› 2qnc

X-ray diffraction
3.1Å resolution

Crystal structure of T4 Endonuclease VII N62D mutant in complex with a DNA Holliday junction

Released:
DOI: 10.2210/pdb2qnc/pdb
PDB entry 2qnc coloured by chain, front view.
PDB entry 2qnc coloured by chain, side view.
PDB entry 2qnc coloured by chain, top view.
Source organism: Tequatrovirus T4
Primary publication:
Crystal structure of T4 endonuclease VII resolving a Holliday junction.
Biertümpfel C, Yang W, Suck D
Nature 449 616-20 (2007)
PMID: 17873859

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-115808 (preferred)
Entry contents:
1 distinct polypeptide molecule
4 distinct DNA molecules
Macromolecules (5 distinct):
Recombination endonuclease VII Chains: A, B
Molecule details ›
Chains: A, B
Length: 157 amino acids
Theoretical weight: 18.17 KDa
Source organism: Escherichia virus T4
Expression system: Escherichia coli
UniProt:
  • Canonical: P13340 (Residues: 1-157; Coverage: 100%)
Gene name: 49
Sequence domains:
Structure domains:
DNA (5'-D(*DCP*DG*DAP*DAP*DGP*DAP*DAP*DTP*DTP*DCP*DCP*DGP*DGP*DAP*DTP*DTP*DAP*DGP*DGP*DGP*DAP*DTP*DCP*DC)-3') Chain: C
Molecule details ›
Chain: C
Length: 24 nucleotides
Theoretical weight: 7.42 KDa
Source organism: Tequatrovirus T4
Expression system: Not provided
DNA (5'-D(*DGP*DGP*DAP*DTP*DCP*DCP*DCP*DTP*DAP*DAP*DGP*DCP*DTP*DCP*DCP*DAP*DTP*DCP*DGP*DAP*DTP*DGP*DTP*DG)-3') Chain: D
Molecule details ›
Chain: D
Length: 24 nucleotides
Theoretical weight: 7.35 KDa
Source organism: Tequatrovirus T4
Expression system: Not provided
DNA (5'-D(*DCP*DAP*DCP*DAP*DTP*DCP*DGP*DAP*DTP*DGP*DGP*DAP*DGP*DCP*DCP*DGP*DCP*DTP*DAP*DGP*DGP*DCP*DCP*DT)-3') Chain: E
Molecule details ›
Chain: E
Length: 24 nucleotides
Theoretical weight: 7.36 KDa
Source organism: Tequatrovirus T4
Expression system: Not provided
DNA (5'-D(*DAP*DGP*DGP*DCP*DCP*DTP*DAP*DGP*DCP*DGP*DTP*DCP*DCP*DGP*DGP*DAP*DAP*DTP*DTP*DCP*DTP*DTP*DCP*DG)-3') Chain: F
Molecule details ›
Chain: F
Length: 24 nucleotides
Theoretical weight: 7.36 KDa
Source organism: Tequatrovirus T4
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand MG 2 x MG
Ligand ZN 2 x ZN
Ligand EDO 2 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-1
Spacegroup: P43212
Unit cell:
a: 99.197Å b: 99.197Å c: 186.884Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.258 0.258 0.278
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

9 review citations

Nucleases: diversity of structure, function and mechanism.
Yang W. (2011)
8 more

13 mentions without citation

Holliday junction resolvases.
Wyatt et al. (2014)
12 more