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]
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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.)
The PDB database is updated weekly (on Tuesday). Likewise, the PDB Holdings List is also updated weekly. As of 20 July 2010[update], the breakdown of current holdings was as follows:
| Experimental Method |
Proteins | Nucleic Acids | Protein/Nucleic Acid complexes |
Other | Total |
|---|---|---|---|---|---|
| X-ray diffraction | 53916 | 1212 | 2530 | 17 | 57675 |
| NMR | 7409 | 917 | 158 | 7 | 8492 |
| Electron microscopy | 202 | 17 | 77 | 0 | 296 |
| Hybrid | 21 | 1 | 1 | 1 | 24 |
| Other | 125 | 4 | 4 | 13 | 146 |
| Total: | 61673 | 2151 | 2771 | 38 | 66633 |
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", where the electron maps can be viewed.
In the past the number of structures in the PDB has grown at an approximately exponentially rate. However, since 2007 the rate of accumulation of new proteins seems to have plateaued, with 7263 proteins added in 2007, 7073 in 2008, and 7448 in 2009.
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:
http://www.pdb.org/pdb/files/4hhb.pdb.gzhttp://www.pdb.org/pdb/files/4hhb.xml.gzThe "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.)
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), 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.