4bnq

The structure of the Staphylococcus aureus Ham1 protein

spinqualitylabelsall models 4bnq, resolution 2.28Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 4bnq is a 2 chain structure with sequence from Staphylococcus aureus aureus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: GOL, PO4 Activity: Nucleoside-triphosphate diphosphatase, with EC number 3.6.1.19 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function [NTPA_STAAN] Pyrophosphatase that hydrolyzes non-canonical purine nucleotides such as XTP and ITP/dITP to their respective monophosphate derivatives. Might exclude non-canonical purines from DNA precursor pool, thus preventing their incorporation into DNA and avoiding chromosomal lesions (By similarity). Publication Abstract from PubMed Molecular replacement is the method of choice for X-ray crystallographic structure determination provided that suitable structural homologues are available in the PDB. Presently, there are ~80,000 structures in the PDB (8074 were deposited in the year 2012 alone), of which ~70% have been solved by molecular replacement. For successful molecular replacement the model must cover at least 50% of the total structure and the Calpha r.m.s.d. between the core model and the structure to be solved must be less than 2 A. Here, an approach originally implemented in the CaspR server (https://www.igs.cnrs-mrs.fr/Caspr2/index.cgi) based on homology modelling to search for a molecular-replacement solution is discussed. How the use of as much information as possible from different sources can improve the model(s) is briefly described. The combination of structural information with distantly related sequences is crucial to optimize the multiple alignment that will define the boundaries of the core domains. PDB clusters (sequences with >/=30% identical residues) can also provide information on the eventual changes in conformation and will help to explore the relative orientations assumed by protein subdomains. Normal-mode analysis can also help in generating series of conformational models in the search for a molecular-replacement solution. Of course, finding a correct solution is only the first step and the accuracy of the identified solution is as important as the data quality to proceed through refinement. Here, some possible reasons for failure are discussed and solutions are proposed using a set of successful examples. Molecular replacement: tricks and treats.,Abergel C Acta Crystallogr D Biol Crystallogr. 2013 Nov;69(Pt 11):2167-73. doi:, 10.1107/S0907444913015291. Epub 2013 Oct 12. PMID:24189227 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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