› 2uyp

X-ray diffraction
2.44Å resolution

Crystal structure of E. coli TdcF with bound propionate

Released:
DOI: 10.2210/pdb2uyp/pdb
PDB entry 2uyp coloured by chain, front view.
PDB entry 2uyp coloured by chain, side view.
PDB entry 2uyp coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
The crystal structure of Escherichia coli TdcF, a member of the highly conserved YjgF/YER057c/UK114 family.
Burman JD, Stevenson CE, Sawers RG, Lawson DM
BMC Struct Biol 7 30 (2007)
PMID: 17506874

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-142843 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Putative reactive intermediate deaminase TdcF Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 129 amino acids
Theoretical weight: 14.07 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0AGL2 (Residues: 1-129; Coverage: 100%)
Gene names: JW5521, b3113, tdcF, yhaR
Sequence domains: Endoribonuclease L-PSP
Structure domains: RutC-like

Ligands and Environments

1 bound ligand:
Ligand PPI 2 x PPI
1 modified residue:
Ligand OCS 3 x OCS

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RUH3R
Spacegroup: P21212
Unit cell:
a: 72.435Å b: 85.744Å c: 62.512Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.171 0.166 0.253
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

5 review citations

The diphthamide modification pathway from Saccharomyces cerevisiae--revisited.
Schaffrath et al. (2014)
4 more

3 mentions without citation

RidA Proteins Protect against Metabolic Damage by Reactive Intermediates.
Irons et al. (2020)
2 more