› 6dp8

X-ray diffraction
1.32Å resolution

Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 5 mM Mg2+ and 200 mM Li+ for 240 s at 21 C

Released:
DOI: 10.2210/pdb6dp8/pdb
PDB entry 6dp8 coloured by chain, front view.
PDB entry 6dp8 coloured by chain, side view.
PDB entry 6dp8 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-510347 (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: synthetic construct
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: synthetic construct
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: synthetic construct
Expression system: Not provided

Ligands and Environments

6 bound ligands:
Ligand MG 2 x MG
Ligand LI 1 x LI
Ligand CL 3 x CL
Ligand GOL 3 x GOL
Ligand EDO 6 x EDO
Ligand PEG 2 x PEG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-BM
Spacegroup: C2
Unit cell:
a: 81.426Å b: 37.747Å c: 61.811Å
α: 90° β: 95.45° γ: 90°
R-values:
R R work R free
0.148 0.147 0.17
Expression systems:
  • Escherichia coli
  • 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)