› 1wdv

X-ray diffraction
1.7Å resolution

Crystal structure of hypothetical protein APE2540

Released:
DOI: 10.2210/pdb1wdv/pdb
PDB entry 1wdv coloured by chain, front view.
PDB entry 1wdv coloured by chain, side view.
PDB entry 1wdv coloured by chain, top view.
Source organism: Aeropyrum pernix K1
Primary publication:
Structure of a putative trans-editing enzyme for prolyl-tRNA synthetase from Aeropyrum pernix K1 at 1.7 A resolution.
Murayama K, Kato-Murayama M, Katsura K, Uchikubo-Kamo T, Yamaguchi-Hirafuji M, Kawazoe M, Akasaka R, Hanawa-Suetsugu K, Hori-Takemoto C, Terada T, Shirouzu M, Yokoyama S
Acta Crystallogr Sect F Struct Biol Cryst Commun 61 26-9 (2005)
PMID: 16508081

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-195420 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
YbaK/aminoacyl-tRNA synthetase-associated domain-containing protein Chains: A, B
Molecule details ›
Chains: A, B
Length: 152 amino acids
Theoretical weight: 16.48 KDa
Source organism: Aeropyrum pernix K1
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9Y8U3 (Residues: 1-151; Coverage: 100%)
Gene name: APE_2540.1
Sequence domains: Aminoacyl-tRNA editing domain
Structure domains: YbaK/aminoacyl-tRNA synthetase-associated domain

Ligands and Environments

No bound ligands
1 modified residue:
Ligand MSE 6 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL26B1
Spacegroup: P21
Unit cell:
a: 47.435Å b: 58.917Å c: 53.603Å
α: 90° β: 106.8° γ: 90°
R-values:
R R work R free
0.169 0.169 0.206
Expression system: Escherichia coli

Quick links

Citations

3 citation in other articles

Two complementary enzymes for threonylation of tRNA in crenarchaeota: crystal structure of Aeropyrum pernix threonyl-tRNA synthetase lacking a cis-editing domain.
Shimizu et al. (2009)
2 more

3 mentions without citation

Rigorous performance evaluation in protein structure modelling and implications for computational biology.
Moult J. (2006)
2 more