› 1eo4

X-ray diffraction
1.9Å resolution

ECORV BOUND TO MN2+ AND COGNATE DNA CONTAINING A 3'S SUBSTITION AT THE CLEAVAGE SITE

Released:
DOI: 10.2210/pdb1eo4/pdb
PDB entry 1eo4 coloured by chain, front view.
PDB entry 1eo4 coloured by chain, side view.
PDB entry 1eo4 coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Inhibition of EcoRV Endonuclease by Deoxyribo-3'-S-phosphorothiolates: A High-Resolution X-ray Crystallographic Study
Horton NC, Connolly BA, Perona JJ
J. Am. Chem. Soc. 122 3314-3324 (2000)

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-113759 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
Type II restriction enzyme EcoRV Chains: A, B
Molecule details ›
Chains: A, B
Length: 245 amino acids
Theoretical weight: 28.69 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P04390 (Residues: 1-245; Coverage: 100%)
Gene name: ecoRVR
Sequence domains: Restriction endonuclease EcoRV
Structure domains: DNA mismatch repair MutH/Restriction endonuclease, type II
DNA (5'-D(*CP*AP*AP*GP*AP*(TSP)P*AP*TP*CP*TP*T)-3') Chains: C, D
Molecule details ›
Chains: C, D
Length: 11 nucleotides
Theoretical weight: 3.35 KDa
Source organism: Escherichia coli
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand MN 5 x MN
Ligand ACY 2 x ACY
1 modified residue:
Ligand TSP 2 x TSP

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL7-1
Spacegroup: P1
Unit cell:
a: 47.7Å b: 48.5Å c: 63.7Å
α: 96.7° β: 109.6° γ: 106.3°
R-values:
R R work R free
0.216 0.213 0.305
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

1 mention without citation

DNA conformations and their sequence preferences.
Svozil et al. (2008)