› 1zcc

X-ray diffraction
2.5Å resolution

Crystal structure of glycerophosphodiester phosphodiesterase from Agrobacterium tumefaciens str.C58

Released:
DOI: 10.2210/pdb1zcc/pdb
PDB entry 1zcc coloured by chain, front view.
PDB entry 1zcc coloured by chain, side view.
PDB entry 1zcc coloured by chain, top view.
Source organism: Agrobacterium fabrum str. C58
Primary publication:
Crystal structure of glycerophosphodiester phosphodiesterase from Agrobacterium tumefaciens by SAD with a large asymmetric unit.
Rao KN, Bonanno JB, Burley SK, Swaminathan S
Proteins 65 514-8 (2006)
PMID: 16909422

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-108857 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
GP-PDE domain-containing protein Chains: A, B, C, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
Length: 248 amino acids
Theoretical weight: 27.36 KDa
Source organism: Agrobacterium fabrum str. C58
Expression system: Escherichia coli
UniProt:
  • Canonical: A9CG82 (Residues: 1-248; Coverage: 100%)
Gene names: Atu4212, ugpQ
Sequence domains: Glycerophosphoryl diester phosphodiesterase family
Structure domains: Phosphatidylinositol (PI) phosphodiesterase

Ligands and Environments

2 bound ligands:
Ligand ACT 6 x ACT
Ligand SO4 6 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X25, NSLS BEAMLINE X12C
Spacegroup: P21
Unit cell:
a: 78.56Å b: 140.22Å c: 88.6Å
α: 90° β: 90.53° γ: 90°
R-values:
R R work R free
0.244 0.244 0.281
Expression system: Escherichia coli

Quick links

Citations

2 review citations

The emerging physiological roles of the glycerophosphodiesterase family.
Corda et al. (2014)
1 more

1 mention without citation

Crystal structure of glycerophosphodiester phosphodiesterase (GDPD) from Thermoanaerobacter tengcongensis, a metal ion-dependent enzyme: insight into the catalytic mechanism.
Shi et al. (2008)