PDBe 1stx

X-ray diffraction
2.1Å resolution

Structure of the K38A mutant of EcoRV bound to cognate DNA and Mn2+

Released:

Function and Biology Details

Reaction catalysed:
Endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. 
Biochemical function:
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Type-2 restriction enzyme EcoRV Chains: A, B
Molecule details ›
Chains: A, B
Length: 244 amino acids
Theoretical weight: 28.5 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: ECO RV Endonuclease; Chain A
5'-D(P*AP*TP*CP*TP*T)-3' Chains: D, F
Molecule details ›
Chains: D, F
Length: 5 nucleotides
Theoretical weight: 1.47 KDa
Source organism: Synthetic construct
Expression system: Not provided
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: Synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU
Spacegroup: P21
Unit cell:
a: 63.71Å b: 58.69Å c: 82.1Å
α: 90° β: 107.7° γ: 90°
R-values:
R R work R free
0.201 0.201 0.262
Expression systems:
  • Escherichia coli
  • Not provided