› 1m68

X-ray diffraction
2.3Å resolution

YCDX PROTEIN, TRINUCLEAR ZINC SITE

Released:
DOI: 10.2210/pdb1m68/pdb
PDB entry 1m68 coloured by chain, front view.
PDB entry 1m68 coloured by chain, side view.
PDB entry 1m68 coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Crystal structure of the Escherichia coli YcdX protein reveals a trinuclear zinc active site.
Teplyakov A, Obmolova G, Khil PP, Howard AJ, Camerini-Otero RD, Gilliland GL
Proteins 51 315-8 (2003)
PMID: 12661000

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-160022 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Probable phosphatase YcdX Chain: A
Molecule details ›
Chain: A
Length: 245 amino acids
Theoretical weight: 26.93 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P75914 (Residues: 1-245; Coverage: 100%)
Gene names: JW1017, b1034, ycdX
Sequence domains: PHP domain
Structure domains: Metal-dependent hydrolases

Ligands and Environments

2 bound ligands:
Ligand ZN 3 x ZN
Ligand SO4 2 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P321
Unit cell:
a: 77.35Å b: 77.35Å c: 80.05Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.165 0.162 0.225
Expression system: Escherichia coli BL21

Quick links

Citations

3 review citations

DNA replicases from a bacterial perspective.
McHenry CS. (2011)
2 more

4 mentions without citation

Combining specificity determining and conserved residues improves functional site prediction.
Kalinina et al. (2009)
3 more