In this topic, firstly, we discussed about the definition of Protein Data Bank (PDB). PDB is a
repository for 3-D biological macromolecular structure. All data are available
to the public. It includes proteins, nucleic acids and viruses. The PDB is obtained
by X-Ray crystallography (80%) or NMR spectroscopy (16%).
Protein Data Bank founded
in 1971 by Brookhaven National Laboratory, New York. First set of data were
entered on punched cards. Currently it holds 29,000 released structures.
X
Ray Crystallography
X-ray
crystallography is a method of
determining the atomic and molecular structure of a crystal, in which the crystalline atoms cause a beam of X-rays to diffract into many specific directions. By measuring the angles and intensities
of these diffracted beams, a crystallographer can produce a three-dimensional picture of the density of electrons within the crystal.
Some examples of protein images :
mmCIF
mmCIF dictionary
contains 2,500 definitions for terms used to describe the crystallographic
experiment. For examples, _chem_comp_link.details, _atom_type.description, and
so on. The dictionary definition language (DDL) is structured in a way that
data files that conform to this syntax can be readily loaded into a database.
Data
Deposition
Getting the Most Out of the PDB
References
- http://en.wikipedia.org/wiki/Protein_Data_Bank
- http://proteopedia.org/wiki/index.php/PDB_identification_code
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