2ZE4 | pdb_00002ze4

Crystal structure of phospholipase D from streptomyces antibioticus

• PDB DOI: https://doi.org/10.2210/pdb2ZE4/pdb

• Classification: HYDROLASE
• Organism(s): Streptomyces antibioticus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-12-05 Released: 2007-12-25 
• Deposition Author(s): Suzuki, A., Kakuno, K., Saito, R., Iwasaki, Y., Yamane, T., Yamane, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.171 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.121 (Depositor), 0.120 (DCC) 
• R-Value Observed: 
  0.124 (Depositor) 

Literature

Crystal structure of phospholipase D from streptomyces antibioticus

Suzuki, A., Kakuno, K., Saito, R., Iwasaki, Y., Yamane, T., Yamane, T.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 54.23 kDa 
• Atom Count: 3,959 
• Modeled Residue Count: 501 
• Deposited Residue Count: 509 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phospholipase D	A	509	Streptomyces antibioticus	Mutation(s): 0  EC: 3.1.4.4
UniProt
Find proteins for Q53728 (Streptomyces antibioticus) Explore Q53728  Go to UniProtKB:  Q53728

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MES	B [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.171 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.121 (Depositor), 0.120 (DCC) 
• R-Value Observed: 0.124 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.004	α = 90
b = 85.008	β = 90
c = 99.343	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Weissenberg	data collection
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-12-25 
Deposition Author(s): Suzuki, A., Kakuno, K., Saito, R., Iwasaki, Y., Yamane, T., Yamane, T.

Revision History  

• Version 1.0: 2007-12-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary