› 1io2

X-ray diffraction
2Å resolution

Crystal structure of type 2 ribonuclease h from hyperthermophilic archaeon, thermococcus kodakaraensis kod1

Released:
DOI: 10.2210/pdb1io2/pdb
PDB entry 1io2 coloured by chain, front view.
PDB entry 1io2 coloured by chain, side view.
PDB entry 1io2 coloured by chain, top view.
Source organism: Thermococcus kodakarensis KOD1
Primary publication:
Catalytic center of an archaeal type 2 ribonuclease H as revealed by X-ray crystallographic and mutational analyses.
Muroya A, Tsuchiya D, Ishikawa M, Haruki M, Morikawa M, Kanaya S, Morikawa K
Protein Sci 10 707-14 (2001)
PMID: 11274461

Function and Biology Details

Reaction catalysed: 
Endonucleolytic cleavage to 5'-phosphomonoester.
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-130755 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Ribonuclease HII Chain: A
Molecule details ›
Chain: A
Length: 213 amino acids
Theoretical weight: 23.97 KDa
Source organism: Thermococcus kodakarensis KOD1
Expression system: Escherichia coli
UniProt:
  • Canonical: O74035 (Residues: 1-213; Coverage: 93%)
Gene names: TK0805, rnhB
Sequence domains: Ribonuclease HII
Structure domains:

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-6A
Spacegroup: P212121
Unit cell:
a: 43.54Å b: 72.99Å c: 78.32Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.223 0.223 0.274
Expression system: Escherichia coli

Quick links

Citations

7 review citations

Ribonuclease H: molecular diversities, substrate binding domains, and catalytic mechanism of the prokaryotic enzymes.
Tadokoro et al. (2009)
6 more

6 mentions without citation

Reviewing Challenges of Predicting Protein Melting Temperature Change Upon Mutation Through the Full Analysis of a Highly Detailed Dataset with High-Resolution Structures.
Louis et al. (2021)
5 more