› 1ydy

X-ray diffraction
1.7Å resolution

Crystal structure of periplasmic glycerophosphodiester phosphodiesterase from Escherichia coli

Released:
DOI: 10.2210/pdb1ydy/pdb
PDB entry 1ydy coloured by chain, front view.
PDB entry 1ydy coloured by chain, side view.
PDB entry 1ydy coloured by chain, top view.
Source organism: Escherichia coli
Entry authors: Malashkevich VN, Fedorov E, Almo SC, Burley SK, 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 domain:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-140645 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Glycerophosphodiester phosphodiesterase, periplasmic Chains: A, B
Molecule details ›
Chains: A, B
Length: 356 amino acids
Theoretical weight: 40.64 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P09394 (Residues: 1-356; Coverage: 99%)
Gene names: JW2233, b2239, glpQ
Sequence domains: Glycerophosphoryl diester phosphodiesterase family
Structure domains: Phosphatidylinositol (PI) phosphodiesterase

Ligands and Environments

2 bound ligands:
Ligand CA 2 x CA
Ligand GOL 2 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU300
Spacegroup: P212121
Unit cell:
a: 63.789Å b: 74.469Å c: 157.219Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.187 0.187 0.228
Expression system: Escherichia coli BL21

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