› 3vrh

X-ray diffraction
2.1Å resolution

Crystal structure of ph0300

Released:
DOI: 10.2210/pdb3vrh/pdb
PDB entry 3vrh coloured by chain, front view.
PDB entry 3vrh coloured by chain, side view.
PDB entry 3vrh coloured by chain, top view.
Source organism: Pyrococcus horikoshii OT3
Primary publication:
Crystallographic and mutational studies on the tRNA thiouridine synthetase TtuA.
Nakagawa H, Kuratani M, Goto-Ito S, Ito T, Katsura K, Terada T, Shirouzu M, Sekine S, Shigi N, Yokoyama S
Proteins 81 1232-44 (2013)
PMID: 23444054

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-129662 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
tRNA-5-methyluridine(54) 2-sulfurtransferase Chain: A
Molecule details ›
Chain: A
Length: 310 amino acids
Theoretical weight: 35.69 KDa
Source organism: Pyrococcus horikoshii OT3
Expression system: Escherichia coli
UniProt:
  • Canonical: O58038 (Residues: 1-310; Coverage: 100%)
Gene names: PH0300, ttuA
Sequence domains:
Structure domains: HUPs

Ligands and Environments

2 bound ligands:
Ligand ZN 2 x ZN
Ligand BCN 1 x BCN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL32XU
Spacegroup: P43212
Unit cell:
a: 70.071Å b: 70.071Å c: 128.636Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.208 0.206 0.244
Expression system: Escherichia coli

Quick links

Citations

7 review citations

Wobble uridine modifications-a reason to live, a reason to die?!
Schaffrath et al. (2017)
6 more

3 mentions without citation

Nonredox thiolation in tRNA occurring via sulfur activation by a [4Fe-4S] cluster.
Arragain et al. (2017)
2 more