› 2drv

X-ray diffraction
1.6Å resolution

Structure of PH1069 protein from Pyrococcus horikoshii OT3

Released:
DOI: 10.2210/pdb2drv/pdb
PDB entry 2drv coloured by chain, front view.
PDB entry 2drv coloured by chain, side view.
PDB entry 2drv coloured by chain, top view.
Source organism: Pyrococcus horikoshii OT3
Entry authors: Lokanath NK, Kunishima N, RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Function and Biology Details

Reaction catalysed: 
S-adenosyl-L-methionine + 7-((3S)-(3-amino-3-carboxypropyl))-4-demethylwyosine(37) in tRNA(Phe) = S-adenosyl-L-homocysteine + 7-((3S)-(3-amino-3-carboxypropyl))wyosine(37) in tRNA(Phe)
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-129769 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
tRNA(Phe) 7-((3-amino-3-carboxypropyl)-4-demethylwyosine(37)-N(4))-methyltransferase 1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 200 amino acids
Theoretical weight: 23.54 KDa
Source organism: Pyrococcus horikoshii OT3
Expression system: Escherichia coli
UniProt:
  • Canonical: O58796 (Residues: 1-196; Coverage: 100%)
Gene names: PH1069, taw3-1
Sequence domains: Methyltransferase TYW3
Structure domains: tRNA wybutosine-synthesizing-like

Ligands and Environments

1 bound ligand:
Ligand SO4 1 x SO4
1 modified residue:
Ligand MSE 14 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL26B1
Spacegroup: P1
Unit cell:
a: 37.346Å b: 52.898Å c: 53.125Å
α: 104.65° β: 102.96° γ: 109.25°
R-values:
R R work R free
0.218 0.218 0.245
Expression system: Escherichia coli

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