Protein Data Bank

Protein Data Bank

Content
Description	Protein structure X-ray crystallography NMR Structure Determination
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Access
Data format	PDB
Website	.org.wwpdbwww .org.pdbewww /pdb.org.rcsbwww .org.pdbjwww
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The Protein Data Bank (PDB) is a repository for the three-dimensional structural data of large biological molecules, such as 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, 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.^[4]

History

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.^[5] 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,

• 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

External links

References

• Crystallographic database
• Protein structure
• Protein structure prediction
• Protein structure database
• 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

See also

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,^[18] VMD, MDL Chime, Pymol, UCSF Chimera, Rasmol, Swiss-PDB Viewer,^[19] StarBiochem^[20] (a Java-based interactive molecular viewer with integrated search of protein databank), Sirius, and VisProt3DS^[21] (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.

Viewing the data

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.)

• 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 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.^[17] 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:

File format

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

Growth trend

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".^[13][14]

These data show that most structures are determined by X-ray diffraction, but about 10% 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.)

81,076 structures in the PDB have a structure factor file.

7,912 structures have an NMR restraint file.

1,669 structures in the PDB have a chemical shifts file.

798 structures in the PDB have a 3DEM map file deposited in EM Data Bank

Examples of protein structures from the PDB (created with UCSF Chimera)

Contents

for this validation software has been made available to the public at no charge). ^[11] The data are then automatically checked for plausibility (the source code^[10] 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.wwPDB joined in 2006. Each of the four members of ^[9] The BMRB^[2] RCSB (USA), and PDBj (Japan).[1]