3C8P | pdb_00003c8p

X-ray structure of Viscotoxin A1 from Viscum album L.

• PDB DOI: https://doi.org/10.2210/pdb3C8P/pdb

• Classification: TOXIN
• Organism(s): Viscum album
• Mutation(s): No 


• Deposited: 2008-02-13 Released: 2008-06-17 
• Deposition Author(s): Pal, A., Debreczeni, J.E., Sevvana, M., Gruene, T., Kahle, B., Zeeck, A., Sheldrick, G.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free: 
  0.191 (Depositor) 
• R-Value Work: 
  0.148 (DCC) 
• R-Value Observed: 
  0.151 (Depositor) 

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

• PubMed: 18703848 
• DOI: https://doi.org/10.1107/S0907444908022646
• Primary Citation 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.

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Organizational Affiliation: 
• Lehrstuhl für Strukturchemie, Georg-August-Universität, Tammannstrasse 4, D-37077 Göttingen, Germany.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 9.79 kDa 
• Atom Count: 809 
• Modeled Residue Count: 92 
• Deposited Residue Count: 92 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Viscotoxin A1	A, B	46	Viscum album	Mutation(s): 0
UniProt
Find proteins for P83554 (Viscum album) Explore P83554  Go to UniProtKB:  P83554

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free:  0.191 (Depositor) 
• R-Value Work:  0.148 (DCC) 
• R-Value Observed: 0.151 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.73	α = 90
b = 65.73	β = 90
c = 47.16	γ = 90

Software Package:

Software Name	Purpose
SHELX	refinement
PDB_EXTRACT	data extraction
SAINT	data reduction
SADABS	data scaling
XPREP	data reduction
SHELXD	phasing
SHELXE	model building
SHELXL-97	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-06-17 
Deposition Author(s): Pal, A., Debreczeni, J.E., Sevvana, M., Gruene, T., Kahle, B., Zeeck, A., Sheldrick, G.M.

Revision History  

• Version 1.0: 2008-06-17
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-10-30
  Changes: Data collection, Database references, Structure summary