3T0R | pdb_00003t0r

Crystal Structure of MjTX-I, a myotoxic Lys49-phospholipase A2 from Bothrops moojeni

• PDB DOI: https://doi.org/10.2210/pdb3T0R/pdb

• Classification: TOXIN
• Organism(s): Bothrops moojeni
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2011-07-20 Released: 2012-08-01 
• Deposition Author(s): Salvador, G.H.M., Marchi-Salvador, D.P., Fontes, M.R.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free: 
  0.267 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.231 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.233 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of MjTX-I, a myotoxic Lys49-phospholipase A2 from Bothrops moojeni

Salvador, G.H.M., Marchi-Salvador, D.P., Fontes, M.R.M.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: SAXS

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors.

Biological Assembly Evidence: SAXS

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 generated by PISA (software)

Biological Assembly 5  

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

Biological assembly 5 generated by PISA (software)

Biological Assembly 6  

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

Biological assembly 6 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 55.41 kDa 
• Atom Count: 3,684 
• Modeled Residue Count: 475 
• Deposited Residue Count: 484 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phospholipase A2 homolog 1	A, B, C, D	121	Bothrops moojeni	Mutation(s): 0  EC: 3.1.1.4 Membrane Entity: Yes
UniProt
Find proteins for P82114 (Bothrops moojeni) Explore P82114  Go to UniProtKB:  P82114

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PE4	E [auth A]	2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL C16 H34 O8 PJWQOENWHPEPKI-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free:  0.267 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.231 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.233 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.593	α = 90
b = 125.848	β = 105.91
c = 65.327	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-08-01 
Deposition Author(s): Salvador, G.H.M., Marchi-Salvador, D.P., Fontes, M.R.M.

Revision History  

• Version 1.0: 2012-08-01
  Type: Initial release
  
• Version 1.1: 2017-10-25
  Changes: Author supporting evidence
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-11-27
  Changes: Structure summary