› 1zbi

X-ray diffraction
1.85Å resolution

Bacillus halodurans RNase H catalytic domain mutant D132N in complex with 12-mer RNA/DNA hybrid

Released:
DOI: 10.2210/pdb1zbi/pdb
PDB entry 1zbi coloured by chain, front view.
PDB entry 1zbi coloured by chain, side view.
PDB entry 1zbi coloured by chain, top view.
Source organism: Halalkalibacterium halodurans C-125
Primary publication:
Crystal structures of RNase H bound to an RNA/DNA hybrid: substrate specificity and metal-dependent catalysis.
Nowotny M, Gaidamakov SA, Crouch RJ, Yang W
Cell 121 1005-16 (2005)
PMID: 15989951

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-114889 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
1 distinct RNA molecule
Macromolecules (3 distinct):
Ribonuclease H Chains: A, B
Molecule details ›
Chains: A, B
Length: 142 amino acids
Theoretical weight: 16.33 KDa
Source organism: Alkalihalobacillus halodurans C-125
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9KEI9 (Residues: 59-196; Coverage: 70%)
Gene names: BH0863, rnhA
Structure domains: Ribonuclease H-like superfamily/Ribonuclease H
5'-D(*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*C)-3' Chain: D
Molecule details ›
Chain: D
Length: 12 nucleotides
Theoretical weight: 3.7 KDa
Source organism: Halalkalibacterium halodurans C-125
Expression system: Not provided
5'-R(*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP*C)-3' Chain: C
Molecule details ›
Chain: C
Length: 12 nucleotides
Theoretical weight: 3.77 KDa
Source organism: Halalkalibacterium halodurans C-125
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand MG 4 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: C2
Unit cell:
a: 136.393Å b: 36.964Å c: 93.202Å
α: 90° β: 121.51° γ: 90°
R-values:
R R work R free
0.206 0.206 0.248
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

87 review citations

Ribonuclease H: the enzymes in eukaryotes.
Cerritelli et al. (2009)
86 more

33 mentions without citation

From guide to target: molecular insights into eukaryotic RNA-interference machinery.
Ipsaro et al. (2015)
32 more