› 1odg

X-ray diffraction
2.8Å resolution

Very-short-patch DNA repair endonuclease bound to its reaction product site

Released:
DOI: 10.2210/pdb1odg/pdb
PDB entry 1odg coloured by chain, front view.
PDB entry 1odg coloured by chain, side view.
PDB entry 1odg coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Crystal structure of the Escherichia coli dcm very-short-patch DNA repair endonuclease bound to its reaction product-site in a DNA superhelix.
Bunting KA, Roe SM, Headley A, Brown T, Savva R, Pearl LH
Nucleic Acids Res 31 1633-9 (2003)
PMID: 12626704

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-114301 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
DNA mismatch endonuclease Vsr Chain: A
Molecule details ›
Chain: A
Length: 134 amino acids
Theoretical weight: 15.57 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P09184 (Residues: 23-156; Coverage: 86%)
Gene names: JW1943, b1960, vsr
Sequence domains: DNA mismatch endonuclease Vsr
Structure domains: VSR Endonuclease
5'-D(*TP*AP*GP*GP*CP*5CM*TP*GP*GP*AP*TP*CP)-3' Chains: F, W
Molecule details ›
Chains: F, W
Length: 12 nucleotides
Theoretical weight: 3.69 KDa
Source organism: Escherichia coli

Ligands and Environments

1 bound ligand:
Ligand ZN 1 x ZN
1 modified residue:
Ligand 5CM 2 x 5CM

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-2
Spacegroup: P61
Unit cell:
a: 102.805Å b: 102.805Å c: 64.29Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.287 0.287 0.356
Expression system: Escherichia coli

Quick links

Citations

3 review citations

Nucleases: diversity of structure, function and mechanism.
Yang W. (2011)
2 more

4 mentions without citation

An inactivated nuclease-like domain in RecC with novel function: implications for evolution.
Rigden DJ. (2005)
3 more