2ISD | pdb_00002isd

PHOSPHOINOSITIDE-SPECIFIC PHOSPHOLIPASE C-DELTA1 FROM RAT

• PDB DOI: https://doi.org/10.2210/pdb2ISD/pdb
• Entry: 2ISD supersedes: 1ISD

• Classification: LIPID DEGRADATION
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1997-03-31 Released: 1997-07-07 
• Deposition Author(s): Essen, L.-O., Perisic, O., Williams, R.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.280 (Depositor) 
• R-Value Work: 
  0.227 (Depositor) 

Literature

Crystal structure of a mammalian phosphoinositide-specific phospholipase C delta.

Essen, L.O., Perisic, O., Cheung, R., Katan, M., Williams, R.L.

(1996) Nature 380: 595-602

• PubMed: 8602259 
• DOI: https://doi.org/10.1038/380595a0
• Primary Citation Related Structures: 
  2ISD


• PubMed Abstract: 
  

  Mammalian phosphoinositide-specific phospholipase C enzymes (PI-PLC) act as signal transducers that generate two second messengers, inositol-1,4,5-trisphosphate and diacylglycerol. The 2.4-A structure of phospholipase C delta 1 reveals a multidomain protein incorporating modules shared by many signalling proteins. The structure suggests a mechanism for membrane attachment and Ca2+-dependent hydrolysis of second-messenger precursors. The regulation and reversible membrane association of PI-PLC may serve as a model for understanding other multidomain enzymes involved in phospholipid signalling.

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Organizational Affiliation: 
• Center for Protein Engineering, MRC Centre, Cambridge, UK.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 141.27 kDa 
• Atom Count: 9,216 
• Modeled Residue Count: 1,074 
• Deposited Residue Count: 1,248 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOSPHOINOSITIDE-SPECIFIC PHOSPHOLIPASE C, ISOZYME DELTA1	A, B	624	Rattus norvegicus	Mutation(s): 0  Gene Names: CDNA FRAGMENT EC: 3.1.4.11
UniProt
Find proteins for P10688 (Rattus norvegicus) Explore P10688  Go to UniProtKB:  P10688

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	C [auth A], D [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.280 (Depositor) 
• R-Value Work:  0.227 (Depositor) 

Space Group: F 4₁ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 397.36	α = 90
b = 397.36	β = 90
c = 397.36	γ = 90

Software Package:

Software Name	Purpose
SHELX-90	model building
SOLOMON	phasing
TNT	refinement
MOSFLM	data reduction
CCP4	data scaling
SHELX-90	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1997-07-07 
Deposition Author(s): Essen, L.-O., Perisic, O., Williams, R.L.
• This entry supersedes: 1ISD

Revision History  

• Version 1.0: 1997-07-07
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references, Derived calculations