› 1oup

X-ray diffraction
2.3Å resolution

Crystal structure of the periplasmic endonuclease Vvn complexed with octamer double stranded DNA

Released:
DOI: 10.2210/pdb1oup/pdb
PDB entry 1oup coloured by chain, front view.
PDB entry 1oup coloured by chain, side view.
PDB entry 1oup coloured by chain, top view.
Source organism: Vibrio vulnificus
Primary publication:
DNA binding and cleavage by the periplasmic nuclease Vvn: a novel structure with a known active site.
Li CL, Hor LI, Chang ZF, Tsai LC, Yang WZ, Yuan HS
EMBO J 22 4014-25 (2003)
PMID: 12881435

Function and Biology Details

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

Structure analysis Details

Assemblies composition:
hetero trimer
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-114326 (preferred)
Entry contents:
1 distinct polypeptide molecule
3 distinct DNA molecules
Macromolecules (4 distinct):
Endonuclease I Chains: A, B
Molecule details ›
Chains: A, B
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*CP*GP*AP*TP*CP*GP*C)-3' Chains: C, D, F
Molecule details ›
Chains: C, D, F
Length: 8 nucleotides
Theoretical weight: 2.43 KDa
Source organism: Vibrio vulnificus
Expression system: Not provided
5'-D(*GP*CP*GP*AP*TP*C)-3' Chain: E
Molecule details ›
Chain: E
Length: 6 nucleotides
Theoretical weight: 1.81 KDa
Source organism: Vibrio vulnificus
Expression system: Not provided
5'-D(P*GP*C)-3' Chain: G
Molecule details ›
Chain: G
Length: 2 nucleotides
Theoretical weight: 573 Da
Source organism: Vibrio vulnificus
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand CA 2 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL12B2
Spacegroup: P21
Unit cell:
a: 53.74Å b: 50.11Å c: 89.61Å
α: 90° β: 97.53° γ: 90°
R-values:
R R work R free
0.191 0.191 0.26
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

2 review citations

Applications of the CRISPR/Cas system beyond gene editing.
Anton et al. (2018)
1 more

16 mentions without citation

Crystal structure of Cas9 in complex with guide RNA and target DNA.
Nishimasu et al. (2014)
15 more