Hi everyone...it's me again.!!
uppss sorry..>.<
Assalamualaikum..^.^
How was ur day? extremely good..Not so bad..or teribble?
Huh whatever it is life must go on. The problems that you face will make you appreciate about life..
Let go of all the stresses and devastations.
Let go of all the insults and underestimations.
Let go of all your enemies.
Let go of those who are insignificant and contributing unenthusiastically in your life.
Let go of those who edify your criminal deeds.
Let go and move on...keep smiling,and remember LIFE GOES ON
http://sphotos-e.ak.fbcdn.net/hphotos-ak-snc7/384201_476021729086334_1599055143_n.jpg
Aha..!!
Wednesday is back and you know what..!! my COMPUTER IN SCIENCE class..!!! I'd really love this class and the most awaited time by all students because we will play around with computer (the important technology nowadays)..yeah..
New lesson for today that I would like to share with all of you around the globe is PDB. A useful knowledge for sciences students especially whoever persue their study in BOITECHNOLOGY (like me).
Protein Data Bank (PDB) is
a repository for 3-D biological macromolecular structure includes proteins, nucleic acids and viruses which obtained
by X-Ray crystallography (80%) or NMR spectroscopy (16%)that is submitted
by biologists and biochemists from around the world. First set of data were entered on punched
cards. Later on it use magnetic tapes.
It is founded in 1971 by Brookhaven National
Laboratory, New York and then transferred to the Research Collaborators for
Structural Bioinformatics (RCSB) in 1998. Currently it holds 29,000 released structures. All
data are available to the public.
PDB is an important resource for research in
the academic, pharmaceutical, and biotechnology sectors. For examples :-
- Will this molecule turns into a cancer cell?
- Can this combination of molecules cure common cold?
- How does radiation affect the RNA and DNA?
This is howw it will look like..
PDB is consist of :-
- PDB data (Information required)
- Data deposition and validation
- Software tools ((Help scientists deposit their results quicker and validate their results)
- Data query
- PDB Beta
- 3D interaction
PDB is used together with RASMOL..(what is that)
RASMOL is a sophisticated, yet user-friendly, interactive molecular graphics program
intended for viewing molecules. proteins, nucleic acids and small
molecules. The program reads in the 3-D coordinates for a molecule using
the pdb file format and aimed at display, teaching and generation of
publication quality images.
It reads in molecule coordinate file and interactively
displays the molecule on the screen in a variety of colour schemes and
molecule representations. Currently available representations include
depth-cued wireframes, `Dreiding` sticks, spacefilling (CPK) spheres,
ball and stick, solid and strand biomolecular ribbons, atom labels and
dot surfaces. It displays the molecule in various representations
and allows one to rotate the molecule interactively, translated, zoomed and z-clipped
(slabbed) interactively using either the mouse, the scroll bars, the
command line or an attached dial box.. RasMol-ucb allows
simultaneous viewing of multiple molecules. Different parts of the molecule
may be represented and coloured independently of the rest of the
molecule or displayed in several representations simultaneously. Alternate conformers and multiple NMR models may be specially
coloured and identified in atom labelsAtoms may also be labelled with arbitrary text
strings.
Supported input file formats include Protein Data Bank
(PDB), Tripos Associates` Alchemy and Sybyl Mol2 formats, Molecular
Design Limited`s (MDL) Mol file format, Minnesota Supercomputer Center`s
(MSC) XYZ (XMol) format, CHARMm format, CIF format and mmCIF format
files.
The program is provided as freeware, available for
internet downloading, by Roger Sayle at the BioMolecular Structures Group
of Glaxo Research & Development (UK). When the program is compiled
for use by Microsoft Windows users, it is called RASWIN.
Here are few example of protein display using RASWIN.
- Trypsin
- Htr A
- Lex A
- Clp P
- Clp B
TRYPSIN
-a serine protease found in the digestive system of many vertebrates, where it hydrolyses proteins.
Molecule above is a molecule of Pancreatic Trypsin Inhibitor
Precursor. This picture is obtained from Raswin software and it is displayed in
ball and stick style and coloured in group. These are the description of this
molecule:
Classification : Proteinase Inhibitor (
Trypsin)
Weight : 6622.57
Polymer : 1
Type : Protein
Length : 58
Num. of chains : 2
Num. of groups : 57 [74]
Num. of atoms :
458 [78]
Num. of bonds :
476
Scientific Name :
Bos Taurus
Common Name :
Cattle
Method Of Experiment : X-Ray Diffraction
By:
Authors :
Wlodawer, A.
Deposition :
1987-05-13
Release :
1987-10-16
Last Modified (REVDAT) : 2009-02-24
CLP P
-an enzyme that in humans is encoded by the CLPP gene. It is found in mitochondria
and is widely distributed in bacterial species.
Molecular above is a molecule of ATP-Dependant Clp Protease
Proteolytic Subunit P. This picture is obtain from Raswin software and it is
displayed in cartoon style and coloured in group. These are the description of
this molecule:
Classification :
Hydrolase
Weight :
162599.63
Polymer :
1
Type :
Protein
Length :
201
Num. of chains :21
Num. of groups :
1246 [461]
Num. of atoms :
9661 [1090]
Num. of bonds :
10403
Scientific Name :
Francisella tularensis
subsp. tularensi
Common Name :
-
Method Of Experiment : X-Ray Diffraction
By:
Author :
Kim, Y., Zhou, M., Gu, M., Anderson, W.F., Joachimiak, A., Center for
Structural Genomics of Infectious
Diseases
Deposition :
2010-10-02
Release :
2010-10-20
Caseinolytic
peptidase B protein homolog (ClpB)
chaperone; it is a chaperone involved in disaggregating proteins and also has a role in de novo
protein
synthesis under mild stress conditions.
Molecule above is a molecule of Chaperone Protein ClpB. This
picture is obtained from Raswin software
and it is displayed in backbone style
and coloured in group. These are the description of this molecule:
Classification :
Chaperone
Weight :
34931.60
Polymer :
1
Type :
Protein
Length :
308
Num. of chains :
-
Num. of groups :
292
Num. of atoms :
2348
Num. of bonds :
2385
Scientific Name :
Thermus
thermophilus
Common Name :
-
Method of Experiment : X-Ray Diffraction
By;
Authors : Biter, A.B., Lee,
S., Sung, N., Tsai, F.T.F.
Deposition : 2012-05-25
Release : 2012-07-18
Last Modified (REVDAT) : 2012-08-22
Human telomerase RNA (HTR A).
-HTR-like protein from Haloarcula marismortui. Htr A protein can be portrayed as below. This picture is obtained from RasWin and it is displayed in Ribbon style and colured in Group.
The molecule above is named as Sensor Protein. These are the descriptions
regarding this molecule.
Classification : Transferase
Weight : 60054.17
Polymer : 1
Type : Protein
Length : 126
Num. of chains : 12
Num of groups : 471 [491]
Num of atoms : 4102 [629]
Num. of bonds : 4330
Scientific name : Haloarcula marismortui atcc 43049
Common name : -
Method of experiment : X-RAY DIFFRACTION
By:
Author : Osipiuk, J., Zhou, M., Freeman, L., Joachimiak, A., Midwest Center for Structural Genomics.
Repressor LexA (LexA)
LexA is a repressor enzyme (EC 3.4.21.88) that represses SOS response genes coding for DNApolymerases required for repairing DNA damage. The picture of Lex A enzyme be portrayed as below. This picture is obtained from RasWin software and it is displayed in Strands style and colured in Group.
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