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Structure of IDP00649

2.1 Angstrom Resolution Crystal Structure of Metallo-beta-lactamase Family Protein from Staphylococcus aureus subsp. aureus COL.

Edit deposit information
CSGID target
IDP00649 
PDB Id
3R2U (NCBI MMDB
Authors
G.Minasov,Z.Wawrzak,A.Halavaty,L.Shuvalova,I.Dubrovska,J.Winsor,O.Kiryukhina,L.Papazisi,W.F.Anderson,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
George Minasov 
Responsible lab
Northwestern University 
Deposition Date
Mar 14, 2011 
Release Date
Mar 23, 2011 

Annotation

Description
The target protein idp00649 was assign as a protein with unknown function. It consists of two domains: N-terminal Domain, which is similar to metallo-beta-lactamase family proteins (PF00753) and C-terminal Rhodanese-like Domain (PF00581). Metallo-beta-lactamases are important enzymes, which are involved in the breakdown of antibiotics by antibiotic-resistant bacteria. Usually these proteins bind two zinc ions per molecule as cofactor. The superposition of N-terminal domain of idp00649 with the metallo-beta-lactamase from Bacillus cereus (PDB code 1BMC) shows close match in the fold for these proteins, and the match in the position of metals bound to the active site. But these two proteins have very low sequence homology. C-terminal domain, which has Rhodanese-like fold, also shows very low sequence homology to the proteins of this family. Furthermore, very important Cysteine in the active site of Rhodanese, which is involved in detoxification of cyanide, is missing in the C-terminal Domain of idp00649. So, function and specificity of these domain and protein as whole still remains unknown. 
Functional assignment
metallo-beta-lactamase 

Ligands

Ligand code Name Ligand type
FE biological
CL crystallization
175 3,5-dihydro-5-methylidene-4h-imidazol-4-on

Structure information

Unit cell parameters

Space Group
P 43 21 2  
Unit Cell

a=92.48Å, b=92.48Å, c=385.39Å
α=90.00, β=90.00, γ=90.00 
Solvent content
 
Matthews coefficient
 

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
29.98-2.10Å (2.16-2.10Å)  
Rall(%)
15.8 
Rwork(%)
15.6 (18.5) 
Rfree(%)
19.7 (25.1) 
Num. observed reflections
98323 (7010) 
Num. Rfree reflections
4916 (343) 
Completeness(%)
99.9 (98.7) 

Model parameters

Num Atoms
11213  
Num Waters
1214  
Num Hetatoms
1246  
Model mean isotropic B factor
30.320Å2  
RMSD bond length
0.011Å  
RMSD bond angle
1.398°  
Filename uploaded
rcsb064418.pdb (uploaded on Mar 24, 2011 12:24 PM)  
Inserted
Mar 24, 2011