› 2ivk

X-ray diffraction
2.9Å resolution

Crystal structure of the periplasmic endonuclease Vvn complexed with a 16-bp DNA

Released:
DOI: 10.2210/pdb2ivk/pdb
PDB entry 2ivk coloured by chain, front view.
PDB entry 2ivk coloured by chain, side view.
PDB entry 2ivk coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis for sequence-dependent DNA cleavage by nonspecific endonucleases.
Wang YT, Yang WJ, Li CL, Doudeva LG, Yuan HS
Nucleic Acids Res 35 584-94 (2007)
PMID: 17175542

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
hetero decamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-115416 (preferred)
Entry contents:
1 distinct polypeptide molecule
3 distinct DNA molecules
Macromolecules (4 distinct):
Endonuclease I Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 213 amino acids
Theoretical weight: 24.75 KDa
Source organism: Vibrio vulnificus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q7MHK3 (Residues: 19-231; Coverage: 100%)
Gene name: VV2866
Sequence domains: Endonuclease I
5'-D(*GP*AP*AP*TP*TP*CP*GP*AP*TP*CP *GP*AP*AP*TP*T)-3' Chains: E, G
Molecule details ›
Chains: E, G
Length: 15 nucleotides
Theoretical weight: 4.61 KDa
Source organism: synthetic construct
Expression system: Not provided
5'-D(*AP*AP*TP*TP*CP*GP*AP*TP*CP*GP *AP*AP*TP*TP*C)-3' Chains: F, H
Molecule details ›
Chains: F, H
Length: 15 nucleotides
Theoretical weight: 4.57 KDa
Source organism: synthetic construct
Expression system: Not provided
5'-D(*GP*AP*AP*TP*TP*CP*GP*AP*TP*CP *GP*AP*AP*TP*TP*C)-3' Chains: I, J
Molecule details ›
Chains: I, J
Length: 16 nucleotides
Theoretical weight: 4.9 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE AR-NW12A
Spacegroup: P1
Unit cell:
a: 64.636Å b: 64.705Å c: 79.157Å
α: 74.45° β: 73.56° γ: 75.56°
R-values:
R R work R free
0.237 0.237 0.284
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

1 review citation

Nucleases: diversity of structure, function and mechanism.
Yang W. (2011)
22 other articles

3 mentions without citation

Structural basis for sequence-dependent DNA cleavage by nonspecific endonucleases.
Wang et al. (2007)
2 more