1F0I

THE FIRST CRYSTAL STRUCTURE OF A PHOSPHOLIPASE D

• PDB DOI: https://doi.org/10.2210/pdb1F0I/pdb

• Classification: HYDROLASE
• Organism(s): Streptomyces sp. PMF
• Mutation(s): No 


• Deposited: 2000-05-16 Released: 2001-05-16 
• Deposition Author(s): Leiros, I., Secundo, F., Zambonelli, C., Servi, S., Hough, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.185 
• R-Value Work: 0.130 
• R-Value Observed: 0.130 

Literature

The first crystal structure of a phospholipase D.

Leiros, I., Secundo, F., Zambonelli, C., Servi, S., Hough, E.

(2000) Structure 8: 655-667

• PubMed: 10873862 
• DOI: https://doi.org/10.1016/s0969-2126(00)00150-7
• Primary Citation of Related Structures:  
  1F0I


• PubMed Abstract: 
  

  The phospholipase D (PLD) superfamily includes enzymes that are involved in phospholipid metabolism, nucleases, toxins and virus envelope proteins of unknown function. PLD hydrolyzes the terminal phosphodiester bond of phospholipids to phosphatidic acid and a hydrophilic constituent. Phosphatidic acid is a compound that is heavily involved in signal transduction. PLD also catalyses a transphosphatidylation reaction in the presence of phosphatidylcholine and a short-chained primary or secondary alcohol.

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Organizational Affiliation: 

Department of Chemistry, Faculty of Science, University of Tromso, Norway.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 53.91 kDa 
• Atom Count: 4,468 
• Modelled Residue Count: 496 
• Deposited Residue Count: 504 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOSPHOLIPASE D	A	504	Streptomyces sp. PMF	Mutation(s): 0  EC: 3.1.4.4
UniProt
Find proteins for P84147 (Streptomyces sp. (strain PMF)) Explore P84147  Go to UniProtKB:  P84147

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	B [auth A], C [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.185 
• R-Value Work: 0.130 
• R-Value Observed: 0.130 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.28	α = 90
b = 57.42	β = 93.17
c = 68.7	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALA	data scaling
MLPHARE	phasing
SHELXL-97	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-05-16 
Deposition Author(s): Leiros, I., Secundo, F., Zambonelli, C., Servi, S., Hough, E.

Revision History  

• Version 1.0: 2001-05-16
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance