› 2dvk

X-ray diffraction
1.8Å resolution

Crystal Structure of Hypothetical protein from Aeropyrum pernix

Released:
DOI: 10.2210/pdb2dvk/pdb
PDB entry 2dvk coloured by chain, front view.
PDB entry 2dvk coloured by chain, side view.
PDB entry 2dvk coloured by chain, top view.
Source organism: Aeropyrum pernix
Entry authors: Lokanath NK, 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-195481 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
tRNA(Phe) 7-((3-amino-3-carboxypropyl)-4-demethylwyosine(37)-N(4))-methyltransferase Chain: A
Molecule details ›
Chain: A
Length: 188 amino acids
Theoretical weight: 21.02 KDa
Source organism: Aeropyrum pernix
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9YDV3 (Residues: 1-188; Coverage: 100%)
Gene names: APE_0816, taw3
Sequence domains: Methyltransferase TYW3
Structure domains: tRNA wybutosine-synthesizing-like

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL26B1
Spacegroup: C2221
Unit cell:
a: 55.87Å b: 70.232Å c: 91.579Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.234 0.234 0.249
Expression system: Escherichia coli

Quick links