› 2ze4

X-ray diffraction
2.5Å resolution

Crystal structure of phospholipase D from streptomyces antibioticus

Released:
DOI: 10.2210/pdb2ze4/pdb
PDB entry 2ze4 coloured by chain, front view.
PDB entry 2ze4 coloured by chain, side view.
PDB entry 2ze4 coloured by chain, top view.
Source organism: Streptomyces antibioticus
Entry authors: Suzuki A, Kakuno K, Saito R, 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: 54.04 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

1 bound ligand:
Ligand MES 1 x MES
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: P212121
Unit cell:
a: 61.004Å b: 85.008Å c: 99.343Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.124 0.121 0.171
Expression system: Escherichia coli BL21(DE3)

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