› 1rvc

X-ray diffraction
2.1Å resolution

MG2+ BINDING TO THE ACTIVE SITE OF ECO RV ENDONUCLEASE: A CRYSTALLOGRAPHIC STUDY OF COMPLEXES WITH SUBSTRATE AND PRODUCT DNA AT 2 ANGSTROMS RESOLUTION

Released:
DOI: 10.2210/pdb1rvc/pdb
PDB entry 1rvc coloured by chain, front view.
PDB entry 1rvc coloured by chain, side view.
PDB entry 1rvc coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Mg2+ binding to the active site of EcoRV endonuclease: a crystallographic study of complexes with substrate and product DNA at 2 A resolution.
Kostrewa D, Winkler FK
Biochemistry 34 683-96 (1995)
PMID: 7819264

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 hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-114547 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 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
Expression system: 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
DNA (5'-D(*AP*AP*AP*GP*AP*T)-3') Chains: C, E
Molecule details ›
Chains: C, E
Length: 6 nucleotides
Theoretical weight: 1.84 KDa
Source organism: Escherichia coli
Expression system: Not provided
DNA (5'-D(*AP*TP*CP*TP*T)-3') Chains: D, F
Molecule details ›
Chains: D, F
Length: 5 nucleotides
Theoretical weight: 1.47 KDa
Source organism: Escherichia coli
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand MG 4 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
Spacegroup: P1
Unit cell:
a: 49.29Å b: 50.34Å c: 63.88Å
α: 96.66° β: 108.76° γ: 108.41°
R-values:
R R work R free
0.156 0.156 not available
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

20 review citations

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

5 mentions without citation

A tool written in Scala for preparation and analysis in MD simulation and 3D-RISM calculation of biomolecules.
Onishi et al. (2019)
4 more