Research Collaboratory for Structural Bioinformatics’ Protein Data

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB-PDB at http //www.rcsb.org/pdb/) is the online source for X-ray and NMR structural data. Many software programs mentioned in Section 3.12 include the facility to visualize imported data however, two free software programs operate well in this regard. These are RasMol and Chime, described below. 

Research Collaboratory for Structural Bioinformatics Protein Data Bank... 

The Research Collaboratory for Structural Bioinformatics— Protein Data Bank (RCSB—PDB) is available online at http www.pdb.org. (accessed April 2003). 

There are many ways to assess the structure of a folded protein. Many of them are spectroscopic, such as circular dichroism (CD), fluorescence, infrared, and Raman. These methods can be combined with the use of stress to measure the stability of the folded structure by perturbing it with heat or chemicals (Figure 8). High resolution structural information (determined in atomic detail) is often obtained by X-ray crystallography or nuclear magnetic resonance (NMR). These data are routinely deposited in the RSCB (Research Collaboratory for Structural Bioinformatics) protein database for public access. ... 

In 1971 the Protein Data Bank - PDB [146] (see Section 5.8 for a complete story and description) - was established at Brookhaven National Laboratories - BNL -as an archive for biological macromolccular cr7stal structures. This database moved in 1998 to the Research Collaboratory for Structural Bioinformatics -RCSB. A key component in the creation of such a public archive of information was the development of a method for effreient and uniform capture and curation of the data [147], The result of the effort was the PDB file format [53], which evolved over time through several different and non-uniform versions. Nevertheless, the PDB file format has become the standard representation for exchanging inacromolecular information derived from X-ray diffraction and NMR studies, primarily for proteins and nucleic acids. In 1998 the database was moved to the Research Collaboratory for Structural Bioinformatics - RCSB. 

Data formats in the Brookhaven Protein Databank have become an intensively discussed topic in the last few years. The original PDB file format [17] was created in the late 1970s and maintained by the Research Collaboratory for Structural Bioinformatics [13]. In order to improve the organization of bibliographic... 

The Protein Data Bank (PDB) is the collection of publicly available structures of proteins, nucleic acids, and other biological macromolecules initiated by Brook-haven National Laboratory and now maintained by the Research Collaboratory for Structural Bioinformatics (RCSB) at http //www.rcsb.org/pdb/ (Berman et al., 2000). The PDB coordinates of biomacromolecules can be classified into the following ... 

At this writing, the three-dimensional sttuctures of eight different naturally occurring type 1 copper proteins are known. These include the cupredoxins plastocyanin at 1.33 A resolution (pdb code 1 PTC), azurin at 1.8 A (pdb code 2AZA), pseudoazurin at 1.55 A (pdb code IPAZ), amicyanin at 1.3 A (pdb code lAAC), auracyanin at 1.55 A (pdb code IQHQ), rusticyanin at 1.9 A (pdb code IRCY), and the phytocyanins cucumber basic protein at 1.8 A (pdb code2CBP), and stellacyanin at 1.6 A (pdb code IJER) Atomic coordinates for these and all other single-domain type 1 copper proteins are available from the Research Collaboratory for Structural Bioinformatics (RCSB) Protein Data Bank (PDB) and can be accessed online at www.rcsb.org/pdb/. 

RCSB PDB Research Collaboratory for Structural Bioinformatics (RCSB), the non-profit consortium that manages the Protein Data Bank (PDB)... 

Perhaps the most useful of all biological databases is the Protein Data Bank (PDB), operated by the Research Collaboratory for Structural Bioinformatics (RCSB). The PDB is a worldwide repository of X-ray and N.VIR structural data for biological macromolecules. In early 2007, data for more than 40,000 structures were available, and more than 6000 new structures were being added yearly. To access the Protein Data Bank, go to http //w W W,rcsb.org/pdb/ and a home page like that shown in Figure 26.11 will appear. As wdth much that is available online, however, the PDB site is changing rapidly, so you may not see quite the same thing. 

Research Collaboratory for Structural Bioinformatics — Maintains the Protein Data Bank (PDB), a file of 3-dimensional structures of proteins and other biological macromolecules. Address Department of Chemistry and Chemical Biology, Rutgers University, 610 Taylor Road, Piscataway, NJ 08854-8087 [www.rcsb.org]. 

RCSB, Protein Data Bank, operated by the Research Collaboratory for Structural Bioinformatics, http //www.rcsb.org/pdb/index.html. 

PDB PROTEIN DATA BANK AT THE RESEARCH COLLABORATORY FOR STRUCTURAL BIOINFORMATICS (RCSB)... 

Brookhaven Protein Data Bank http //www.rcsb.org/ pdb/ Research Collaboratory for Structural Bioinformatics (RCSB), non-profit consortium, CA, USA World-wide repository for the processing and distribution of 3-D biological macro-molecular structure data. X-ray crystallographic and NMR data. Freely downloadable stmcture files. Display of stmctures via free programs of other vendors (e.g. Chime, Rasmol, WebLab Viewer)... 

Fig. 1. Resolution histogram in resolution bins of 0.25 A for the hyperthetmophilic proteins (solid bars) listed in Table I and for the entire Protein Data Base (PDB) [cross-hatched bars J. Sussman, D. Lin, J. Jiang, N. Manning, J. Prilusky, O. Ritter, and E. Abola, Acta Crystallogr. D54,1078 (1998) Research Collaboratory for Structural Bioinformatics PDB, http //www.rcsb.oig/pdb/], as estimated in October, 1999 from http //db2.sdsc.edu/moose/images/summary.gif.

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