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Structure of IDP01318

CRYSTAL STRUCTURE OF DPS PROTEIN FROM VIBRIO CHOLERAE O1, A MEMBER OF A BROAD SUPERFAMILY OF FERRITIN-LIKE DIIRON-CARBOXYLATE PROTEINS

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CSGID target
IDP01318 
PDB Id
3IQ1 (NCBI MMDB
Authors
B.Nocek,S.Peterson,M.Gu,Z.Otwinowski,W.Anderson,A.Joachimiak 
Responsible person
Boguslaw Nocek 
Responsible lab
Argonne National Laboratory 
Deposition Date
Aug 18, 2009 
Release Date
Sep 08, 2009 

Annotation

Description
DNA-binding proteins from starved cells (Dps-like proteins) are key factors involved in oxidative stress protection in bacteria. They bind and oxidize iron to prevent the formation of harmful reactive oxygen species that can interact and damage DNA. We have determined the crystal structure of Vibrio cholerae O1 in iron-free form at 1.67-Å resolution. This Dps-like protein is composed of 12 identical subunits assembled in a spherical structure with an internal cavity. Each subunit is composed of a four-helix bundle. Fold analysis using the SSM server reveals close structural similarity to a Dps-like protein from Listeria monocytogene (PDB id 2iy4, Z-score 7.7, rmsd 1.03 Å) and a Dps protein from Bacillus brevis (PDB id 1n1q, Z-score 7.8, rmsd 1.05 Å).  
Functional assignment
 

Ligands

Ligand code Name Ligand type
CL CHLORIDE ION
MSE modified residue

Structure information

Unit cell parameters

Space Group
H 3  
Unit Cell

a=93.82Å, b=93.82Å, c=225.56Å
α=90.00, β=90.00, γ=120.00 
Solvent content
52.49  
Matthews coefficient
2.59  

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
35.00-1.67Å (1.71-1.67Å)  
Rall(%)
17.8 
Rwork(%)
13.9 (20.4) 
Rfree(%)
17.4 (25.0) 
Num. observed reflections
85070 (5927) 
Num. Rfree reflections
4253 (285) 
Completeness(%)
98.8 (93.1) 

Model parameters

Num Atoms
5020  
Num Waters
777  
Num Hetatoms
973  
Model mean isotropic B factor
7.710Å2  
RMSD bond length
0.020Å  
RMSD bond angle
1.502°  
Filename uploaded
rcsb054721.pdb (uploaded on Aug 31, 2009 12:33 PM)  
Inserted
Aug 31, 2009