› 4pdn

X-ray diffraction
1.45Å resolution

Crystal structure of E. coli YfcM

Released:
DOI: 10.2210/pdb4pdn/pdb
PDB entry 4pdn coloured by chain, front view.
PDB entry 4pdn coloured by chain, side view.
PDB entry 4pdn coloured by chain, top view.
Source organism: Escherichia coli KTE5
Primary publication:
The non-canonical hydroxylase structure of YfcM reveals a metal ion-coordination motif required for EF-P hydroxylation.
Kobayashi K, Katz A, Rajkovic A, Ishii R, Branson OE, Freitas MA, Ishitani R, Ibba M, Nureki O
Nucleic Acids Res 42 12295-305 (2014)
PMID: 25274739

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-102248 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Elongation factor P hydroxylase Chain: A
Molecule details ›
Chain: A
Length: 190 amino acids
Theoretical weight: 22.22 KDa
Source organism: Escherichia coli KTE5
Expression system: Escherichia coli
UniProt:
  • Canonical: A0A0J9X1Z5 (Residues: 1-182; Coverage: 96%)
Gene name: WCE_02429
Sequence domains: Elongation factor P hydroxylase

Ligands and Environments

1 bound ligand:
Ligand MG 1 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL32XU
Spacegroup: C2
Unit cell:
a: 124.36Å b: 36.968Å c: 37.636Å
α: 90° β: 101.22° γ: 90°
R-values:
R R work R free
0.149 0.148 0.174
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Stall no more at polyproline stretches with the translation elongation factors EF-P and IF-5A.
Lassak et al. (2016)
1 more

1 mention without citation

The non-canonical hydroxylase structure of YfcM reveals a metal ion-coordination motif required for EF-P hydroxylation.
Kobayashi et al. (2014)