further variety into nonribosomal peptide products. Linear gramicidin synthetase contains a unique formylation-tailoring domain in its initiation module (F-A-PCP). The structure of the F-A di-domain has previously been determined in a crystal form which had large solvent channels and no density for the minor Asub subdomain. An attempt was made to take advantage of this packing by removing the Asub subdomain from the construct (F-AΔsub) in order to produce a crystal that could accommodate the PCP domain...
October 1, 2016: Acta Crystallographica. Section D, Structural Biology
John J Tanner
The radius of gyration is a fundamental structural parameter that is particularly useful for describing polymers. It has been known since Flory's seminal work in the mid-20th century that polymers show a power-law dependence, where the radius of gyration is proportional to the number of residues raised to a power. The power-law exponent has been measured experimentally for denatured proteins and derived empirically for folded monomeric proteins using crystal structures. Here, the biological assemblies in the Protein Data Bank are surveyed to derive the power-law parameters for protein oligomers having degrees of oligomerization of 2-6 and 8...
October 1, 2016: Acta Crystallographica. Section D, Structural Biology
Wouter G Touw, Bart van Beusekom, Jochem M G Evers, Gert Vriend, Robbie P Joosten
Many crystal structures in the Protein Data Bank contain zinc ions in a geometrically distorted tetrahedral complex with four Cys and/or His ligands. A method is presented to automatically validate and correct these zinc complexes. Analysis of the corrected zinc complexes shows that the average Zn-Cys distances and Cys-Zn-Cys angles are a function of the number of cysteines and histidines involved. The observed trends can be used to develop more context-sensitive targets for model validation and refinement.
October 1, 2016: Acta Crystallographica. Section D, Structural Biology
Inseong Jo, Nohra Park, In Young Chung, You Hee Cho, Nam Chul Ha
In bacteria, many Dsb-family proteins play diverse roles in the conversion between the oxidized and reduced states of cysteine residues of substrate proteins. Most Dsb enzymes catalyze disulfide formation in periplasmic or secreted substrate proteins. Recently, a DsbM protein has been found in a Gram-negative bacterium, and was characterized as a cytosolic Dsb member with the conserved CXXC motif on the basis of sequence homology to the Dsb-family proteins. The protein was implicated in the reduction of the cytoplasmic redox-sensor protein OxyR in Pseudomonas aeruginosa...
October 1, 2016: Acta Crystallographica. Section D, Structural Biology
Stephanie Hutin, Martha Brennich, Benoit Maillot, Adam Round
Biological small-angle X-ray scattering (BioSAXS) is a powerful technique to determine the solution structure, particle size, shape and surface-to-volume ratio of macromolecules. However, a drawback is that the sample needs to be monodisperse. To ensure this, size-exclusion chromatography (SEC) has been implemented on many BioSAXS beamlines. Here, the integration of ion-exchange chromatography (IEC) using both continuous linear and step gradients on a beamline is described. Background subtraction for continuous gradients by shifting a reference measurement and two different approaches for step gradients, which are based on interpolating between two background measurements, are discussed...
October 1, 2016: Acta Crystallographica. Section D, Structural Biology
Kaushik Hatti, Ashutosh Gulati, Narayanaswamy Srinivasan, M R N Murthy
During the past decade, the authors have collected a few X-ray diffraction data sets from protein crystals that appeared to be easy cases of molecular replacement but failed to yield structures even after extensive trials. Here, the use of a large-scale molecular replacement method that explores all structurally characterized domains as phasing models to determine the structure corresponding to two data sets collected at 1.9 and 2.3 Å resolution is reported. These two structures were of the same protein independently crystallized in 2007 and 2011...
October 1, 2016: Acta Crystallographica. Section D, Structural Biology
Michael Blaber
No abstract text is available yet for this article.
September 2016: Acta Crystallographica. Section D, Structural Biology
Alexandre Urzhumtsev, Pavel V Afonine, Andrew H Van Benschoten, James S Fraser, Paul D Adams
Researcher feedback has indicated that in Urzhumtsev et al. [(2015) Acta Cryst. D71, 1668-1683] clarification of key parts of the algorithm for interpretation of TLS matrices in terms of elemental atomic motions and corresponding ensembles of atomic models is required. Also, it has been brought to the attention of the authors that the incorrect PDB code was reported for one of test models. These issues are addressed in this article.
September 1, 2016: Acta Crystallographica. Section D, Structural Biology
Pawel A Janowski, Nigel W Moriarty, Brian P Kelley, David A Case, Darrin M York, Paul D Adams, Gregory L Warren
Modern crystal structure refinement programs rely on geometry restraints to overcome the challenge of a low data-to-parameter ratio. While the classical Engh and Huber restraints work well for standard amino-acid residues, the chemical complexity of small-molecule ligands presents a particular challenge. Most current approaches either limit ligand restraints to those that can be readily described in the Crystallographic Information File (CIF) format, thus sacrificing chemical flexibility and energetic accuracy, or they employ protocols that substantially lengthen the refinement time, potentially hindering rapid automated refinement workflows...
September 2016: Acta Crystallographica. Section D, Structural Biology
Maria Rutkiewicz-Krotewicz, Agnieszka J Pietrzyk-Brzezinska, Bartosz Sekula, Hubert Cieśliński, Anna Wierzbicka-Woś, Józef Kur, Anna Bujacz
The crystal structure of a novel dimeric β-D-galactosidase from Paracoccus sp. 32d (ParβDG) was solved in space group P212121 at a resolution of 2.4 Å by molecular replacement with multiple models using the BALBES software. This enzyme belongs to glycoside hydrolase family 2 (GH2), similar to the tetrameric and hexameric β-D-galactosidases from Escherichia coli and Arthrobacter sp. C2-2, respectively. It is the second known structure of a cold-active GH2 β-galactosidase, and the first in the form of a functional dimer, which is also present in the asymmetric unit...
September 2016: Acta Crystallographica. Section D, Structural Biology
Arnau Casanas, Rangana Warshamanage, Aaron D Finke, Ezequiel Panepucci, Vincent Olieric, Anne Nöll, Robert Tampé, Stefan Brandstetter, Andreas Förster, Marcus Mueller, Clemens Schulze-Briese, Oliver Bunk, Meitian Wang
The development of single-photon-counting detectors, such as the PILATUS, has been a major recent breakthrough in macromolecular crystallography, enabling noise-free detection and novel data-acquisition modes. The new EIGER detector features a pixel size of 75 × 75 µm, frame rates of up to 3000 Hz and a dead time as low as 3.8 µs. An EIGER 1M and EIGER 16M were tested on Swiss Light Source beamlines X10SA and X06SA for their application in macromolecular crystallography. The combination of fast frame rates and a very short dead time allows high-quality data acquisition in a shorter time...
September 2016: Acta Crystallographica. Section D, Structural Biology
Ulrich Zander, Michele Cianci, Nicolas Foos, Catarina S Silva, Luca Mazzei, Chloe Zubieta, Alejandro de Maria, Max H Nanao
Recent advances in macromolecular crystallography have made it practical to rapidly collect hundreds of sub-data sets consisting of small oscillations of incomplete data. This approach, generally referred to as serial crystallography, has many uses, including an increased effective dose per data set, the collection of data from crystals without harvesting (in situ data collection) and studies of dynamic events such as catalytic reactions. However, selecting which data sets from this type of experiment should be merged can be challenging and new methods are required...
September 2016: Acta Crystallographica. Section D, Structural Biology
Pavel Mikulecký, Jirí Zahradník, Petr Kolenko, Jiří Černý, Tatsiana Charnavets, Lucie Kolářová, Iva Nečasová, Phuong Ngoc Pham, Bohdan Schneider
Interferon-γ receptor 2 is a cell-surface receptor that is required for interferon-γ signalling and therefore plays a critical immunoregulatory role in innate and adaptive immunity against viral and also bacterial and protozoal infections. A crystal structure of the extracellular part of human interferon-γ receptor 2 (IFNγR2) was solved by molecular replacement at 1.8 Å resolution. Similar to other class 2 receptors, IFNγR2 has two fibronectin type III domains. The characteristic structural features of IFNγR2 are concentrated in its N-terminal domain: an extensive π-cation motif of stacked residues KWRWRH, a NAG-W-NAG sandwich (where NAG stands for N-acetyl-D-glucosamine) and finally a helix formed by residues 78-85, which is unique among class 2 receptors...
September 2016: Acta Crystallographica. Section D, Structural Biology
Tristan Ian Croll, Gregers Rom Andersen
While the rapid proliferation of high-resolution structures in the Protein Data Bank provides a rich set of templates for starting models, it remains the case that a great many structures both past and present are built at least in part by hand-threading through low-resolution and/or weak electron density. With current model-building tools this task can be challenging, and the de facto standard for acceptable error rates (in the form of atomic clashes and unfavourable backbone and side-chain conformations) in structures based on data with dmax not exceeding 3...
September 2016: Acta Crystallographica. Section D, Structural Biology
Shun Zhao, Xiao Wang, Guoqi Niu, Wei Dong, Jia Wang, Ying Fang, Yajing Lin, Lin Liu
Copper homeostasis integrates multiple processes from sensing to storage and efflux out of the cell. CopM is a cyanobacterial metallochaperone, the gene for which is located upstream of a two-component system for copper resistance, but the molecular basis for copper recognition by this four-helical bundle protein is unknown. Here, crystal structures of CopM in apo, copper-bound and silver-bound forms are reported. Monovalent copper/silver ions are buried within the bundle core; divalent copper ions are found on the surface of the bundle...
September 2016: Acta Crystallographica. Section D, Structural Biology
Hong Wen Zhou, Christian Burger, Hao Wang, Benjamin S Hsiao, Benjamin Chu, Lila Graham
The evolution of vertebrates required a key development in supramolecular evolution: internally mineralized collagen fibrils. In bone, collagen molecules and mineral crystals form a nanocomposite material comparable to cast iron in tensile strength, but several times lighter and more flexible. Current understanding of the internal nanoscale structure of collagen fibrils, derived from studies of rat tail tendon (RTT), does not explain how nucleation and growth of mineral crystals can occur inside a collagen fibril...
September 2016: Acta Crystallographica. Section D, Structural Biology
Jung Hyun Na, Sun Shin Cha
AmpC BER is an extended substrate spectrum class C β-lactamase with a two-amino-acid insertion in the R2 loop compared with AmpC EC2. The crystal structures of AmpC BER (S64A mutant) and AmpC EC2 were determined. Structural comparison of the two proteins revealed that the insertion increases the conformational flexibility of the R2 loop. Two citrate molecules originating from the crystallization solution were observed in the active site of the S64A mutant. One citrate molecule makes extensive interactions with active-site residues that are highly conserved among class C β-lactamases, whereas the other one is weakly bound...
August 2016: Acta Crystallographica. Section D, Structural Biology
Didier Nurizzo, Matthew W Bowler, Hugo Caserotto, Fabien Dobias, Thierry Giraud, John Surr, Nicolas Guichard, Gergely Papp, Matias Guijarro, Christoph Mueller-Dieckmann, David Flot, Sean McSweeney, Florent Cipriani, Pascal Theveneau, Gordon A Leonard
Automation of the mounting of cryocooled samples is now a feature of the majority of beamlines dedicated to macromolecular crystallography (MX). Robotic sample changers have been developed over many years, with the latest designs increasing capacity, reliability and speed. Here, the development of a new sample changer deployed at the ESRF beamline MASSIF-1 (ID30A-1), based on an industrial six-axis robot, is described. The device, named RoboDiff, includes a high-capacity dewar, acts as both a sample changer and a high-accuracy goniometer, and has been designed for completely unattended sample mounting and diffraction data collection...
August 2016: Acta Crystallographica. Section D, Structural Biology
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