Citations
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Ribonuclease from Streptomyces aureofaciens at atomic resolution.
TL;DR: Refinement with anisotropic atomic temperature factors resulted in increased accuracy of the structure and revealed density for a partially occupied anion in the nucleotide binding site of molecule A in the native structure which was not seen at lower resolution.
Journal ArticleDOI
The protein common interface database (ProtCID)—a comprehensive database of interactions of homologous proteins in multiple crystal forms
Qifang Xu,Roland L. Dunbrack +1 more
TL;DR: By examining interfaces that are shared by many homologous proteins in different CFs, it is found that the PDB and the Protein Interfaces, Surfaces, and Assemblies (PISA) are not always consistent in their annotations of biological assemblies in a homologueous family.
Journal ArticleDOI
The Time-resolved and Extreme-conditions XAS (TEXAS) facility at the European Synchrotron Radiation Facility: the energy-dispersive X-ray absorption spectroscopy beamline ID24
Sakura Pascarelli,Olivier Mathon,Trevor Mairs,Innokenty Kantor,Giovanni Agostini,C. Strohm,Sebastien Pasternak,François Perrin,G. Berruyer,P. Chappelet,C. Clavel,M.C. Dominguez +11 more
TL;DR: The new energy-dispersive XAS beamline at the European Synchrotron Radiation Facility is presented and its performance is illustrated with a few recent examples of experiments by different user groups.
Journal ArticleDOI
Detection of ligand binding hot spots on protein surfaces via fragment-based methods: application to DJ-1 and glucocerebrosidase
Melissa R. Landon,Raquel L. Lieberman,Quyen Q. Hoang,Shulin Ju,Jose M. M. Caaveiro,Jose M. M. Caaveiro,Susan D. Orwig,Dima Kozakov,Ryan Brenke,Gwo-Yu Chuang,Dmitry Beglov,Sandor Vajda,Gregory A. Petsko,Dagmar Ringe +13 more
TL;DR: Comparison of data derived via MSCS and FTMap shows that FTMap, a computational method for the identification of fragment binding hot spots, is an accurate and robust alternative to the performance of expensive and difficult crystallographic experiments.
Journal ArticleDOI
ElaC Encodes a Novel Binuclear Zinc Phosphodiesterase
TL;DR: Analysis of the primary sequence indicates homology to an arylsulfatase and predicts a metallo-β-lactamase fold, and these results identify the currently unassigned gene product ElaC to be a novel binuclear zinc phosphodiesterase.
References
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The Protein Data Bank
Helen M. Berman,John D. Westbrook,Zukang Feng,Gary L. Gilliland,Talapady N. Bhat,Helge Weissig,Ilya N. Shindyalov,Philip E. Bourne +7 more
TL;DR: The goals of the PDB are described, the systems in place for data deposition and access, how to obtain further information and plans for the future development of the resource are described.
Journal ArticleDOI
Crystal structure refinement with SHELXL
TL;DR: New features added to the refinement program SHELXL since 2008 are described and explained.
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Coot: model-building tools for molecular graphics.
Paul Emsley,Kevin Cowtan +1 more
TL;DR: CCP4mg is a project that aims to provide a general-purpose tool for structural biologists, providing tools for X-ray structure solution, structure comparison and analysis, and publication-quality graphics.
Journal ArticleDOI
PHENIX: a comprehensive Python-based system for macromolecular structure solution
Paul D. Adams,Paul D. Adams,Pavel V. Afonine,Gábor Bunkóczi,Vincent B. Chen,Ian W. Davis,Nathaniel Echols,Jeffrey J. Headd,Li-Wei Hung,Gary J. Kapral,Ralf W. Grosse-Kunstleve,Airlie J. McCoy,Nigel W. Moriarty,Robert D. Oeffner,Randy J. Read,David S. Richardson,Jane S. Richardson,Thomas C. Terwilliger,Peter H. Zwart +18 more
TL;DR: The PHENIX software for macromolecular structure determination is described and its uses and benefits are described.
Journal ArticleDOI
Phaser crystallographic software
Airlie J. McCoy,Ralf W. Grosse-Kunstleve,Paul D. Adams,Martyn Winn,Laurent C. Storoni,Randy J. Read +5 more
TL;DR: A description is given of Phaser-2.1: software for phasing macromolecular crystal structures by molecular replacement and single-wavelength anomalous dispersion phasing.