› 2ze9

X-ray diffraction
2.3Å resolution

Crystal structure of H168A mutant of phospholipase D from Streptomyces antibioticus, as a complex with phosphatidylcholine

Released:
DOI: 10.2210/pdb2ze9/pdb
PDB entry 2ze9 coloured by chain, front view.
PDB entry 2ze9 coloured by chain, side view.
PDB entry 2ze9 coloured by chain, top view.
Source organism: Streptomyces antibioticus
Entry authors: Suzuki A, Toda H, Iwasaki Y, Yamane T, Yamane T

Function and Biology Details

Reaction catalysed: 
A phosphatidylcholine + H(2)O = choline + a phosphatidate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-176073 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Phospholipase D Chain: A
Molecule details ›
Chain: A
Length: 509 amino acids
Theoretical weight: 53.97 KDa
Source organism: Streptomyces antibioticus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q53728 (Residues: 48-556; Coverage: 100%)
Sequence domains: PLD-like domain
Structure domains: Endonuclease Chain A

Ligands and Environments

2 bound ligands:
Ligand MES 1 x MES
Ligand PD7 1 x PD7
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU300
Spacegroup: P212121
Unit cell:
a: 60.868Å b: 78.232Å c: 98.603Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.174 0.17 0.251
Expression system: Escherichia coli BL21(DE3)

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