1OKH

Viscotoxin A3 from Viscum album L.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.257 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure of Viscotoxin A3: Disulfide Location from Weak Sad Data

Debreczeni, J.E.Girmann, B.Zeeck, A.Kratzner, R.Sheldrick, G.M.

(2003) Acta Crystallogr.,Sect.D 59: 2125


  • PubMed Abstract: 
  • The crystal structure of viscotoxin A3 (VT A3) extracted from European mistletoe (Viscum album L.) has been solved using the anomalous diffraction of the native S atoms measured in-house with Cu Kalpha radiation to a resolution of 2.2 A and truncated ...

    The crystal structure of viscotoxin A3 (VT A3) extracted from European mistletoe (Viscum album L.) has been solved using the anomalous diffraction of the native S atoms measured in-house with Cu Kalpha radiation to a resolution of 2.2 A and truncated to 2.5 A. A 1.75 A resolution synchrotron data set was used for phase expansion and refinement. An innovation in the dual-space substructure-solution program SHELXD enabled the individual S atoms of the disulfide bonds to be located using the Cu Kalpha data; this resulted in a marked improvement in the phasing compared with the use of super-S atoms. The VT A3 monomer consists of 46 amino acids with three disulfide bridges and has an overall fold resembling the canonical architecture of the alpha- and beta-thionins, a capital letter L. The asymmetric unit consists of two monomers related by a local twofold axis and held together by hydrophobic interactions between the monomer units. One phosphate anion (confirmed by 31P-NMR and MS) is associated with each monomer.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
VISCOTOXIN A3
A, B
46Viscum albumGene Names: THI2.1
Find proteins for P01538 (Viscum album)
Go to UniProtKB:  P01538
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.257 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 47.995α = 90.00
b = 68.593β = 90.00
c = 25.264γ = 90.00
Software Package:
Software NamePurpose
SHELXEphasing
SCALEPACKdata scaling
SHELXL-97refinement
DENZOdata reduction
SHELXDphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-12-04
    Type: Initial release
  • Version 1.1: 2016-12-14
    Type: Data collection, Database references, Derived calculations, Non-polymer description, Other, Version format compliance