Protein Data Bank

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, can be accessed at no charge on the internet. 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.^[1]

History

The PDB originated as a grassroots effort.^[1] In 1971, Walter Hamilton of the Brookhaven National Laboratory agreed to set up the data bank at Brookhaven. Upon Hamilton's death in 1973, Tom Koeztle took over direction of the PDB. In January 1994, Joel Sussman was appointed head of the PDB. In October 1998,^[2] the PDB was transferred to the Research Collaboratory for Structural Bioinformatics (RCSB); 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).^[3] In 2003, with the formation of the wwPDB, the PDB became an international organization. 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 annotates 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

The PDB database is updated weekly. Likewise, the PDB Holdings List is also updated weekly. As of 3 November 2009 (2009 -11-03)^[update], the breakdown of current holdings was as follows:

41,933 structures in the PDB have a structure factor file.

5,384 structures have an NMR restraint file.

These data show that most structures are determined by X-ray diffraction, but about 15% of structures are now determined by protein NMR, and a few are even 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", where the electron maps can be viewed.

In the past, the number of structures in the PDB has grown nearly exponentially. In 2007, 7263 structures were added. However, in 2008, only 7073 structures were added, so the rate of production of structures has appeared to start to decrease.

File format

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.^[4] 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
• For PDBML (XML) files, use, e.g., http://www.pdb.org/pdb/files/4hhb.xml.gz

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

The structure files may be viewed using one of several open source computer programs. Some other free, but not open source programs include VMD, MDL Chime, Swiss-PDB Viewer, StarBiochem (a Java-based interactive molecular viewer with integrated search of protein databank), and Sirius. The RCSB PDB website contains an extensive list of both free and commercial molecule visualization programs and web browser plugins.

References

See also

• Crystallographic database
• Protein structure
• Protein structure databases
• PDBWiki — a website for community annotation of PDB structures
• Proteopedia — a collaborative 3D encyclopedia of proteins and other molecules

External links

• 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 PDB'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