› 6dmn

X-ray diffraction
1.27Å resolution

Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Soaked in 2 mM Ca2+ and 200 mM K+ at 21 C

Released:
DOI: 10.2210/pdb6dmn/pdb
PDB entry 6dmn coloured by chain, front view.
PDB entry 6dmn coloured by chain, side view.
PDB entry 6dmn 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-510308 (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: 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
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: Alkalihalobacillus halodurans
Expression system: Not provided
RNA (5'-R(*AP*CP*AP*U)-3') Chain: B
Molecule details ›
Chain: B
Length: 4 nucleotides
Theoretical weight: 1.22 KDa
Source organism: Alkalihalobacillus halodurans
Expression system: Not provided
RNA (5'-R(P*CP*G)-3') Chain: b
Molecule details ›
Chain: b
Length: 2 nucleotides
Theoretical weight: 605 Da
Source organism: Alkalihalobacillus halodurans
Expression system: Not provided

Ligands and Environments

5 bound ligands:
Ligand CA 2 x CA
Ligand IOD 4 x IOD
Ligand GOL 2 x GOL
Ligand EDO 4 x EDO
Ligand K 1 x K
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-BM-B
Spacegroup: C2
Unit cell:
a: 81.465Å b: 37.681Å c: 62.022Å
α: 90° β: 95.93° γ: 90°
R-values:
R R work R free
0.151 0.15 0.171
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

4 review citations

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

3 mentions without citation

Not making the cut: Techniques to prevent RNA cleavage in structural studies of RNase-RNA complexes.
Jones et al. (2022)
2 more