4F2U

Structure of the N254Y/H258Y double mutant of the Phosphatidylinositol-Specific Phospholipase C from S.aureus

• PDB DOI: https://doi.org/10.2210/pdb4F2U/pdb

• Classification: LYASE
• Organism(s): Staphylococcus aureus subsp. aureus str. Newman
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2012-05-08 Released: 2012-12-12 
• Deposition Author(s): Cheng, J., Goldstein, R., Stec, B., Gershenson, A., Roberts, M.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free: 0.236 
• R-Value Work: 0.158 
• R-Value Observed: 0.162 

Literature

Competition between Anion Binding and Dimerization Modulates Staphylococcus aureus Phosphatidylinositol-specific Phospholipase C Enzymatic Activity.

Cheng, J., Goldstein, R., Stec, B., Gershenson, A., Roberts, M.F.

(2012) J Biol Chem 287: 40317-40327

• PubMed: 23038258 
• DOI: https://doi.org/10.1074/jbc.M112.395277
• Primary Citation of Related Structures:  
  4F2B, 4F2T, 4F2U


• PubMed Abstract: 
  

  Bacterial phosphatidylinositol-specific phospholipase C targets PI and glycosylphosphatidylinositol-linked proteins of eukaryotic cells.

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Organizational Affiliation: 

Department of Chemistry, Boston College, Chestnut Hill, MA 02467, USA.

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: 35.89 kDa 
• Atom Count: 2,759 
• Modelled Residue Count: 304 
• Deposited Residue Count: 310 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
1-phosphatidylinositol phosphodiesterase	A	310	Staphylococcus aureus subsp. aureus str. Newman	Mutation(s): 2  Gene Names: plc, NWMN_0041 EC: 4.6.1.13
UniProt
Find proteins for P45723 (Staphylococcus aureus (strain Newman)) Explore P45723  Go to UniProtKB:  P45723

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	B [auth A], C [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free: 0.236 
• R-Value Work: 0.158 
• R-Value Observed: 0.162 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.22	α = 90
b = 56.119	β = 90
c = 61.708	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-12-12 
Deposition Author(s): Cheng, J., Goldstein, R., Stec, B., Gershenson, A., Roberts, M.F.

Revision History  

• Version 1.0: 2012-12-12
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description