1ZLB

Crystal structure of catalytically-active phospholipase A2 in the absence of calcium


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.97 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Insights into metal ion binding in phospholipases A(2): ultra high-resolution crystal structures of an acidic phospholipase A(2) in the Ca(2+) free and bound states.

Murakami, M.T.Gabdoulkhakov, A.Genov, N.Cintra, A.C.Betzel, C.Arni, R.K.

(2006) Biochimie 88: 543-549

  • DOI: 10.1016/j.biochi.2005.10.014
  • Primary Citation of Related Structures:  
    1ZL7, 1ZLB

  • PubMed Abstract: 
  • The electrophile Ca(2+) is an essential multifunctional co-factor in the phospholipase A(2) mediated hydrolysis of phospholipids. Crystal structures of an acidic phospholipase A(2) from the venom of Bothrops jararacussu have been determined both in t ...

    The electrophile Ca(2+) is an essential multifunctional co-factor in the phospholipase A(2) mediated hydrolysis of phospholipids. Crystal structures of an acidic phospholipase A(2) from the venom of Bothrops jararacussu have been determined both in the Ca(2+) free and bound states at 0.97 and 1.60 A resolutions, respectively. In the Ca(2+) bound state, the Ca(2+) ion is penta-coordinated by a distorted pyramidal cage of oxygen and nitrogen atoms that is significantly different to that observed in structures of other Group I/II phospholipases A(2). In the absence of Ca(2+), a water molecule occupies the position of the Ca(2+) ion and the side chain of Asp49 and the calcium-binding loop adopts a different conformation.


    Related Citations: 
    • Crystallization and high-resolution X-ray diffraction data collection of an Asp49 PLA2 from Bothrops jararacussu venom both in the presence and absence of Ca2+ ions.
      Murakami, M.T., Michelan-Duarte, S., Cintra, A.C.O., Arni, R.K.
      (2004) Biochim Biophys Acta 1703: 79

    Organizational Affiliation

    Department of Physics, IBILCE/UNESP, Cristovão Colombo 2265, São José do Rio Preto, SP 15054-000, Brazil.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
hypotensive phospholipase A2A122Bothrops jararacussuMutation(s): 0 
EC: 3.1.1.4
Find proteins for Q8AXY1 (Bothrops jararacussu)
Explore Q8AXY1 
Go to UniProtKB:  Q8AXY1
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.97 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.168 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.964α = 90
b = 53.794β = 90
c = 89.816γ = 90
Software Package:
Software NamePurpose
SHELXmodel building
SHELXL-97refinement
MAR345data collection
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-04-25
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description