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Structure of IDP04482

Crystal Structure of Thioredoxin 2 from Yersinia pestis

Edit deposit information
CSGID target
IDP04482 
PDB Id
3P2A (NCBI MMDB
Authors
Y.Kim,M.Zhou,S.Grimshaw,W.F.Anderson,A.Joachimiak,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Youngchang Kim 
Responsible lab
Argonne National Laboratory 
Deposition Date
Oct 01, 2010 
Release Date
Oct 13, 2010 

Annotation

Description
Thioredoxin is a small (~13 Kd) disulphide oxidoreductase found in all living organism interact with a broad range of proteins participating in reversible oxidation to convert two cysteine thiol groups to a disulphide and dithiol. The structure has a common beta-alpha fold shared with glutaredoxin, glutathione peroxidase, bacterial protein disulphide isomerase DsbA, and the N-terminal domain of glutathione transferase. Thioredoxin 2 from Yersinia pestis belongs to group 2 by having a small beta-hairpin containing domain fused at the N-terminus of the Trx domain.  
Functional assignment
 

Ligands

Ligand code Name Ligand type
ZN ZINC ION biological
MSE modified residue
175 3,5-dihydro-5-methylidene-4h-imidazol-4-on

Structure information

Unit cell parameters

Space Group
P 1 21 1  
Unit Cell

a=53.97Å, b=75.58Å, c=81.51Å
α=90.00, β=90.85, γ=90.00 
Solvent content
50.46  
Matthews coefficient
2.48  

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
34.29-2.20Å (2.27-2.20Å)  
Rall(%)
18.6 
Rwork(%)
18.4 (23.7) 
Rfree(%)
23.4 (32.8) 
Num. observed reflections
34941 (3196) 
Num. Rfree reflections
1778 (160) 
Completeness(%)
98.9 (95.0) 

Model parameters

Num Atoms
4458  
Num Waters
353  
Num Hetatoms
360  
Model mean isotropic B factor
37.340Å2  
RMSD bond length
0.014Å  
RMSD bond angle
1.556°  
RMSD dihedral angle
16.643°
 
Filename uploaded
dep.pdb (uploaded on Oct 05, 2010 7:06 AM)  
Inserted
Oct 05, 2010