3RLG

Crystal structure of Loxosceles intermedia phospholipase D isoform 1 H12A mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 

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Literature

Crystallization and preliminary X-ray diffraction analysis of a class II phospholipase D from Loxosceles intermedia venom.

Ullah, A.de Giuseppe, P.O.Murakami, M.T.Trevisan-Silva, D.Wille, A.C.Chaves-Moreira, D.Gremski, L.H.da Silveira, R.B.Sennf-Ribeiro, A.Chaim, O.M.Veiga, S.S.Arni, R.K.

(2011) Acta Crystallogr Sect F Struct Biol Cryst Commun 67: 234-236

  • DOI: 10.1107/S1744309110050931
  • Primary Citation of Related Structures:  
    3RLG

  • PubMed Abstract: 
  • Phospholipases D are the major dermonecrotic component of Loxosceles venom and catalyze the hydrolysis of phospholipids, resulting in the formation of lipid mediators such as ceramide-1-phosphate and lysophosphatidic acid which can induce pathological and biological responses ...

    Phospholipases D are the major dermonecrotic component of Loxosceles venom and catalyze the hydrolysis of phospholipids, resulting in the formation of lipid mediators such as ceramide-1-phosphate and lysophosphatidic acid which can induce pathological and biological responses. Phospholipases D can be classified into two classes depending on their catalytic efficiency and the presence of an additional disulfide bridge. In this work, both wild-type and H12A-mutant forms of the class II phospholipase D from L. intermedia venom were crystallized. Wild-type and H12A-mutant crystals were grown under very similar conditions using PEG 200 as a precipitant and belonged to space group P12(1)1, with unit-cell parameters a = 50.1, b = 49.5, c = 56.5 Å, β = 105.9°. Wild-type and H12A-mutant crystals diffracted to maximum resolutions of 1.95 and 1.60 Å, respectively.


    Organizational Affiliation

    Centro Multiusuário de Inovação Biomolecular, Departamento de Física, Universidade Estadual Paulista (UNESP), São José do Rio Preto-SP, Brazil.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Sphingomyelin phosphodiesterase D LiSicTox-alphaIA1aA302Loxosceles intermediaMutation(s): 1 
EC: 3.1.4.41 (PDB Primary Data), 4.6.1 (UniProt)
UniProt
Find proteins for P0CE80 (Loxosceles intermedia)
Explore P0CE80 
Go to UniProtKB:  P0CE80
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CE80
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.575α = 90
b = 49.455β = 105.56
c = 56.395γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-08-24
    Type: Initial release