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Acta Crystallographica. Section D, Structural Biology

Massimiliano Veroux
No abstract text is available yet for this article.
November 1, 2016: Acta Crystallographica. Section D, Structural Biology
Armin Ruf, Tim Tetaz, Brigitte Schott, Catherine Joseph, Markus G Rudolph
Fructose-1,6-bisphosphatase (FBPase) is a key regulator of gluconeogenesis and a potential drug target for type 2 diabetes. FBPase is a homotetramer of 222 symmetry with a major and a minor dimer interface. The dimers connected via the minor interface can rotate with respect to each other, leading to the inactive T-state and active R-state conformations of FBPase. Here, the first crystal structure of human liver FBPase in the R-state conformation is presented, determined at a resolution of 2.2 Å in a tetragonal setting that exhibits an unusual arrangement of noncrystallographic symmetry (NCS) elements...
November 1, 2016: Acta Crystallographica. Section D, Structural Biology
Pawel Drozdzal, Miroslaw Gilski, Mariusz Jaskolski
The self-complementary d(CGCGCG) hexanucleotide was synthesized with both D-2'-deoxyribose (the natural enantiomer) and L-2'-deoxyribose, and the two enantiomers were mixed in racemic (1:1) proportions and crystallized, producing a new crystal form with C2/c symmetry that diffracted X-rays to 0.78 Å resolution. The structure was solved by direct, dual-space and molecular-replacement methods and was refined to an R factor of 13.86%. The asymmetric unit of the crystal contains one Z-DNA duplex and three Mg(2+) sites...
November 1, 2016: Acta Crystallographica. Section D, Structural Biology
Francesco Manzoni, Kadhirvel Saraboji, Janina Sprenger, Rohit Kumar, Ann Louise Noresson, Ulf J Nilsson, Hakon Leffler, S Zoë Fisher, Tobias E Schrader, Andreas Ostermann, Leighton Coates, Matthew P Blakeley, Esko Oksanen, Derek T Logan
Galectin-3 is an important protein in molecular signalling events involving carbohydrate recognition, and an understanding of the hydrogen-bonding patterns in the carbohydrate-binding site of its C-terminal domain (galectin-3C) is important for the development of new potent inhibitors. The authors are studying these patterns using neutron crystallography. Here, the production of perdeuterated human galectin-3C and successive improvement in crystal size by the development of a crystal-growth protocol involving feeding of the crystallization drops are described...
November 1, 2016: Acta Crystallographica. Section D, Structural Biology
Marek Grabowski, Karol M Langner, Marcin Cymborowski, Przemyslaw J Porebski, Piotr Sroka, Heping Zheng, David R Cooper, Matthew D Zimmerman, Marc André Elsliger, Stephen K Burley, Wladek Minor
The low reproducibility of published experimental results in many scientific disciplines has recently garnered negative attention in scientific journals and the general media. Public transparency, including the availability of `raw' experimental data, will help to address growing concerns regarding scientific integrity. Macromolecular X-ray crystallography has led the way in requiring the public dissemination of atomic coordinates and a wealth of experimental data, making the field one of the most reproducible in the biological sciences...
November 1, 2016: Acta Crystallographica. Section D, Structural Biology
Andrew F Bent, Greg Mann, Wael E Houssen, Vitaliy Mykhaylyk, Ramona Duman, Louise Thomas, Marcel Jaspars, Armin Wagner, James H Naismith
Determination of protein crystal structures requires that the phases are derived independently of the observed measurement of diffraction intensities. Many techniques have been developed to obtain phases, including heavy-atom substitution, molecular replacement and substitution during protein expression of the amino acid methionine with selenomethionine. Although the use of selenium-containing methionine has transformed the experimental determination of phases it is not always possible, either because the variant protein cannot be produced or does not crystallize...
November 1, 2016: Acta Crystallographica. Section D, Structural Biology
Filipe Freire, Anil Verma, Pedro Bule, Victor D Alves, Carlos M G A Fontes, Arun Goyal, Shabir Najmudin
Glucuronoxylan endo-β-1,4-xylanases cleave the xylan chain specifically at sites containing 4-O-methylglucuronic acid substitutions. These enzymes have recently received considerable attention owing to their importance in the cooperative hydrolysis of heteropolysaccharides. However, little is known about the hydrolysis of glucuronoxylans in extreme environments. Here, the structure of a thermostable family 30 glucuronoxylan endo-β-1,4-xylanase (CtXyn30A) from Clostridium thermocellum is reported. CtXyn30A is part of the cellulosome, a highly elaborate multi-enzyme complex secreted by the bacterium to efficiently deconstruct plant cell-wall carbohydrates...
November 1, 2016: 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
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