1QAT | pdb_00001qat

1-PHOSPHATIDYLINOSITOL-4,5-BISPHOSPHATE PHOSPHODIESTERASE DELTA COMPLEX WITH SAMARIUM (III) CHLORIDE

• PDB DOI: https://doi.org/10.2210/pdb1QAT/pdb

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


• Deposited: 1996-08-02 Released: 1997-02-12 
• Deposition Author(s): Grobler, J.A., Hurley, J.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.261 (Depositor) 
• R-Value Work: 
  0.194 (Depositor) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: experimental

Literature

C2 domain conformational changes in phospholipase C-delta 1.

Grobler, J.A., Essen, L.O., Williams, R.L., Hurley, J.H.

(1996) Nat Struct Biol 3: 788-795

• PubMed: 8784353 
• DOI: https://doi.org/10.1038/nsb0996-788
• Primary Citation Related Structures: 
  1QAS, 1QAT


• PubMed Abstract: 
  

  The structure of the PH-domain truncated core of rat phosphoinositide-specific phospholipase C-delta 1 has been determined at 2.4 A resolution and compared to the structure previously determined in a different crystal form. The stereochemical relationship between the EF, catalytic, and C2 domains is essentially identical. The Ca2+ analogue Sm3+ binds at two sites between the jaws of the C2 domain. Sm3+ binding ejects three lysine residues which bridge the gap between the jaws and occupy the Ca2+ site in the apoenzyme, triggering a conformational change in the jaws. The distal sections of the C2 jaws move apart, opening the mouth by 9 A and creating a gap large enough to bind a phospholipid headgroup.

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Organizational Affiliation: 
• Laboratory of Molecular Biology, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0580, USA.

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: 141.61 kDa 
• Atom Count: 8,022 
• Modeled Residue Count: 1,016 
• Deposited Residue Count: 1,244 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOSPHOLIPASE C DELTA-1	A, B	622	Rattus norvegicus	Mutation(s): 0  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
SM	C [auth A], D [auth A], E [auth B], F [auth B], G [auth B]	SAMARIUM (III) ION Sm DOSGOCSVHPUUIA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.261 (Depositor) 
• R-Value Work:  0.194 (Depositor) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.6	α = 66.4
b = 75.1	β = 85.6
c = 86.4	γ = 89.8

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1997-02-12 
Deposition Author(s): Grobler, J.A., Hurley, J.H.

Revision History  

• Version 1.0: 1997-02-12
  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: 2024-02-14
  Changes: Data collection, Database references, Derived calculations, Other
• Version 1.4: 2024-04-03
  Changes: Refinement description