› 2ihn

X-ray diffraction
3Å resolution

Co-crystal of Bacteriophage T4 RNase H with a fork DNA substrate

Released:
DOI: 10.2210/pdb2ihn/pdb
PDB entry 2ihn coloured by chain, front view.
PDB entry 2ihn coloured by chain, side view.
PDB entry 2ihn coloured by chain, top view.
Source organism: Tequatrovirus T4
Primary publication:
Crystal structure of bacteriophage T4 5' nuclease in complex with a branched DNA reveals how flap endonuclease-1 family nucleases bind their substrates.
Devos JM, Tomanicek SJ, Jones CE, Nossal NG, Mueser TC
J Biol Chem 282 31713-24 (2007)
PMID: 17693399

Function and Biology Details

Reaction catalysed: 
Endonucleolytic cleavage to 5'-phosphomonoester.
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-115401 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Ribonuclease H Chain: A
Molecule details ›
Chain: A
Length: 305 amino acids
Theoretical weight: 35.61 KDa
Source organism: Escherichia virus T4
Expression system: Escherichia coli
UniProt:
  • Canonical: P13319 (Residues: 1-305; Coverage: 100%)
Gene names: 33.2, das, rnh
Sequence domains:
Structure domains:
5'-D(*CP*TP*AP*AP*CP*TP*TP*TP*GP*AP*GP*GP*CP*AP*GP*AP*CP*C)-3' Chain: C
Molecule details ›
Chain: C
Length: 18 nucleotides
Theoretical weight: 5.5 KDa
Source organism: Tequatrovirus T4
Expression system: Not provided
5'-D(*GP*GP*TP*CP*TP*GP*CP*CP*TP*CP*AP*AP*GP*AP*CP*GP*GP*TP*AP*GP*TP*CP*AP*A)-3' Chain: D
Molecule details ›
Chain: D
Length: 24 nucleotides
Theoretical weight: 7.39 KDa
Source organism: Tequatrovirus T4
Expression system: Not provided

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU FR-E+ SUPERBRIGHT
Spacegroup: P212121
Unit cell:
a: 68.16Å b: 84.99Å c: 89.29Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.225 0.222 0.282
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

8 review citations

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

11 mentions without citation

Unpairing and gating: sequence-independent substrate recognition by FEN superfamily nucleases.
Grasby et al. (2012)
10 more