1AHO

THE AB INITIO STRUCTURE DETERMINATION AND REFINEMENT OF A SCORPION PROTEIN TOXIN

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.96 Å
  • R-Value Work: 0.158 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Ab initio structure determination and refinement of a scorpion protein toxin.

Smith, G.D., Blessing, R.H., Ealick, S.E., Fontecilla-Camps, J.C., Hauptman, H.A., Housset, D., Langs, D.A., Miller, R.

(1997) Acta Crystallogr D Biol Crystallogr 53: 551-557

  • DOI: https://doi.org/10.1107/S0907444997005386
  • Primary Citation of Related Structures:  
    1AHO

  • PubMed Abstract: 

    The structure of toxin II from the scorpion Androctonus australis Hector has been determined ab initio by direct methods using SnB at 0.96 A resolution. For the purpose of this structure redetermination, undertaken as a test of the minimal function and the SnB program, the identity and sequence of the protein was withheld from part of the research team. A single solution obtained from 1 619 random atom trials was clearly revealed by the bimodal distribution of the final value of the minimal function associated with each individual trial. Five peptide fragments were identified from a conservative analysis of the initial E-map, and following several refinement cycles with X-PLOR, a model was built of the complete structure. At the end of the X-PLOR refinement, the sequence was compared with the published sequence and 57 of the 64 residues had been correctly identified. Two errors in sequence resulted from side chains with similar size while the rest of the errors were a result of severe disorder or high thermal motion in the side chains. Given the amino-acid sequence, it is estimated that the initial E-map could have produced a model containing 99% of all main-chain and 81% of side-chain atoms. The structure refinement was completed with PROFFT, including the contributions of protein H atoms, and converged at a residual of 0.158 for 30 609 data with F >or= 2sigma(F) in the resolution range 8.0-0.964 A. The final model consisted of 518 non-H protein atoms (36 disordered), 407 H atoms, and 129 water molecules (43 with occupancies less than unity). This total of 647 non-H atoms represents the largest light-atom structure solved to date.

    • Organizational Affiliation: 

    Hauptman-Woodward Medical Research Institute, Buffalo, NY 14203, USA.


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TOXIN II64Androctonus australis hectorMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P01484 (Androctonus australis)
Explore P01484 
Go to UniProtKB:  P01484
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01484
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.96 Å
  • R-Value Work: 0.158 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.9α = 90
b = 40.7β = 90
c = 30.1γ = 90
Software Package:
Software NamePurpose
MOSFILMdata collection
ROTAVATAdata reduction
AGROVATAdata reduction
SHAKE-N-BAKEmodel building
PROFFTrefinement
MOSFLMdata reduction
CCP4data scaling
ROTAVATA)data scaling
SHAKE-N-BAKEphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-10-15
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance