› 3ca8

X-ray diffraction
1.8Å resolution

Crystal structure of Escherichia coli YdcF, an S-adenosyl-L-methionine utilizing enzyme

Released:
DOI: 10.2210/pdb3ca8/pdb
PDB entry 3ca8 coloured by chain, front view.
PDB entry 3ca8 coloured by chain, side view.
PDB entry 3ca8 coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
The Escherichia coli YdcF binds S-adenosyl-L-methionine and adopts an alpha/beta-fold characteristic of nucleotide-utilizing enzymes.
Chao KL, Lim K, Lehmann C, Doseeva V, Howard AJ, Schwarz FP, Herzberg O
Proteins 72 506-9 (2008)
PMID: 18393394

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-152696 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Protein YdcF Chains: A, B
Molecule details ›
Chains: A, B
Length: 266 amino acids
Theoretical weight: 29.74 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: P34209 (Residues: 1-266; Coverage: 100%)
Gene names: JW1411, b1414, ydcF
Sequence domains: DUF218 domain
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand SO4 8 x SO4
Ligand MPD 14 x MPD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 17-ID
Spacegroup: P21
Unit cell:
a: 64.795Å b: 39.71Å c: 122.645Å
α: 90° β: 96.34° γ: 90°
R-values:
R R work R free
0.195 0.195 0.238
Expression system: Escherichia coli

Quick links

Citations

6 citation in other articles

The major facilitator superfamily (MFS) revisited.
Reddy et al. (2012)
5 more

1 mention without citation

Identification and characterization of molecular entities differentially expressed in bacteria genome upon treatment with glyphosate shock.
Fabunmi et al. (2023)