3ODV

X-ray structure of kaliotoxin by racemic protein crystallography

• PDB DOI: https://doi.org/10.2210/pdb3ODV/pdb

• Classification: TOXIN
• Organism(s): Androctonus mauritanicus mauritanicus
• Mutation(s): No 


• Deposited: 2010-08-11 Released: 2010-10-20 
• Deposition Author(s): Pentelute, B.L., Mandal, K., Gates, Z.P., Sawaya, M.R., Yeates, T.O., Kent, S.B.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.95 Å
• R-Value Free: 0.203 
• R-Value Work: 0.188 
• R-Value Observed: 0.189 

Literature

Total chemical synthesis and X-ray structure of kaliotoxin by racemic protein crystallography.

Pentelute, B.L., Mandal, K., Gates, Z.P., Sawaya, M.R., Yeates, T.O., Kent, S.B.

(2010) Chem Commun (Camb) 46: 8174-8176

• PubMed: 20877851 
• DOI: https://doi.org/10.1039/c0cc03148h
• Primary Citation of Related Structures:  
  3ODV


• PubMed Abstract: 
  

  Here we report the total synthesis of kaliotoxin by 'one pot' native chemical ligation of three synthetic peptides. A racemic mixture of D- and L-kaliotoxin synthetic protein molecules gave crystals in the centrosymmetric space group P1 that diffracted to atomic-resolution (0.95 Å), enabling the X-ray structure of kaliotoxin to be determined by direct methods.

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Organizational Affiliation: 

Department of Chemistry, Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 8.94 kDa 
• Atom Count: 906 
• Modelled Residue Count: 76 
• Deposited Residue Count: 76 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Potassium channel toxin alpha-KTx 3.1	A, B	38	Androctonus mauritanicus mauritanicus	Mutation(s): 0
UniProt
Find proteins for P24662 (Androctonus mauritanicus mauritanicus) Explore P24662  Go to UniProtKB:  P24662

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	E [auth B], F [auth B]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
TFA	C [auth A], D [auth B]	trifluoroacetic acid C2 H F3 O2 DTQVDTLACAAQTR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.95 Å
• R-Value Free: 0.203 
• R-Value Work: 0.188 
• R-Value Observed: 0.189 
• Space Group: P -1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 25.15	α = 109.39
b = 30.511	β = 97.39
c = 41.097	γ = 97.09

Software Package:

Software Name	Purpose
SHELXD	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-10-20 
Deposition Author(s): Pentelute, B.L., Mandal, K., Gates, Z.P., Sawaya, M.R., Yeates, T.O., Kent, S.B.H.

Revision History  

• Version 1.0: 2010-10-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2012-03-28
  Changes: Other