› 6dor

X-ray diffraction
1.5Å resolution

Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 2 mM Mg2+ and 300 mM K+ for 120 s at 21 C (dataset 1)

Released:
DOI: 10.2210/pdb6dor/pdb
PDB entry 6dor coloured by chain, front view.
PDB entry 6dor coloured by chain, side view.
PDB entry 6dor 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-119767 (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: 136 amino acids
Theoretical weight: 15.72 KDa
Source organism: Alkalihalobacillus halodurans
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9KEI9 (Residues: 61-196; 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
5'-R(*AP*CP*AP*U)-3' portion of cleaved RNA 5'-R(*AP*CP*AP*UP*CP*G)-3' Chain: B
Molecule details ›
Chain: B
Length: 4 nucleotides
Theoretical weight: 1.22 KDa
Source organism: synthetic construct
Expression system: Not provided
5'-R(P*CP*G)-3' portion of cleaved RNA (5'-R(*AP*CP*AP*UP*CP*G)-3') Chain: b
Molecule details ›
Chain: b
Length: 2 nucleotides
Theoretical weight: 605 Da
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

6 bound ligands:
Ligand MG 2 x MG
Ligand K 3 x K
Ligand IOD 4 x IOD
Ligand GOL 5 x GOL
Ligand PGE 1 x PGE
Ligand EDO 1 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-BM
Spacegroup: C2
Unit cell:
a: 81.544Å b: 37.711Å c: 62.779Å
α: 90° β: 96.56° γ: 90°
R-values:
R R work R free
0.156 0.155 0.194
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)