2ZE9

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

• PDB DOI: https://doi.org/10.2210/pdb2ZE9/pdb

• Classification: HYDROLASE
• Organism(s): Streptomyces antibioticus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2007-12-06 Released: 2007-12-25 
• Deposition Author(s): Suzuki, A., Toda, H., Iwasaki, Y., Yamane, T., Yamane, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.251 
• R-Value Work: 0.170 
• R-Value Observed: 0.174 

Literature

Crystal structure of phospholipase D from streptomyces antibioticus

Suzuki, A., Toda, H., 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: 54.56 kDa 
• Atom Count: 4,161 
• Modelled Residue Count: 504 
• 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): 1  EC: 3.1.4.4
UniProt
Find proteins for Q53728 (Streptomyces antibioticus) Explore Q53728  Go to UniProtKB:  Q53728

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PD7	C [auth A]	(2R)-3-(phosphonooxy)propane-1,2-diyl diheptanoate C17 H33 O8 P JAXUAGQDLYDLQB-OAHLLOKOSA-N
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: 2.30 Å
• R-Value Free: 0.251 
• R-Value Work: 0.170 
• R-Value Observed: 0.174 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.868	α = 90
b = 78.232	β = 90
c = 98.603	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystalClear	data collection
DENZO	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-12-25 
Deposition Author(s): Suzuki, A., Toda, H., 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: 2021-11-10
  Changes: Database references, Derived calculations
• Version 1.3: 2023-11-01
  Changes: Data collection, Refinement description