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PDB Entries (pdb + entry)
Selected AbstractsPDB_REDO: automated re-refinement of X-ray structure models in the PDBJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 3 2009Robbie P. Joosten Structural biology, homology modelling and rational drug design require accurate three-dimensional macromolecular coordinates. However, the coordinates in the Protein Data Bank (PDB) have not all been obtained using the latest experimental and computational methods. In this study a method is presented for automated re-refinement of existing structure models in the PDB. A large-scale benchmark with 16,807 PDB entries showed that they can be improved in terms of fit to the deposited experimental X-ray data as well as in terms of geometric quality. The re-refinement protocol uses TLS models to describe concerted atom movement. The resulting structure models are made available through the PDB_REDO databank (http://www.cmbi.ru.nl/pdb_redo/). Grid computing techniques were used to overcome the computational requirements of this endeavour. [source] Analysis and validation of carbohydrate three-dimensional structuresACTA CRYSTALLOGRAPHICA SECTION D, Issue 2 2009Thomas Lütteke Knowledge of the three-dimensional structures of the carbohydrate molecules is indispensable for a full understanding of the molecular processes in which carbohydrates are involved, such as protein glycosylation or protein,carbohydrate interactions. The Protein Data Bank (PDB) is a valuable resource for three-dimensional structural information on glycoproteins and protein,carbohydrate complexes. Unfortunately, many carbohydrate moieties in the PDB contain inconsistencies or errors. This article gives an overview of the information that can be obtained from individual PDB entries and from statistical analyses of sets of three-dimensional structures, of typical problems that arise during the analysis of carbohydrate three-dimensional structures and of the validation tools that are currently available to scientists to evaluate the quality of these structures. [source] Re-refinement from deposited X-ray data can deliver improved models for most PDB entriesACTA CRYSTALLOGRAPHICA SECTION D, Issue 2 2009Robbie P. Joosten The deposition of X-ray data along with the customary structural models defining PDB entries makes it possible to apply large-scale re-refinement protocols to these entries, thus giving users the benefit of improvements in X-ray methods that have occurred since the structure was deposited. Automated gradient refinement is an effective method to achieve this goal, but real-space intervention is most often required in order to adequately address problems detected by structure-validation software. In order to improve the existing protocol, automated re-refinement was combined with structure validation and difference-density peak analysis to produce a catalogue of problems in PDB entries that are amenable to automatic correction. It is shown that re-refinement can be effective in producing improvements, which are often associated with the systematic use of the TLS parameterization of B factors, even for relatively new and high-resolution PDB entries, while the accompanying manual or semi-manual map analysis and fitting steps show good prospects for eventual automation. It is proposed that the potential for simultaneous improvements in methods and in re-refinement results be further encouraged by broadening the scope of depositions to include refinement metadata and ultimately primary rather than reduced X-ray data. [source] Crystallization and preliminary X-ray analysis of a cohesin-like module from AF2375 of the archaeon Archaeoglobus fulgidusACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 3 2009Milana Voronov-Goldman A cohesin-like module of 160 amino-acid residues from the hypothetical protein AF2375 of the noncellulolytic, hyperthermophilic, sulfate-reducing archaeon Archaeoglobus fulgidus was cloned, expressed, purified, crystallized and subjected to X-ray structural study in order to compare its structure with those of cellulolytic cohesins. The crystals had cubic symmetry, with unit-cell parameters a = b = c = 101.75,Å in space group P4332, and diffracted to 1.82,Å resolution. The asymmetric unit contained a single cohesin molecule. A model assembled from six cohesin structures (PDB entries 1anu, 1aoh, 1g1k, 1qzn, 1zv9 and 1tyj) of very low sequence identity to the cohesin-like module was used in molecular-replacement attempts, producing a marginal solution. [source] Crystallization and preliminary X-ray diffraction analysis of the Thermoanaerobacter ethanolicus secondary alcohol dehydrogenase I86A mutantACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 7 2010Carla Protsko The Thermoanaerobacter ethanolicus secondary alcohol dehydrogenase I86A mutant is stereospecific for (R)-alcohols instead of (S)-alcohols. Pyramidal crystals grown in the presence of (R)-phenylethanol via the hanging-drop vapour-diffusion method diffracted to 3.2,Å resolution at the Canadian Light Source. The crystal belonged to the orthorhombic space group P212121, with unit-cell parameters a = 80.23, b = 124.90, c = 164.80,Å. The structure was solved by molecular replacement using the structure of T. brockii SADH (PDB entry 1ykf). 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