Assalamualaikum.Today we will explain about PBD protein Data Bank.
The Protein Data Bank (PDB) is a repository for the three-dimensional 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
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[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 |
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- 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.
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 | 87,089 |
| 2011 | 8072 | 78,111 |
| 2010 | 7897 | 70,039 |
| 2009 | 7380 | 62,142 |
| 2008 | 6956 | 54,762 |
| 2007 | 7198 | 47,806 |
| 2006 | 6473 | 40,608 |
| 2005 | 5359 | 34,135 |
| 2004 | 5180 | 28,776 |
| 2003 | 4167 | 23,596 |
| 2002 | 3001 | 19,429 |
| 2001 | 2831 | 16,428 |
| 2000 | 2627 | 13,597 |
| 1999 | 2360 | 10,970 |
| 1998 | 2057 | 8,610 |
| 1997 | 1565 | 6,553 |
| 1996 | 1172 | 4,988 |
| 1995 | 945 | 3,816 |
| 1994 | 1289 | 2,871 |
| 1993 | 696 | 1,582 |
| 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
Various software tools can minimize the amount of manual labor.Help scientists deposit their results quicker.Also help validate their results
Commonly used software:
– pdb_extract
– ADIT
– PDB Validation Suite
PDB Extract Tool
pdb_extract can extract information from the output of
standard crystallographic programs. It merges the information into mmC.IF files
at each step of the structure-determination process.These mmCIF files are then
ready for validation and deposition.
Data Deposition
AutoDep Input Tool
ADIT is available
both as web-based tool and a standalone tool.It is used for assembling,
editing, validating and deposition structural data.ADIT is built on top of the
mmCIF dictionary.Data will go through series of computerized validation
procedures.
PDB Validation Suite
PDB Validation Suite creates reports based upon the
validation results.Reports are generated in plain text and PostScript formats.It
also calculates derived information that could be used for assessing the
quality of a structure.
PDB Validation
The geometry of the macromolecule is checked against known
standards for distances and angles.Coordinate data are checked against results
from other experiments.Results of the validations are reviewed by the
annotation staff and then returned to the author for review.
Data Deposition
Processing time, including all author correspondence average
about two weeks.ADIT along with other data collection and validation tools
enables the depositors to pre-check all aspects of the structure before
submission.Besides the RCSB site, data are processed by PDBj in Osaka and
European Bioinformatics Institute
Introduction To Rasmol
You can download from this website RaSmOL
| protein picture | description |
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Glucose is a major source of energy in your body, but unfortunately, free glucose is relatively rare in our typical diet. Instead, glucose is locked up in many larger forms, including lactose and sucrose, where two small sugars are connected together, and long chains of glucose like starches and glycogen. One of the major jobs of digestion is to break these chains into their individual glucose units, which are then delivered by the blood to hungry cells throughout your body. |
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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. |
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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... |
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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. |
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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. |
![(2S,5R)-2-ethyl-1,6-dioxaspiro[4.4]nonane](http://en.wikipedia.org/wiki/File:2S,5R-chalcogran-skeletal.svg)
