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Encyclopedia > Protein Data Bank

The Protein Data Bank (PDB) is a repository for 3-D structural data of proteins and nucleic acids. These data, typically obtained by X-ray crystallography or NMR spectroscopy and submitted by biologists and biochemists from around the world, are released into the public domain, and can be accessed for free. See also protein structure. Through the years the Protein Data Bank has undergone many, many changes and revisions. ... A representation of the 3D structure of myoglobin showing coloured alpha helices. ... Look up nucleic acid in Wiktionary, the free dictionary. ... X-ray crystallography, also known as single-crystal X-ray diffraction, is the oldest and most common crystallographic method for determining the structure of molecules. ... Pacific Northwest National Laboratorys high magnetic field (800 MHz) NMR spectrometer being loaded with a sample. ... A biologist is a scientist devoted to and producing results in biology through the study of organisms. ... Biochemistry (from Greek: , bios, life and Egyptian kÄ“me, earth[1]) is the study of the chemical processes in living organisms. ... The public domain comprises the body of all creative works and other knowledge—writing, artwork, music, science, inventions, and others—in which no person or organization has any proprietary interest. ... Proteins are an important class of biological macromolecules present in all biological organisms, made up of such elements as carbon, hydrogen, nitrogen, oxygen, and sulfur. ...

Contents

History

Founded in 1971 by Drs. Edgar Meyer and Walter Hamilton Brookhaven National Laboratory, management of the Protein Data Bank was transferred in 1998 to members of the Research Collaboratory for Structural Bioinformatics (RCSB). Rutgers University is the lead site and is currently under the direction of Helen M. Berman. [1] ≠ Aerial view of Brookhaven National Laboratory. ... “Rutgers” redirects here. ...


The Worldwide Protein Data Bank (wwPDB) consists of organizations that act as deposition, data processing and distribution centers for PDB data. The founding members are RCSB PDB (USA), MSD-EBI (Europe) and PDBj (Japan). The BMRB (USA) group joined the wwPDB in 2006. The mission of the wwPDB is to maintain a single Protein Data Bank Archive of macromolecular structural data that is freely and publicly available to the global community. PDB can be an acronym for any of the following: the Presidents Daily Briefing the Protein Data Bank the trio Pastorius, Dennard, and Bullock, and a jazz album by that trio a file format, Palm database, generally used to store data for an application a (proprietary) Microsoft file format... A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. ...


The PDB is a key resource in structural biology and is critical to more recent work in structural genomics. Structural biology is a branch of molecular biology concerned with the study of the architecture and shape of biological macromolecules--proteins and nucleic acids in particular—and what causes them to have the structures they have. ... Structural genomics or structural bioinformatics refers to the analysis of macromolecular structure particularly proteins. ...


Countless derived databases and projects have been developed to integrate and classify the PDB in terms of protein structure, protein function and protein evolution. Proteins are an important class of biological macromolecules present in all biological organisms, made up of such elements as carbon, hydrogen, nitrogen, oxygen, and sulfur. ...


Growth

When the PDB was originally founded it contained just 7 protein structures. Since then it has undergone an approximate exponential growth in the number of structures, which does not show any sign of falling off.


The growth rate of the PDB has been the subject of fairly extensive analysis.


Contents

As of 15 April 2008, the database contained 50,277 released atomic coordinate entries (or "structures"), 46,400 of that proteins, the rest being nucleic acids, nucleic acid-protein complexes, and a few other molecules. About 5,000 new structures are released each year. Data are stored in the mmCIF format specifically developed for the purpose. It is estimated that the size of the PDB archive will triple to 150,000 structures by the year 2014.[2] is the 105th day of the year (106th in leap years) in the Gregorian calendar. ... 2008 (MMVIII) is the current year, a leap year that started on Tuesday of the Anno Domini (or common era), in accordance to the Gregorian calendar. ...


Note that the database stores information about the exact location of all atoms in a large biomolecule (although, usually without the hydrogen atoms, as their positions are more of a statistical estimate); if one is only interested in sequence data, i.e., the list of amino acids making up a particular protein or the list of nucleotides making up a particular nucleic acid, the much larger databases from Swiss-Prot and the International Nucleotide Sequence Database Collaboration should be used. For other uses, see Atom (disambiguation). ... This article is about the chemistry of hydrogen. ... This article is about the class of chemicals. ... A representation of the 3D structure of myoglobin showing coloured alpha helices. ... A nucleotide is a chemical compound that consists of 3 portions: a heterocyclic base, a sugar, and one or more phosphate groups. ... Look up nucleic acid in Wiktionary, the free dictionary. ... Swiss-Prot is a curated biological database of protein sequences created in 1986 by Amos Bairoch during his PhD and developed by the Swiss Institute of Bioinformatics and the European Bioinformatics Institute. ... The International Nucleotide Sequence Database (INSD) consists of a joint effort to collect and disseminate databases about DNA and RNA sequences. ...


Statistics

As of 9 April 2008, the "PDB Holdings List" at RCSB reported the following statistics: is the 99th day of the year (100th in leap years) in the Gregorian calendar. ... 2008 (MMVIII) is the current year, a leap year that started on Tuesday of the Anno Domini (or common era), in accordance to the Gregorian calendar. ...

Proteins Nucleic Acids Protein/NA complexes Other Total
X-ray diffraction 39791 1024 1813 24 42652
NMR 6291 804 137 7 7239
Electron microscopy 117 11 43 0 171
Other 88 4 4 2 98
Total 46287 1843 1997 33 50160

Note that theoretical models are no longer accepted in the PDB. A representation of the 3D structure of myoglobin, showing coloured alpha helices. ... Look up nucleic acid in Wiktionary, the free dictionary. ... X-ray crystallography is a technique in crystallography in which the pattern produced by the diffraction of x-rays through the closely spaced lattice of atoms in a crystal is recorded and then analyzed to reveal the nature of that lattice. ... Nuclear magnetic resonance spectroscopy most commonly known as NMR spectroscopy is the name given to the technique which exploits the magnetic properties of certain nuclei. ... The electron microscope is a microscope that can magnify very small details with high resolving power due to the use of electrons rather than light to scatter off material, magnifying at levels up to 500,000 times. ...


22,461 structures in the PDB have a structure factor file. 3,138 structures in the PDB have an NMR restraint file. In physics, in the area of crystallography, the structure factor of a crystal is a mathematical description of how the crystal scatters incident radiation. ...


The current breakdown of holdings is updated weekly.


File format

Through the years the PDB file format has undergone many, many changes and revisions. Its original format was dictated by the width of computer punch cards. Through the years the Protein Data Bank has undergone many, many changes and revisions. ...

  • PDB Format Guide - Prepared by the PDB Staff at BNL The PDB format specification can be found here, and it is vital that you read this before looking at the raw data.
  • Recently PDB provides a representation of PDB data in XML format, PDBML format.
  • ftp.rcsb.org The raw data can be downloaded from here.
  • PDB format files can be downloaded using HTTP with URLs like this: http://www.pdb.org/pdb/files/4hhb.pdb.gz
  • PDBML (XML) files can be downloaded using HTTP with URLs like this: http://www.pdb.org/pdb/files/4hhb.xml.gz
  • ftp.ebi.ac.uk/pub/databases/rcsb/ Alternate download location for the PDB archive.
  • www.pdb.org Statistics about the PDB can be found here.

This legacy format has caused many problems with the format, and consequently there are 'clean-up' projects;

The MMDB uses ASN.1 (and an XML conversion of this format). The wwPDB members RCSB PDB, MSD-EBI, and PDBj are working together to make the data uniform across the archive. Some believe this to be desirable; others argue that, without a universal repository of information (i.e., a common dictionary), it is not possible to draw comparisons.[citation needed] National Center for Biotechnology Information logo The National Center for Biotechnology Information (NCBI) is part of the United States National Library of Medicine (NLM), a branch of the National Institutes of Health. ...


Each structure published in PDB receives a four-character alphanumeric identifier, its PDB ID. This should not be used as an identifier for biomolecules, since often several structures for the same molecule (in different environments or conformations) are contained in PDB with different PDB IDs.


If a biologist submits structure data for a protein or nucleic acid, wwPDB staff reviews and annotates the entry. The data are then automatically checked for plausibility. The source code for this validation software has been released for free. The main data base accepts only experimentally derived structures, and not theoretically predicted ones (see protein structure prediction). Source code (commonly just source or code) is any series of statements written in some human-readable computer programming language. ... Protein structure prediction is one of the most significant technologies pursued by computational structural biology and theoretical chemistry. ...


Various funding agencies and scientific journals now require scientists to submit their structure data to PDB.


Viewing the data

The structural data can be used to visualize the biomolecules with appropriate software, such as VMD, RasMol, PyMOL, Jmol, MDL Chime, QuteMol, web browser VRML plugin or any web-based software designed to visualize and analyse the protein structures such as STING. A recent desktop software addition is Sirius. The RCSB PDB website also contains resources for education, structural genomics, and related software. A representation of the 3D structure of myoglobin, showing coloured alpha helices. ... Screenshot of VMD 1. ... RasMol is a computer program written for molecular graphics visualization intended and used primarily for the depiction and exploration of biological macromolecule structures, such as those found in the Protein Data Bank. ... PyMOL is an open-source, user-sponsored, molecular visualization system created by Warren Lyford DeLano and commercialized by DeLano Scientific LLC, which is a private software company dedicated to creating useful tools that become universally accessible to scientific and educational communities. ... Jmol is molecule viewer for use in chemistry and biochemistry. ... MDL Chime is a plugin used by web browsers to display the three dimensional structures of molecules. ... QuteMol QuteMol is an open source, interactive, high quality molecular visualization system. ... An example of a Web browser (Mozilla Firefox) A web browser is a software application that enables a user to display and interact with text, images, videos, music and other information typically located on a Web page at a website on the World Wide Web or a local area network. ... VRML (Virtual Reality Modeling Language, pronounced vermal or by its initials, originally known as the Virtual Reality Markup Language) is a standard file format for representing 3-dimensional (3D) interactive vector graphics, designed particularly with the World Wide Web in mind. ... This article is about the musician. ... Sirius is a molecular modeling and analysis system developed by Oleksandr (Sasha) Buzko at San Diego Supercomputer Center. ...


References

  1. ^ Helen M. Berman - Rutgers Chemistry and Chemical Biology Department
  2. ^ PDB Archive Contains More Than 50,000 Structures. Retrieved on 2008-04-12.

2008 (MMVIII) is the current year, a leap year that started on Tuesday of the Anno Domini (or common era), in accordance to the Gregorian calendar. ... is the 102nd day of the year (103rd in leap years) in the Gregorian calendar. ...

Printed

  • H.M. Berman, K. Henrick, H. Nakamura (2003): Announcing the worldwide Protein Data Bank. Nature Structural Biology 10 (12), p. 980 PMID 14634627.
  • H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, P.E. Bourne: The Protein Data Bank. Nucleic Acids Research, 28 pp. 235-242 (2000). PMID 10592235
  • Bernstein FC, Koetzle TF, Williams GJ, Meyer Jr EF, Brice MD, Rodgers JR, Kennard O, Shimanouchi T, Tasumi M. The Protein Data Bank: a computer-based archival file for macromolecular structures. J Mol Biol 1977;112:535-542. PMID 875032.
  • E.F. Meyer “The First Years of the Protein Data Bank“, Protein Science 6:1591-1597 (1997)
  • Sussman, JL, Lin, D, Jiang, J, Manning, NO, Prilusky, J, Ritter, O & Abola, EE. Protein data bank (PDB): a database of 3D structural information of biological macromolecules. Acta Cryst 1998; D54:1078-1084. PMID 10089483.

External links

Related (derived) resources

Main article: Protein structure databases
  • Macromolecular Structure Database — MSD Home Page - project for data about macromolecular structures from the PDB.
  • PDBWiki — PDBWiki Home Page - a website for community annotation of PDB structures.
  • PDBsum — PDBsum Home Page - an overview of macromolecular structures in the PDB.
  • PROTEOPEDIA: The collaborative, 3D encyclopedia of proteins and other molecules

The European Bioinformatics Institute (EBI) is a centre for research and services in bioinformatics, and is part of European Molecular Biology Laboratory (EMBL). ...

Enzyme database data

  • [1] The best mapping is provided by Kim Henrick's group at EBI as part of the MSD SIFTS initiative.
  • [2] PDB provide a mapping on their beta site, but it is at the whole PDB level not chain level.
  • [3] Search at BRENDA enzyme database portal.
  • [4] PDBSProtEC:

Molecular graphic visualisation tools

PyMOL is an open-source, user-sponsored, molecular visualization system created by Warren Lyford DeLano and commercialized by DeLano Scientific LLC, which is a private software company dedicated to creating useful tools that become universally accessible to scientific and educational communities. ... Sirius is a molecular modeling and analysis system developed by Oleksandr (Sasha) Buzko at San Diego Supercomputer Center. ... This article is about the musician. ... RasMol is a computer program written for molecular graphics visualization intended and used primarily for the depiction and exploration of biological macromolecule structures, such as those found in the Protein Data Bank. ... Jmol is molecule viewer for use in chemistry and biochemistry. ... QuteMol QuteMol is an open source, interactive, high quality molecular visualization system. ...

  Results from FactBites:
 
Protein Data Bank - Wikipedia, the free encyclopedia (971 words)
The Protein Data Bank (PDB) is a repository for 3-D structural data of proteins and nucleic acids.
This data, typically obtained by X-ray crystallography or NMR spectroscopy, is submitted by biologists and biochemists from around the world, is released into the public domain, and can be accessed for free.
Founded in 1971 by Brookhaven National Laboratory, the Protein Data Bank was transferred in 1998 to the Research Collaboratory for Structural Bioinformatics (RCSB), which is composed of Rutgers University, the University of Wisconsin, Madison, NIST and the San Diego Supercomputer Center.
Protein Data Bank (372 words)
This data, typically obtained by X-ray crystallography or NMR spectroscopy, is submitted by biologists from around the world, is released into the public domain, and can be accessed for free.
The structural data can be used to visualize the biomolecules with appropriate software, such as rasmol[?], chime or a VRML plugin.
Founded in 1971 by Brookhaven National Laboratory, the Protein Data Bank was transferred in 1998 to the Research Collaboratoy for Structural Bioinformatics (RCSB), which is composed of Rutgers University, the University of Wisconsin, Madison, NIST and the San Diego Supercomputer Center[?].
  More results at FactBites »

 
 

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