1QAT

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


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


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

  • DOI: 10.1038/nsb0996-788
  • Primary Citation of Related Structures:  
    1QAT, 1QAS

  • 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 relatio ...

    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.


    Related Citations: 
    • 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
    • Expression, Characterization, and Crystallization of the Catalytic Core of Rat Phosphatidylinositide-Specific Phospholipase C Delta 1
      Grobler, J.A., Hurley, J.H.
      (1996) Protein Sci 5: 680

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PHOSPHOLIPASE C DELTA-1AB622Rattus norvegicusMutation(s): 0 
Gene Names: Plcd1
EC: 3.1.4.11
Find proteins for P10688 (Rattus norvegicus)
Explore P10688 
Go to UniProtKB:  P10688
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SM
Query on SM

Download CCD File 
A, B
SAMARIUM (III) ION
Sm
DOSGOCSVHPUUIA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.194 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.6α = 66.4
b = 75.1β = 85.6
c = 86.4γ = 89.8
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

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