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Structure of IDP00511

1.1 Angstrom Crystal Structure of Putative Modulator of Drug Activity (MdaB) from Yersinia pestis CO92.

Edit deposit information
CSGID target
IDP00511 
PDB Id
3RPE (NCBI MMDB
Authors
G.Minasov,A.Halavaty,L.Shuvalova,I.Dubrovska,J.Winsor,L.Papazisi,W.F.Anderson,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
George Minasov 
Responsible lab
Northwestern University 
Deposition Date
Apr 26, 2011 
Release Date
May 04, 2011 

Annotation

Description
A putative modulator of drug activity (MdaB) from Yersinia pesttis shows 66% homology to MdaB from E. coli, RCSB Protein Data Bank 2AMJ (in complex with FAD) and 2B3D (apo- structure). Authors demonstrated, that MdaB had close structural relation to known members of DT-diaphorase family and suggested that redox cycle formed by this protein protects E. coli from toxic effects of polyketide compounds rather than the oxidative stress of menadione alone as it was proposed earlier. Menadione has been used experimentally as a chemotherapeutic agent for cancer. More recently it was studied as a potential treatment for prostate cancer. 
Functional assignment
A putative modulator of drug activity 

Ligands

Ligand code Name Ligand type
PEG polyethylene glycol crystallization
175 3,5-dihydro-5-methylidene-4h-imidazol-4-on biological

Structure information

Unit cell parameters

Space Group
P 32  
Unit Cell

a=66.50Å, b=66.50Å, c=76.21Å
α=90.00, β=90.00, γ=120.00 
Solvent content
 
Matthews coefficient
 

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
28.80-1.10Å (1.13-1.10Å)  
Rall(%)
10.0 
Rwork(%)
10.0 (22.4) 
Rfree(%)
11.7 (25.7) 
Num. observed reflections
152994 (11305) 
Num. Rfree reflections
7802 (593) 
Completeness(%)
99.9 (99.3) 

Model parameters

Num Atoms
3406  
Num Waters
473  
Num Hetatoms
641  
Model mean isotropic B factor
13.420Å2  
RMSD bond length
0.010Å  
RMSD bond angle
1.547°  
Filename uploaded
3RPE.pdb (uploaded on May 26, 2011 12:58 PM)  
Inserted
May 26, 2011