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                              Introduction

What is PDB?

(1) The PDB is the Protein Data Bank, a single worlwide repository for 3D structural data of biological molecules.

(2) A PDB is a file, typically with a "pdb" file extension, contains 3D structural data of a particular biological molecule. In short, a PDB file is broken into two sections: (i) a header that contains much background information on the molecule in question such as authors and experimental conditions, (ii) 3D coordinate data that contain the vital experimental data in the form of 3D cartesian coordinates, B-factors, atom information, and more.

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                         How can PDB's be visualized?

     Protein Data Bank files, containing some form of macromolecular coordinate set, are visualized via graphic computing. A myriad of advanced molecular visualization programs are used in academic and industrial setting, and some of these are specific to the field of research or the techniques used to collect the coordinate data. For example, X-ray crystallographers use O, XtalView, MAIN, or other programs for crystallographic modeling. These allow the researcher to model the coordinate set into the electron density from the collected X-ray data.

However, PDB files are "final" deposited coordinates. This means that the depositor has made their best effort to provide a final model that is as accurate as they could make it. Programs like Molscript, Pymol, SwissPDBview/DeepView, Molmol, SETOR, DINO and others are routinely used to visualize deposited coordinates.

In order to produce molecular graphics, one requires the following: graphics workstation computer, some form of molecular graphics software, and most importantly, training.

Symmation has been formally trained in X-ray crystallography and bioinformatics. We have the software and computer equipment, aside from our 8 years of experience. We are able to provide a complete solution to molecular graphics visualization that includes raw data interpretation, remodeling, refinement, structure analysis, and of course publication-quality graphics.

We can reduce your costs of operation, whatever sector you are in. Request information on PDB visualization and read our client testimonials that speak on our expertise!

 SUBTILISIN_3LPA

SIMPLE INFO:

        Subtilisin (serine endopeptidase) is a non-specific protease (a protein-digesting enzyme) initially obtained from Bacillus subtilis.

Subtilisins belong to subtilases, a group of serine proteases that initiate the nucleophilic attack on the peptide (amide) bond through a serine residue at the active site. They are physically and chemically well-characterized enzymes. Subtilisins typically have molecular weights of about 20,000 to 45,000 dalton. They can be obtained from soil bacteria, for example, Bacillus amyloliquefaciens. Subtilisins are secreted in large amounts from many Bacillus species.

Subtilisins are widely used in commercial products, for example, in laundry^[2] and dishwashing detergents, cosmetics, food processing^[3], skin care ointments^[4], contact lens cleaners, and for research purposes in synthetic organic chemistry.

The structure of subtilisin has been determined by X-ray crystallography. It is a 275-residue globular protein with several alpha-helices, and a large beta-sheet. It is structurally unrelated to the chymotrypsin-clan of serine proteases, but uses the same type of catalytic triad in the active site. This makes it the classic example of convergent evolution.

In molecular biology using B. subtilis as a model organism, the gene encoding subtilisin (aprE) is often the second gene of choice after amyE for integrating reporter constructs into, due to its dispensability.

		EXAMPLE:

      PROLYL AMINOPEPTIDASE 3CTZ

                                                                 

                                                  SIMPLE INFO:                                     

Structure of human cytosolic X-prolyl aminopeptidase

Prolyl aminopeptidase from Serratia marcescens specifically catalyzes the removal of N-termlnal proline residues from peptides. We have solved its three-dimensional structure at 2.3 A resolution by the multiple isomorphous replacement method. The enzyme consists of two contiguous domains. The larger domain shows the general topology of the a/0 hydrolase fold, with a central eight-stranded /?-sheet and six helices. The smaller domain consists of six helices. The catalytic triad (SerllS, His296, and Asp268) is located near the large cavity at the interface between the two domains. Cys271, which is sensitive to SH reagents, is located near the catalytic residues, in spite of the fact that the enzyme is a serine peptidase. The specific residues which make up the hydrophobic pocket line the smaller domain, and the specificity of the exo-type enzyme originates from this smaller domain, which blocks the N-terminal of PI proline.

LEX A REPRESSOR             SIMPLE INFO Repressor LexA or LexA is a repressor enzyme (EC 3.4.21.88) that represses SOS response genes coding for DNA polymerases required for repairing DNA damage. LexA is intimately linked to RecA in the biochemical cycle of DNA damage and repair. RecA binds to DNA-bound LexA causing LexA to cleave itself in a process called autoproteolysis. DNA damage can be inflicted by the action of antibiotics. Bacteria require topoisomerases such as DNA gyrase or topoisomerase IV for DNA replication. Antibiotics such as ciprofloxacin are able to prevent the action of these molecules by attaching themselves to the gyrase - DNA complex. This is counteracted by the polymerase repair molecules from the SOS response. Unfortunately the action is partly counterproductive because ciprofloxacin is also involved in the synthetic pathway to RecA type molecules which means that the bacteria responds to an antibiotic by starting to produce more repair proteins. These repair proteins can lead to eventual benevolent mutations which can render the bacteria resistant to ciprofloxacin. Mutations are traditionally thought of as happening as a random process and as a liability to the organism. Many strategies exist in a cell to curb the rate of mutations. Mutations on the other hand can also be part of a survival strategy. For the bacteria under attack from an antibiotic, mutations help to develop the right biochemistry needed for defense. Certain polymerases in the SOS pathway are error-prone in their copying of DNA which leads to mutations. While these mutations are often lethal to the cell, they can also lead to mutations which improve the bacteria's survival. In the specific case of topoisomerases, some bacteria have mutated one of their amino acids so that the ciproflaxin can only create a weak bond to the topoisomerase. This is one of the methods that bacteria use to become resistant to antibiotics. Impaired LexA proteolysis has been shown to interfere with ciprofloxacin resistance.[1] This offers potential for combination therapy that combine quinolones with strategies aimed at interfering with the action of LexA either directly, or via RecA.

LInk:

http://www.symmation.com/content/protein-data-bank.php http://jb.oxfordjournals.org/content/126/3/559.full.pdf    http://www.rcsb.org/pdb/results/results.do?outformat=&qrid=33BF0382&tabtoshow=Current