PDB

    My post today is about Protein Data Bank (PDB). 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. The PDB is overseen by an organization called the Worldwide Protein Data Bank,wwPDB.

The PDB archive contains information about experimentally-determined structures of proteins, nucleic acids, and complex assemblies.The RCSB PDB also provides a variety of tools and resources. Users can perform simple and advanced searches based on annotations relating to sequence, structure and function. These molecules are visualized, downloaded, and analyzed by users who range from students to specialized scientists.

    By using Raswin or Rasmol software, we can see the 3-D structural data of large biological molecules, such as nucleic acids and proteins. Any molecule can be seen in 3-D view from many side. Just click and drag the mouse and then the molecule will start to change it's shape. As you can see below,these four pictures represent the same molecules but in different structure.

picture 1

picture 2

picture 3

picture 4

 If you go to this url , try to type lonA at the search box. Then you'll find out below protein is one of the example of lonA protein.

Crystal structures of Bacillus subtilis Lon protease

Below are some of information about structure displayed above.

scientific name	Bacillus subtilis
expression system	Escherichia Coli
experimental method	x-ray diffraction
classification	hydrolase
structure weight	48027.40
molecule	ATP-dependent protease La 1
polimer type	polipeptide (L)
fragment	BsLon, N-terminal domain