› 2oog

X-ray diffraction
2.2Å resolution

Crystal structure of glycerophosphoryl diester phosphodiesterase from Staphylococcus aureus

Released:
DOI: 10.2210/pdb2oog/pdb
PDB entry 2oog coloured by chain, front view.
PDB entry 2oog coloured by chain, side view.
PDB entry 2oog coloured by chain, top view.
Source organism: Staphylococcus aureus subsp. aureus N315
Entry authors: Patskovsky Y, Fedorov E, Toro R, Sauder JM, Smith D, Freeman J, Maletic M, Powell A, Gheyi T, Wasserman SR, Burley SK, Almo SC, New York SGX Research Center for Structural Genomics (NYSGXRC)

Function and Biology Details

Reaction catalysed: 
A glycerophosphodiester + H(2)O = an alcohol + sn-glycerol 3-phosphate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-102040 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Glycerophosphoryl diester phosphodiesterase Chains: A, B, C, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
Length: 287 amino acids
Theoretical weight: 33.31 KDa
Source organism: Staphylococcus aureus subsp. aureus N315
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A0A0H3K7S1 (Residues: 31-309; Coverage: 100%)
Gene names: NWMN_0830, glpQ
Sequence domains: Glycerophosphoryl diester phosphodiesterase family
Structure domains: Phosphatidylinositol (PI) phosphodiesterase

Ligands and Environments

3 bound ligands:
Ligand ZN 6 x ZN
Ligand SO4 6 x SO4
Ligand GOL 39 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 31-ID
Spacegroup: C2221
Unit cell:
a: 156.312Å b: 183.546Å c: 176.79Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.236 0.235 0.28
Expression system: Escherichia coli BL21(DE3)

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