› 6dp7

X-ray diffraction
1.38Å resolution

Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 500 mM Mn2+ and 200 mM K+ for 40 s at 21 C

Released:
DOI: 10.2210/pdb6dp7/pdb
Model geometry
Fit model/data
PDB entry 6dp7 coloured by chain, front view.
PDB entry 6dp7 coloured by chain, side view.
PDB entry 6dp7 coloured by chain, top view.
Source organisms:
Primary publication:
Cation trafficking propels RNA hydrolysis.
Samara NL, Yang W
Nat Struct Mol Biol 25 715-721 (2018)
PMID: 30076410

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-119783 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
2 distinct RNA molecules
Macromolecules (4 distinct):
Ribonuclease H Chain: A
Molecule details ›
Chain: A
Length: 135 amino acids
Theoretical weight: 15.59 KDa
Source organism: Alkalihalobacillus halodurans C-125
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9KEI9 (Residues: 61-195; Coverage: 69%)
Gene names: BH0863, rnhA
Structure domains: Ribonuclease H-like superfamily/Ribonuclease H
DNA (5'-D(*CP*GP*AP*TP*GP*T)-3') Chain: C
Molecule details ›
Chain: C
Length: 6 nucleotides
Theoretical weight: 1.82 KDa
Source organism: synthetic construct
Expression system: Not provided
RNA (5'-R(*AP*CP*AP*U)-3') Chain: B
RNA (5'-R(P*CP*G)-3') Chain: b

Ligands and Environments

4 bound ligands:
Ligand MN 4 x MN
Ligand K 1 x K
Ligand IOD 3 x IOD
Ligand EDO 2 x EDO
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: APS BEAMLINE 23-BM-B
Spacegroup: C2
Unit cell:
a: 82.013Å b: 37.557Å c: 61.932Å
α: 90° β: 96.79° γ: 90°
R-values:
R R work R free
0.17 0.169 0.192
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

5 review citations

Catalytic mechanism of DNA polymerases-Two metal ions or three?
Tsai MD. (2019)
4 more

1 mention without citation

Cation trafficking propels RNA hydrolysis.
Samara et al. (2018)