› 1vbk

X-ray diffraction
1.9Å resolution

Crystal structure of PH1313 from Pyrococcus horikoshii Ot3

Released:
DOI: 10.2210/pdb1vbk/pdb
PDB entry 1vbk coloured by chain, front view.
PDB entry 1vbk coloured by chain, side view.
PDB entry 1vbk coloured by chain, top view.
Source organism: Pyrococcus horikoshii OT3
Primary publication:
Purification, crystallization and preliminary crystallographic analysis of the putative thiamine-biosynthesis protein PH1313 from Pyrococcus horikoshii OT3.
Sugahara M, Murai S, Sugahara M, Kunishima N
Acta Crystallogr Sect F Struct Biol Cryst Commun 63 56-8 (2007)
PMID: 17183176

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-129801 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
THUMP domain-containing protein Chains: A, B
Molecule details ›
Chains: A, B
Length: 307 amino acids
Theoretical weight: 35.2 KDa
Source organism: Pyrococcus horikoshii OT3
Expression system: Escherichia coli
UniProt:
  • Canonical: O59053 (Residues: 1-307; Coverage: 100%)
Gene name: PH1313
Sequence domains:
Structure domains:

Ligands and Environments

1 bound ligand:
Ligand MRD 4 x MRD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL26B1
Spacegroup: P212121
Unit cell:
a: 71.743Å b: 71.164Å c: 141.774Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.203 0.199 0.222
Expression system: Escherichia coli

Quick links

Citations

1 review citation

A structural perspective on the PP-loop ATP pyrophosphatase family.
Fellner et al. (2018)
3 other articles

4 mentions without citation

Transfer RNA Modification Enzymes with a Thiouridine Synthetase, Methyltransferase and Pseudouridine Synthase (THUMP) Domain and the Nucleosides They Produce in tRNA.
Hori H. (2023)
3 more