› 1rv5

X-ray diffraction
2.1Å resolution

COMPLEX OF ECORV ENDONUCLEASE WITH D(AAAGAT)/D(ATCTT)

Released:
DOI: 10.2210/pdb1rv5/pdb
PDB entry 1rv5 coloured by chain, front view.
PDB entry 1rv5 coloured by chain, side view.
PDB entry 1rv5 coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Role of protein-induced bending in the specificity of DNA recognition: crystal structure of EcoRV endonuclease complexed with d(AAAGAT) + d(ATCTT).
Horton NC, Perona JJ
J Mol Biol 277 779-87 (1998)
PMID: 9545372

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-114544 (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: 244 amino acids
Theoretical weight: 28.56 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P04390 (Residues: 2-245; Coverage: 100%)
Gene name: ecoRVR
Sequence domains: Restriction endonuclease EcoRV
Structure domains: DNA mismatch repair MutH/Restriction endonuclease, type II
5'-D(*AP*AP*AP*GP*AP*T*AP*TP*CP*TP*T)-3' Chains: C, D
Molecule details ›
Chains: C, D
Length: 11 nucleotides
Theoretical weight: 3.36 KDa
Source organism: Escherichia coli
Expression system: Not provided

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Spacegroup: P1
Unit cell:
a: 49.6Å b: 50.4Å c: 63.9Å
α: 96.4° β: 109.2° γ: 108.5°
R-values:
R R work R free
0.193 0.193 0.272
Expression system: Not provided

Quick links

Citations

4 review citations

Structure and function of type II restriction endonucleases.
Pingoud et al. (2001)
3 more

2 mentions without citation

An all-atom knowledge-based energy function for protein-DNA threading, docking decoy discrimination, and prediction of transcription-factor binding profiles.
Xu et al. (2009)
1 more