› 1vrr

X-ray diffraction
2.7Å resolution

Crystal structure of the restriction endonuclease BstYI complex with DNA

Released:
DOI: 10.2210/pdb1vrr/pdb
PDB entry 1vrr coloured by chain, front view.
PDB entry 1vrr coloured by chain, side view.
PDB entry 1vrr coloured by chain, top view.
Source organism: Geobacillus stearothermophilus
Primary publication:
Implications for switching restriction enzyme specificities from the structure of BstYI bound to a BglII DNA sequence.
Townson SA, Samuelson JC, Xu SY, Aggarwal AK
Structure 13 791-801 (2005)
PMID: 15893669

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-114728 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
BstYI Chains: A, B
Molecule details ›
Chains: A, B
Length: 203 amino acids
Theoretical weight: 23.22 KDa
Source organism: Geobacillus stearothermophilus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q84AF2 (Residues: 1-203; Coverage: 100%)
Gene name: bstYIR
Sequence domains: Restriction endonuclease BglII
Structure domains: Restriction Endonuclease
5'-D(*TP*TP*AP*TP*AP*GP*AP*TP*CP*TP*AP*TP*AP*A)-3' Chains: C, D
Molecule details ›
Chains: C, D
Length: 14 nucleotides
Theoretical weight: 4.28 KDa
Source organism: Geobacillus stearothermophilus
Expression system: Not provided

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X12C
Spacegroup: C2
Unit cell:
a: 78.58Å b: 110.91Å c: 80.08Å
α: 90° β: 107.17° γ: 90°
R-values:
R R work R free
0.233 0.23 0.267
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

11 citation in other articles

On the divalent metal ion dependence of DNA cleavage by restriction endonucleases of the EcoRI family.
Pingoud et al. (2009)
10 more

2 mentions without citation

A protein-DNA docking benchmark.
van Dijk et al. (2008)
1 more