Crystallography databases

The authors express their gratitude to the Ministry of Industry and Commerce of the Czech Republic for supporting the work within the framework of research project No. FC-M2/05 and to Grant Agency of the Czech Republic for support of an access to the crystallography database in Cambridge (within the framework of the project No. 203/02/0436). 

Figure 9 The coordination of silver in silver sulfadiazine, the topical agent for bums and wound treatment the Ag-Ag dimeric unit stabilized by two head-to-tail bridging sulfadiazine ligands bound via pyrimidinyl and sulfamido nitrogen donor atoms only the nitrogen and sulfur donor atoms of the third sulfadiazine ligands are shown. SULPMS from the Cambridge Crystallography Database...

The Cambridge Crystallographis Database - Crystallographic Dta Centre, Univ. Chemical Lab.,Lensfield Road, Cambridge, CB 2 1 EW, England. 

PDB, NRL3D Protein Data Bank - protein structures (mostly fror X-ray crystallography). NRL3D is a derived sequence database in PIR format... 

EE Abola, EC Bernstein, SH Bryant, TF Koetzle, J Weng. Protein data bank. In EH Allen, G Bergerhoff, R Sievers, eds. Crystallographic Databases Information, Content, Software Systems, Scientific Applications, Bonn Data Commission of the International Union of Crystallography, 1987, pp 107-132. 

In the protein structure database PDB ( http //www. rcsb.org/pdb), by X-ray crystallography and NMR spectroscopy, experimentally solved 3D-protein structures are available to the public. Homology model building for a query sequence uses protein portions of known 3D-stmctures as structural templates for proteins with high sequence similarity. 

In the case of being successful in calculating multiple conformations by using time- or ensemble-averaged MD restraints the solved molecular structures are presented as 3D models and can be deposited in an electronic structure database (17). Finally, it is recommended to provide an accurate explanation of the procedures used for the structure elucidation because the application of different methods (NMR, DG, MD, SA, Monte-Carlo calculations. X-ray crystallography) may result in varying conformational models which do not implicitly display the real state of a molecule. This aspect should be always kept in mind when dealing with structure determination methods. 

Due to the ready accessibility of SH2 domains by molecular biology techniques, numerous experimentally determined 3D structures of SH2 domains derived by X-ray crystallography as well as heteronuclear multidimensional NMR spectroscopy are known today. The current version of the protein structure database, accessible to the scientific community by, e.g., the Internet (http //www.rcsb.org/pdb/) contains around 80 entries of SH2 domain structures and complexes thereof. Today, the SH2 domain structures of Hck [62], Src [63-66], Abl [67], Grb2 [68-71], Syp [72], PLCy [73], Fyn [74], SAP [75], Lck [76,77], the C- and N-terminal SH2 domain ofp85a [78-80], and of the tandem SH2 domains Syk [81,82], ZAP70 [83,84], and SHP-2 [85] are determined. All SH2 domains display a conserved 3D structure as can be expected from multiple sequence alignments (Fig. 4). The common structural fold consists of a central three-stranded antiparallel ft sheet that is occasionally extended by one to three additional short strands (Fig. 5). This central ft sheet forms the spine of the domain which is flanked on both sides by regular a helices [49, 50,60]. 

For protein crystallography, the repository of most protein crystal structures is the PDB hosted at http // www.rcsb.org/pdb/ (Berman et al., 2000). This database contains the 3-D coordinates (and sometimes the structure factor files) for almost all protein crystal structures. Most journals currently require deposition of the coordinates when pubhshing stmcture papers. Each structure is given a unique identification code that will be listed in the paper (see Figure 22-1 for examples of PDB codes). Structures can be accessed using this code, or using various other search criteria. The PDB also contains structural information for NMR structures. 

Abola EE, Bernstein FC, Bryant SH, Koetzle TF,Weng J (1987) In Allen FH, Bergerhoff G, Sievers R (eds) Protein data bank in crystaUographic databases-information content, software systems, scientific applications. Data Commission of the International Union of Crystallography, Bonn Cambridge Chester, pp 107-132... 

Cambridge Structural Database. A collection of >270K experimental structures for organic and organometallic compounds from X-ray crystallography and neutron diffraction. 

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