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Structure of IDP00895

1.2 Angstrom Crystal Structure of the Glutaredoxin 2 (grxB) from Salmonella typhimurium in complex with Glutathione.

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CSGID target
IDP00895 
PDB Id
3IR4 (NCBI MMDB) 
Authors
G.Minasov,Z.Wawrzak,T.Skarina,O.Onopriyenko,S.N.Peterson,A.Halavaty,Z.Dauter,W.F.Anderson,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
George Minasov 
Responsible lab
Northwestern University 
Deposition Date
Aug 21, 2009 
Release Date
Sep 01, 2009 

Annotation

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Description
Glutaredoxins, also known as thioltransferases (disulphide reductases, are small proteins of approximately one hundred amino-acid residues which utilise glutathione and NADPH as cofactors. Oxidized glutathione is regenerated by glutathione reductase. Together these components compose the glutathione system. Glutaredoxin functions as an electron carrier in the glutathione-dependent synthesis of deoxyribonucleotides by the enzyme ribonucleotide reductase. Like thioredoxin, glutaredoxin possesses an active centre disulphide bond. It exists in either a reduced or an oxidized form where the two cysteine residues are linked in an intramolecular disulphide bond. This family includes the highly abundant Escherichia coli GrxB (Grx2) glutaredoxin which is notably longer than either GrxA or GrxC. Unlike the other two E. coli glutaredoxins, GrxB appears to be unable to reduce ribonucleotide reductase, and may have more to do with resistance to redox stress. The only available structure was solution structure (PDB code 1G7O). Presented crystal structure of the GrxB from Salmonella typhimurium is structurally similar (sequence similarity 86%) to the glutaredoxin from Escherichia coli. High resolution crystal structure of the complex of the GrxB with the glutathione is a important step in understanding of the mechanism of the reaction.  
Functional assignment
Glutaredoxins, thioltransferases. 

Ligands

Ligand code Name Ligand type
CL chloride crystallization
SO4 sulfate crystallization
MSE modified residue
175 3,5-dihydro-5-methylidene-4h-imidazol-4-on biological

Structure information

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Unit cell parameters

Space Group
P 21 21 21  
Unit Cell

a=41.24Å, b=58.76Å, c=87.93Å
α=90.00, β=90.00, γ=90.00 
Solvent content
42.05  
Matthews coefficient
2.12  

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
27.87-1.20Å (1.23-1.20Å)  
Rall(%)
11.8 
Rwork(%)
11.7 (14.6) 
Rfree(%)
14.4 (17.9) 
Num. observed reflections
66655 (4773) 
Num. Rfree reflections
3332 (254) 
Completeness(%)
98.7 (96.9) 

Model parameters

Num Atoms
1951  
Num Waters
489  
Num Hetatoms
600  
Model mean isotropic B factor
6.290Å2  
RMSD bond length
0.013Å  
RMSD bond angle
1.502°  
Filename uploaded
idp00895-5-final.pdb (uploaded on Aug 21, 2009 4:26 PM)  
Inserted
Aug 21, 2009