› 1o9r

X-ray diffraction
1.45Å resolution

The X-ray crystal structure of Agrobacterium tumefaciens Dps, a member of the family that protect DNA without binding

Released:
DOI: 10.2210/pdb1o9r/pdb
PDB entry 1o9r coloured by chain, front view.
PDB entry 1o9r coloured by chain, side view.
PDB entry 1o9r coloured by chain, top view.
Source organism: Agrobacterium tumefaciens
Primary publication:
The Dps protein of Agrobacterium tumefaciens does not bind to DNA but protects it toward oxidative cleavage: x-ray crystal structure, iron binding, and hydroxyl-radical scavenging properties.
Ceci P, Ilari A, Falvo E, Chiancone E
J Biol Chem 278 20319-26 (2003)
PMID: 12660233

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
homo dodecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-186512 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
DNA protection during starvation protein Chains: A, B, C, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
Length: 162 amino acids
Theoretical weight: 17.85 KDa
Source organism: Agrobacterium tumefaciens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q8UCK6 (Residues: 1-162; Coverage: 100%)
Gene names: AGR_C_4495, Atu2477, dps
Sequence domains: Ferritin-like domain
Structure domains: Ferritin

Ligands and Environments

3 bound ligands:
Ligand FE 6 x FE
Ligand TRS 2 x TRS
Ligand EDO 1 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ELETTRA BEAMLINE 5.2R
Spacegroup: P21212
Unit cell:
a: 106.046Å b: 90.349Å c: 105.656Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.18 0.17 0.2
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

10 review citations

The diverse antioxidant systems of Helicobacter pylori.
Wang et al. (2006)
9 more

2 mentions without citation

Structure and mechanism of iron translocation by a Dps protein from Microbacterium arborescens.
Pesek et al. (2011)
1 more