8YK6

Magnetic effects of thaumatin crystals; observation of the crystal growth of magneto-Archimedes levitation and magnetic orientation

• PDB DOI: https://doi.org/10.2210/pdb8YK6/pdb

• Classification: PLANT PROTEIN
• Organism(s): Thaumatococcus daniellii
• Mutation(s): No 


• Deposited: 2024-03-04 Released: 2025-02-26 
• Deposition Author(s): Nakabayashi, M., Inaka, K., Fujiwara, M., Hagiwara, M., Maki, S.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.99 Å
• R-Value Free: 
  0.134 (Depositor), 0.137 (DCC) 
• R-Value Work: 
  0.126 (Depositor), 0.130 (DCC) 
• R-Value Observed: 
  0.126 (Depositor) 

Starting Model: experimental

Literature

Magnetic effects of thaumatin crystals; observation of crystal growth by magneto-Archimedes levitation and magnetic orientation.

Maki, S., Fujiwara, M., Fujiwara, Y., Nakabayashi, M., Morimoto, S., Tanaka, S., Fujiwara, S., Hagiwara, M., Inaka, K.

(2025) PLoS One 20: e0315335-e0315335

• PubMed: 39946396 
• DOI: https://doi.org/10.1371/journal.pone.0315335
• Primary Citation of Related Structures:  
  8YK6


• PubMed Abstract: 
  

  We examined the magnetic effect of thaumatin crystals, which are a well known model of protein crystals but which have hardly been studied for that effect. We succeeded in crystallizing thaumatin by magnetic levitation based on the magneto-Archimedes effect by the addition of the paramagnetic substance gadolinium chloride. We also carried out a chronological observation of the levitation process in a superconducting magnet, and visualized the magnetic orientation of the crystals by applying a magnetic field along the horizontal direction. In another major result, we carried out a diffraction experiment and performed a structural analysis of the crystals. We noticed from the results that no electron density from the gadolinium ion could be observed in the crystals. This suggests the possibility that the paramagnetic substance of the aqueous precipitant solution helps only to promote the crystals' levitation, and has little effect on thaumatin crystallization.

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Organizational Affiliation: 

Institute of Frontier Science and Technology, Okayama University of Science, Okayama, Okayama Pref, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 22.38 kDa 
• Atom Count: 2,205 
• Modelled Residue Count: 206 
• Deposited Residue Count: 207 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thaumatin I	A	207	Thaumatococcus daniellii	Mutation(s): 0
UniProt
Find proteins for P02883 (Thaumatococcus daniellii) Explore P02883  Go to UniProtKB:  P02883

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TLA (Subject of Investigation/LOI)	B [auth A]	L(+)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-JCYAYHJZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.99 Å
• R-Value Free:  0.134 (Depositor), 0.137 (DCC) 
• R-Value Work:  0.126 (Depositor), 0.130 (DCC) 
• R-Value Observed: 0.126 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.083	α = 90
b = 58.083	β = 90
c = 150.47	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-02-26 
Deposition Author(s): Nakabayashi, M., Inaka, K., Fujiwara, M., Hagiwara, M., Maki, S.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-02-26
  Type: Initial release