2V9B

X-ray structure of viscotoxin B2 from Viscum album


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.05 Å
  • R-Value Free: 0.170 

wwPDB Validation   3D Report Full Report


This is version 1.6 of the entry. See complete history


Literature

Structures of viscotoxins A1 and B2 from European mistletoe solved using native data alone.

Pal, A.Debreczeni, J.E.Sevvana, M.Gruene, T.Kahle, B.Zeeck, A.Sheldrick, G.M.

(2008) Acta Crystallogr D Biol Crystallogr 64: 985-992

  • DOI: https://doi.org/10.1107/S0907444908022646
  • Primary Citation of Related Structures:  
    2V9B, 3C8P

  • PubMed Abstract: 

    Crystals of the cytotoxic thionin proteins viscotoxins A1 and B2 extracted from mistletoe diffracted to high resolution (1.25 and 1.05 A, respectively) and are excellent candidates for testing crystallographic methods. Ab initio direct methods were only successful in solving the viscotoxin B2 structure, which with 861 unique non-H atoms is one of the largest unknown structures without an atom heavier than sulfur to be solved in this way, but sulfur-SAD phasing provided a convincing solution for viscotoxin A1. Both proteins form dimers in the crystal and viscotoxin B2 (net charge +4 per monomer), but not viscotoxin A1 (net charge +6), is coordinated by sulfate or phosphate anions. The viscotoxin A1 crystal has a higher solvent content than the viscotoxin B2 crystal (49% as opposed to 28%) with solvent channels along the crystallographic 4(3) axes.


  • Organizational Affiliation

    Lehrstuhl für Strukturchemie, Georg-August-Universität, Tammannstrasse 4, D-37077 Göttingen, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
VISCOTOXIN-B
A, B
46Viscum albumMutation(s): 1 
UniProt
Find proteins for P08943 (Viscum album)
Explore P08943 
Go to UniProtKB:  P08943
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08943
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.05 Å
  • R-Value Free: 0.170 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.819α = 90
b = 40.392β = 90
c = 44.694γ = 90
Software Package:
Software NamePurpose
SHELXL-97refinement
DENZOdata reduction
SADABSdata scaling
SHELXDphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-06-17
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-10-24
    Changes: Data collection, Database references, Structure summary
  • Version 1.4: 2019-05-08
    Changes: Data collection, Experimental preparation
  • Version 1.5: 2019-07-10
    Changes: Data collection
  • Version 1.6: 2019-07-24
    Changes: Data collection