Reference Protein Data Bank

HyperChem contains a database of amino and nucleic acid residues so you can quickly build polymers con laining these subunits. You can also read in structures in files from standard databases, such as the Brookhaven Protein Data Bank (see the HyperChem Reference Manual). 

A model of a Pn helix formed by alanine side chains is illustrated for reference in Figure 13B (see color insert), while Figure 13A illustrates the common occurrence of the Pn backbone conformation among residues outside regions of regular secondary structure (Kleywegt and Jones, 1996 Serrano, 1995 Stapley and Creamer, 1999) in protein structures from the Protein Data Bank. 

Fig. 7.23 Comparison of calculated and observed (x-ray ) mean N-C(a)-C bond angles for 37 proteins selected as described by Jiang et al. (1997,G). This reference is also the source of the values plotted, which are the region-average values, and . Regions of cb/ri-space and region numbering are explained in the lower graph. Experimental values (x-ray) were taken from the Brookhaven Protein Data Bank Chemistry Department, Building 555 Brookhaven National Laboratory, Box 5000, Upton N.Y. 11973-5000). The calculated values were obtained as described in the text.

For updating the information presented in this chapter, a literature search on the keyword nitrogenase modified with structure, X ray, Mossbauer, iron sulfur cluster, or model compound will generate citations referring to the newest research results. A search of the Protein Data Bank (PDB) at the website address http //www.rcsb.org/pdb/ will yield the latest updates on X ray, NMR, and other submitted structural data. 

KcsA crystals suitable for X-ray crystallographic analysis using synchrotron radiation were obtained and the data collected and analyzed for multiple crystals and six different data sets as described in the 1998 Science publication (reference 15). The final KcsA pore structure, including amino acid residues 23 to 119 of the K+ channel, refined to 3.2 A. The X-ray data were deposited in the Protein Data Bank with the accession number 1BL8. 

Proteins are referred to by their identifying codes for the coordinate set in the Brookhaven Protein Data Bank (PDB) (Bernstein et ai, 1977). 

Computational results were obtained using Spartan 08 (Wavefunction Inc., Irvine, CA) and software programs from Accelrys Software Inc. with graphical displays generated by the Discovery Studio Visualizer. Where protein structures have been downloaded from the RCSB Protein Data Bank the full references and PDB IDs have been given. I wish to acknowledge the use of the Chemical Database Service at Daresbury for access to other crystal structures. Again, full primary sources can be found in the references. 

The Protein Data Bank (PDB http //www.pdb.org) is the worldwide repository of three-dimensional structural data of biological macromolecules, such as proteins and nucleic acids (Berman et al. 2003). The Protein Data Bank uses several text file-based formats for data deposition, processing, and archiving. The oldest of these is the Protein Data Bank format (Bernstein 1977), which is used both for deposition and for retrieval of results. It is a plain-text format whose main part, a so-called primary structure section, contains the atomic coordinates within the sequence of residues (e.g., nucleotides or amino acids) in each chain of the macromolecule. Embedded in these records are chain identifiers and sequence numbers that allow other records to reference parts of the sequence. Apart from structural data, the PDB format also allows for storing of various metadata such as bibliographic data, experimental conditions, additional stereochemistry information, and so on. However, the amount of metadata types available is rather limited owing to the age of the PDB format and to its relatively strict syntax rules. 

Protein crystal structures are archived in the Protein Data Bank (PDB) (Bernstein et al. 1977 Berman et al. 2000). About 5 per cent of the approximately 14 000 (December 2000) entries ( 12 500 proteins, peptides, and viruses, 900 nucleic acids, 600 pro-tein/nucleic acid complexes, 20 carbohydrates) contain the qualifier form in the compound name/descriptor field, and most of those refer to polymorphic varieties. In biomolecular crystallography great efforts are expended varying crystallization conditions in the attempts to obtain single crystals suitable for structural investigations... 

Besides differences in the functional form and reference state, from a more practical point of view, the knowledge-based potentials differ also with respect to scope of atom type definitions and the amount of structural data used for their derivation. The number of different atom types ranges from 17 in Drug-Score to 40 nonmetal atom types in BLEEP. In all cases, the Protein Data Bank (321) was the source of the solved crystal structures. For BEEEP 351 selected complexes were used, whereas the PMF function was extracted from 697 complexes, and DrugScore was derived using 1376 complexes. In the latter case, the data have been extracted from Relibase (322,323). 

FIGURE 16.4. Portions of an output file from the Protein Data Bank, (a) Bibliographic information, comments on the structure determination, and the amino-acid sequence. Shown are journal references, information on the resolution, and the amino-acid sequence. Courtesy the Protein Data Bank. 

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