1QKE | pdb_00001qke

ERABUTOXIN

• PDB DOI: https://doi.org/10.2210/pdb1QKE/pdb

• Classification: NEUROTOXIN
• Organism(s): Laticauda semifasciata
• Mutation(s): No 


• Deposited: 1998-01-16 Released: 1999-02-16 
• Deposition Author(s): Nastopoulos, V., Kanellopoulos, P.N., Tsernoglou, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Work: 
  0.162 (DCC) 

Starting Model: experimental

Literature

Structure of dimeric and monomeric erabutoxin a refined at 1.5 A resolution.

Nastopoulos, V., Kanellopoulos, P.N., Tsernoglou, D.

(1998) Acta Crystallogr D Biol Crystallogr 54: 964-974

• PubMed: 9757111 
• DOI: https://doi.org/10.1107/s0907444998005125
• Primary Citation Related Structures: 
  1QKD, 1QKE


• PubMed Abstract: 
  

  Erabutoxin a has been crystallized in its monomeric and dimeric forms. The structures were refined at 1.50 and 1.49 A resolution, respectively, using synchrotron radiation data. The crystals belong to space group P212121, with cell dimensions a = 49.84, b = 46.62, c = 21.22 A for the monomer and a = 55.32, b = 53.54, c = 40.76 A for the dimer. Using starting models from earlier structure determinations, the monomeric structure refined to an R value of 16.7% (8004 unique reflections, 17.0-1.50 A resolution range), while the dimeric structure has been solved by the molecular-replacement method with a final R value of 16.9% (19 444 unique reflections, 17.4-1.49 A resolution range). The high-resolution electron-density maps clearly revealed significant discrete disorder in the proteins and allowed an accurate determination of the solvent structure. For the monomer, the side chains of six residues were modelled with alternate conformers and 106 sites for water molecules and one site for a sulfate ion were included in the final model, whereas for the dimer, 206 sites for water molecules were included and both C-terminal residues together with the side chains of 11 residues adopted alternative conformations. A comparison was made with earlier structure determinations. The features of the solvent structure of the erabutoxin molecules are discussed in detail.

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Organizational Affiliation: 
• Department of Chemistry, University of Patras, 26500 Patras, Greece. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 6.95 kDa 
• Atom Count: 600 
• Modeled Residue Count: 62 
• Deposited Residue Count: 62 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ERABUTOXIN A	A	62	Laticauda semifasciata	Mutation(s): 0
UniProt
Find proteins for P60775 (Laticauda semifasciata) Explore P60775  Go to UniProtKB:  P60775

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Work:  0.162 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.84	α = 90
b = 46.62	β = 90
c = 21.22	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	model building
TNT	refinement
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-02-16 
Deposition Author(s): Nastopoulos, V., Kanellopoulos, P.N., Tsernoglou, D.

Revision History  

• Version 1.0: 1999-02-16
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2016-10-26
  Changes: Other
• Version 1.4: 2023-08-09
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.5: 2024-10-23
  Changes: Data collection, Structure summary