› 5h4g

X-ray diffraction
1.77Å resolution

Structure of PIN-domain protein (VapC4 toxin) from Pyrococcus horikoshii determined at 1.77 A resolution

Released:
DOI: 10.2210/pdb5h4g/pdb
PDB entry 5h4g coloured by chain, front view.
PDB entry 5h4g coloured by chain, side view.
PDB entry 5h4g coloured by chain, top view.
Source organism: Pyrococcus horikoshii OT3
Primary publication:
Structure determination of contaminant proteins using the MarathonMR procedure.
Hatti K, Biswas A, Chaudhary S, Dadireddy V, Sekar K, Srinivasan N, Murthy MRN
J Struct Biol 197 372-378 (2017)
PMID: 28167161

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-129692 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Ribonuclease VapC4 Chains: A, B
Molecule details ›
Chains: A, B
Length: 149 amino acids
Theoretical weight: 17.21 KDa
Source organism: Pyrococcus horikoshii OT3
Expression system: Escherichia coli
UniProt:
  • Canonical: O58236 (Residues: 1-149; Coverage: 100%)
Gene names: PH0500, vapC4
Structure domains: 5'-nuclease

Ligands and Environments

1 bound ligand:
Ligand ZN 1 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE BM14
Spacegroup: P21
Unit cell:
a: 50.78Å b: 44.64Å c: 52.37Å
α: 90° β: 103.4° γ: 90°
R-values:
R R work R free
0.17 0.167 0.221
Expression system: Escherichia coli

Quick links

Citations

3 citation in other articles

findMySequence: a neural-network-based approach for identification of unknown proteins in X-ray crystallography and cryo-EM.
Chojnowski et al. (2022)
2 more

2 mentions without citation

Minimal protein-only RNase P structure reveals insights into tRNA precursor recognition and catalysis.
Teramoto et al. (2021)
1 more