1GOD | pdb_00001god

MONOMERIC LYS-49 PHOSPHOLIPASE A2 HOMOLOGUE ISOLATED FROM THE VENOM OF CERROPHIDION (BOTHROPS) GODMANI

• PDB DOI: https://doi.org/10.2210/pdb1GOD/pdb

• Classification: HYDROLASE
• Organism(s): Cerrophidion godmani
• Mutation(s): No 


• Deposited: 1999-04-16 Released: 1999-04-23 
• Deposition Author(s): Arni, R.K., Fontes, M.R.M., Barberato, C., Gutierrez, J.M., Diaz-Oreiro, C., Ward, R.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.282 (Depositor) 
• R-Value Work: 
  0.188 (Depositor), 0.227 (DCC) 

Starting Model: experimental

Literature

Crystal structure of myotoxin II, a monomeric Lys49-phospholipase A2 homologue isolated from the venom of Cerrophidion (Bothrops) godmani.

Arni, R.K., Fontes, M.R., Barberato, C., Gutierrez, J.M., Diaz, C., Ward, R.J.

(1999) Arch Biochem Biophys 366: 177-182

• PubMed: 10356281 
• DOI: https://doi.org/10.1006/abbi.1999.1210
• Primary Citation Related Structures: 
  1GOD


• PubMed Abstract: 
  

  Lys49-Phospholipase A2 (Lys49-PLA2) homologues damage membranes by a Ca2+-independent mechanism which does not involve catalytic activity. With the aim of determining the structural basis for this novel activity, we have solved the crystal structure of myotoxin-II, a Lys49-PLA2 isolated from the venom of Cerrophidion (Bothrops) godmani (godMT-II) at 2.8 A resolution by molecular replacement. The final model has been refined to a final crystallografic residual (Rfactor) of 18.8% (Rfree = 28.2%), with excellent stereochemistry. godMT-II is also monomeric in the crystalline state, and small-angle X-ray scattering results demonstrate that the protein is monomeric in solution under fisicochemical conditions similar to those used in the crystallographic studies.

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Organizational Affiliation: 
• Department of Physics, IBILCE/UNESP, São José do Rio Preto-SP, Brazil. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 13.73 kDa 
• Atom Count: 999 
• Modeled Residue Count: 121 
• Deposited Residue Count: 121 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (PHOSPHOLIPASE A2)	A	121	Cerrophidion godmani	Mutation(s): 0  EC: 3.1.1.4
UniProt
Find proteins for P81165 (Cerrophidion godmani) Explore P81165  Go to UniProtKB:  P81165

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.282 (Depositor) 
• R-Value Work:  0.188 (Depositor), 0.227 (DCC) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.56	α = 90
b = 60.56	β = 90
c = 84.72	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALEPACK	data scaling
AMoRE	phasing
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-04-23 
Deposition Author(s): Arni, R.K., Fontes, M.R.M., Barberato, C., Gutierrez, J.M., Diaz-Oreiro, C., Ward, R.J.

Revision History  

• Version 1.0: 1999-04-23
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-02
  Changes: Database references, Refinement description
• Version 1.4: 2024-10-09
  Changes: Data collection, Structure summary