› 1wte

X-ray diffraction
1.9Å resolution

Crystal structure of type II restrcition endonuclease, EcoO109I complexed with cognate DNA

Released:
DOI: 10.2210/pdb1wte/pdb
PDB entry 1wte coloured by chain, ensemble of 2 models, front view.
PDB entry 1wte coloured by chain, ensemble of 2 models, side view.
PDB entry 1wte coloured by chain, ensemble of 2 models, top view.
Source organism: Escherichia coli
Primary publication:
Crystal structures of type II restriction endonuclease EcoO109I and its complex with cognate DNA.
Hashimoto H, Shimizu T, Imasaki T, Kato M, Shichijo N, Kita K, Sato M
J Biol Chem 280 5605-10 (2005)
PMID: 15590682

Function and Biology Details

Reaction catalysed: 
Endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-114771 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Restriction endonuclease Chains: A, B
Molecule details ›
Chains: A, B
Length: 272 amino acids
Theoretical weight: 31.48 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9RPJ3 (Residues: 1-272; Coverage: 100%)
Gene name: ecoO109IR
Structure domains:
5'-D(*AP*CP*CP*GP*GP*GP*CP*CP*CP*TP*GP*CP*C)-3' Chain: X
Molecule details ›
Chain: X
Length: 13 nucleotides
Theoretical weight: 3.91 KDa
Source organism: Escherichia coli
Expression system: Not provided
5'-D(*GP*GP*CP*AP*GP*GP*GP*CP*CP*CP*GP*GP*T)-3' Chain: Y
Molecule details ›
Chain: Y
Length: 13 nucleotides
Theoretical weight: 4.03 KDa
Source organism: Escherichia coli
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand NA 2 x NA
No modified residues

Experiments and Validation Details

Entry percentile scores
Spacegroup: P212121
Unit cell:
a: 49.103Å b: 71.879Å c: 203.24Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.173 0.171 0.223
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

16 citation in other articles

Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily.
Steczkiewicz et al. (2012)
15 more

6 mentions without citation

Type II restriction endonucleases--a historical perspective and more.
Pingoud et al. (2014)
5 more