PDB Protein Data Bank

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. 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 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). 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

The PDB database is updated weekly (UTC+0 Wednesday). Likewise, the PDB holdings list is also updated weekly. As of 1 October 2013 (2013-10-01)^[update], the breakdown of current holdings is as follows:

Experimental Method	Proteins	Nucleic Acids	Protein/Nucleic Acid complexes	Other	Total
X-ray diffraction	77781	1484	4074	3	83342
NMR	8867	1047	193	7	10114
Electron microscopy	474	45	129	0	648
Hybrid	52	3	2	1	58
Other	151	4	6	13	174
Total:	87325	2583	4404	24	94336

72,884 structures in the PDB have a structure factor file.

7,424 structures have an NMR restraint file.

1,179 structures in the PDB have a chemical shifts file.

602 structures in the PDB have a 3DEM map file.

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.)
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".

Growth trend

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. Template:SVG Chart

Software Tools

 

  RasMol is an important scientific tool for visualisation of molecules created by Roger Sayle in 1992. RasMol is used by hundreds of thousands of users world-wide to view macromolecules and to prepare publication-quality images. Science is best served when the tools we use are fully understood by those who wield those tools and by those who make used of results obtained with those tools. When a scientific tool exists as software, access to source code is an important element in achieving full understanding of that tool. As our field evolves and new versions of software are required, access to source allows us to adapt our tools quickly and effectively.

protein picture	description
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	Bacteria pull no punches when they fight to protect themselves. Some bacteria build toxins so powerful that a single molecule can kill an entire cell. This is far more effective than chemical poisons like cyanide or arsenic. Chemical poisons attack important molecules one by one, so many, many molecules of cyanide are needed to kill a cell. Bacterial toxins use two strategies to make their toxins far more deadly than this.
	During the holiday season, we often place greater demands on our digestive enzymes than at other times of the year. Our digestive system contains a host of tough, stable enzymes designed to seek out those rich holiday treats and break them into small pieces. Pepsin is the first in a series of enzymes that digest proteins. In the stomach, protein chains bind in the deep active site groove of pepsin, seen in the upper illustration (from PDB entry 5pep), and are broken into smaller pieces. Then, a variety of proteases and peptida...
	As you read this Molecule of the Month, the light from the page is being focused in your eyes by a concentrated solution of crystallin proteins. The lenses in your eyes are built of long cells that, early in their development, filled themselves with crystallins and then made the major sacrifice, ejecting their nuclei and mitochondria and leaving only a smooth, transparent solution of protein. We then rely on these proteins to see for the rest of our lives.
	Bacteria pose a continual threat of infection, both to humans and to other higher organisms. Thus, when looking for new ways to fight infection, it is often productive to look at how other plants, animals and fungi protect themselves. This is how penicillin was discovered. Through a chance observation in 1928, Alexander Fleming discovered that colonies of Penicillium mold growing in his bacterial cultures were able to stave off infection. With more study, he found that the mold was flooding the culture with a molecule that killed the bacteria, penicillin.