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The Protein Data Bank.

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Description	Protein structure X-ray crystallography NMR Structure Determination
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Data format	PDB
Website	www.wwpdb.org www.pdbe.org www.rcsb.org/pdb www.pdbj.org
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The Protein Data Bank (PDB) is a repository for the 3-D structural data of large biological molecules, such as proteins and nucleic acids. (See also crystallographic database.) The data, typically obtained by X-ray crystallography or NMR spectroscopy and submitted by biologists and biochemists from around the world, are freely accessible on the Internet via the websites of its member organisations (PDBe, PDBj, and RCSB). The PDB is overseen by an organization called the Worldwide Protein Data Bank, wwPDB.

The PDB is a key resource in areas of structural biology, such as structural genomics. Most major scientific journals, and some funding agencies, such as the NIH in the USA, now require scientists to submit their structure data to the PDB. If the contents of the PDB are thought of as primary data, then there are hundreds of derived (i.e., secondary) databases that categorize the data differently. For example, both SCOP and CATH categorize structures according to type of structure and assumed evolutionary relations; GO categorize structures based on genes.

History [edit]

Two forces converged to initiate the PDB: 1) a small but growing collection of sets of protein structure data determined by X-ray diffraction; and 2) the newly available (1968) molecular graphics display, the Brookhaven RAster Display (BRAD), to visualize these protein structures in 3-D. In 1969, with the sponsorship of Walter Hamilton at the Brookhaven National Laboratory, Edgar Meyer (Texas A&M University) began to write software to store atomic coordinate files in a common format to make them available for geometric and graphical evaluation. By 1971, one of Meyer's programs, SEARCH, enabled researchers to remotely access information from the database to study protein structures offline. SEARCH was instrumental in enabling networking, thus marking the functional beginning of the PDB.

Upon Hamilton's death in 1973, Tom Koeztle took over direction of the PDB for the subsequent 20 years. In January 1994, Joel Sussman of Israel's Weizmann Institute of Science was appointed head of the PDB. In October 1998, the PDB was transferred to the Collaboratory for Structural Bioinformatics (RCSB); Research the transfer was completed in June 1999. The new director was Helen M. Berman of Rutgers University (one of the member institutions of the RCSB). In 2003, with the formation of the wwPDB, the PDB became an international organization. The founding members are PDBe (Europe), RCSB (USA), and PDBj (Japan). The BMRB joined in 2006. Each of the four members of wwPDB can act as deposition, data processing and distribution centers for PDB data. The data processing refers to the fact that wwPDB staff review and annotate each submitted entry. The data are then automatically checked for plausibility (the source code for this validation software has been made available to the public at no charge).

Contents [edit]

The PDB database is updated weekly (UTC+0 Wednesday). Likewise, the PDB holdings list is also updated weekly. As of 14 May 2013 (2013-05-14)^[update], the breakdown of current holdings is as follows:

Experimental Method	Proteins	Nucleic Acids	Protein/Nucleic Acid complexes	Other	Total
X-ray diffraction	74593	1457	3864	2	79916
NMR	8700	1029	192	7	9928
Electron microscopy	374	45	126	0	545
Hybrid	46	3	2	1	52
Other	147	4	6	13	170
Total:	83860	2538	4190	23	90611

69,415 structures in the PDB have a structure factor file.

7,237 structures have an NMR restraint file.

997 structures in the PDB have a chemical shifts file.

These data show that most structures are determined by X-ray diffraction, but about 15% of structures are now determined by protein NMR. When using X-ray diffraction, approximations of the coordinates of the atoms of the protein are obtained, whereas estimations of the distances between pairs of atoms of the protein are found through NMR experiments. Therefore, the final conformation of the protein is obtained, in the latter case, by solving a distance geometry problem. A few proteins are determined by cryo-electron microscopy. (Clicking on the numbers in the original table will bring up examples of structures determined by that method.)

The significance of the structure factor files, mentioned above, is that, for PDB structures determined by X-ray diffraction that have a structure file, the electron density map may be viewed. The data of such structures is stored on the "electron density server",

In the past, the number of structures in the PDB has grown at an approximately exponential rate. However, since 2007, the rate of accumulation of new proteins appears to have plateaued:

Number of searchable structures per year
Year	# added	Total
2012	8978	700487089000000000087,089
2011	8072	700478111000000000078,111
2010	7897	700470039000000000070,039
2009	7380	700462142000000000062,142
2008	6956	700454762000000000054,762
2007	7198	700447806000000000047,806
2006	6473	700440608000000000040,608
2005	5359	700434135000000000034,135
2004	5180	700428776000000000028,776
2003	4167	700423596000000000023,596
2002	3001	700419429000000000019,429
2001	2831	700416428000000000016,428
2000	2627	700413597000000000013,597
1999	2360	700410970000000000010,970
1998	2057	70038610000000000008,610
1997	1565	70036553000000000006,553
1996	1172	70034988000000000004,988
1995	945	70033816000000000003,816
1994	1289	70032871000000000002,871
1993	696	70031582000000000001,582
1992	192	886
1991	187	694
1990	142	507
1989	74	365
1988	53	291
1987	25	238
1986	18	213
1985	20	195
1984	22	175
1983	36	153
1982	32	117
1981	16	85
1980	16	69
1979	11	53
1978	6	42
1977	23	36
1976	13	13
1975	0	0
1974	0	0
1973	0	0
1972	0	0

Note: searchable structures vary over time as some become obsolete and are removed from the database.

File format [edit]

The file format initially used by the PDB was called the PDB file format. This original format was restricted by the width of computer punch cards to 80 characters per line. Around 1996, the "macromolecular Crystallographic Information file" format, mmCIF, started to be phased in. An XML version of this format, called PDBML, was described in 2005. The structure files can be downloaded in any of these three formats. In fact, individual files are easily downloaded into graphics packages using web addresses:

• For PDB format files, use, e.g., http://www.pdb.org/pdb/files/4hhb.pdb.gz or http://pdbe.org/download/4hhb
• For PDBML (XML) files, use, e.g., http://www.pdb.org/pdb/files/4hhb.xml.gz or http://pdbe.org/pdbml/4hhb

The "4hhb" is the PDB identifier. Each structure published in PDB receives a four-character alphanumeric identifier, its PDB ID. (This cannot be used as an identifier for biomolecules, because often several structures for the same molecule-in different environments or conformations-are contained in PDB with different PDB IDs.)

Viewing the data [edit]

The structure files may be viewed using one of several open source computer programs. Some other free, but not open source programs include ICM-Browser, VMD, MDL Chime, Pymol, UCSF Chimera, Rasmol, Swiss-PDB Viewer, StarBiochem (a Java-based interactive molecular viewer with integrated search of protein databank), Sirius, and VisProt3DS (a tool for Protein Visualization in 3D stereoscopic view in anaglyth and other modes). The RCSB PDB website contains an extensive list of both free and commercial molecule visualization programs and web browser plugins.

See also [edit]

• Crystallographic database
• Protein structure
• Protein structure databases
• PDBREPORT lists all anomalies (also errors) in PDB structures
• PDBsum - extracts data from other databases about PDB structures
• PDBWiki - a website for community annotation of PDB structures
• Proteopedia - a collaborative 3D encyclopedia of proteins and other molecules

References [edit]

External links [edit]

• The Worldwide Protein Data Bank (wwPDB) - parent site to regional hosts (below)
  • RCSB Protein Data Bank (USA)
  • PDBe (Europe)
  • PDBj (Japan)
  • BMRB, Biological Magnetic Resonance Data Bank (USA)
• wwPDB Documentation - documentation on both the PDB and PDBML file formats
• Looking at Structures - The RCSB's introduction to crystallography
• PDBsum Home Page - Extracts data from other databases about PDB structures.
• Nucleic Acid Database, NDB - a PDB mirror especially for searching for nucleic acids
• Introductory PDB tutorial sponsored by PDB
• PDBe: Quick Tour on EBI Train OnLine

v t e Bioinformatics Databases Sequence databases: GenBank, EMBL Nucleotide Sequence Database and DNA Data Bank of Japan Secondary databases: UniProt, database of protein sequences grouping together Swiss-Prot, TrEMBL and Protein Information Resource Other databases: Protein Data Bank, Ensembl and InterPro Specialised genomic databases: Saccharomyces Genome Database, FlyBase, WormBase, Arabidopsis Information Resource and Zebrafish Information Network Other Algorithm: BLAST Server: ExPASy Institutions European Bioinformatics Institute US Center for Biotechnology Information Swiss Institute of Bioinformatics Japanese Institute of Genetics List of biological databases Sequencing Sequence database Sequence alignment Molecular phylogenetics

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Information source: wikipedia.org

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