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 1.3 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: 10.1107/S0907444908022646
  • Primary Citation of Related Structures:  

  • 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 o ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
VISCOTOXIN-B
A, B
46Viscum albumMutation(s): 0 
Gene Names: THI2.2
Find proteins for P08943 (Viscum album)
Go to UniProtKB:  P08943
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
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 = 90.00
b = 40.392β = 90.00
c = 44.694γ = 90.00
Software Package:
Software NamePurpose
SHELXDphasing
DENZOdata reduction
SADABSdata scaling
SHELXL-97refinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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