3AOK

Crystal structure of sweet-tasting protein thaumatin II

• PDB DOI: https://doi.org/10.2210/pdb3AOK/pdb

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


• Deposited: 2010-10-01 Released: 2011-07-27 
• Deposition Author(s): Masuda, T., Mikami, B., Kitabatake, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.27 Å
• R-Value Free: 
  0.148 (Depositor), 0.110 (DCC) 
• R-Value Work: 
  0.110 (DCC) 
• R-Value Observed: 
  0.112 (Depositor) 

Literature

Crystal structure of the sweet-tasting protein thaumatin II at 1.27A

Masuda, T., Ohta, K., Tani, F., Mikami, B., Kitabatake, N.

(2011) Biochem Biophys Res Commun 410: 457-460

• PubMed: 21672520 
• DOI: https://doi.org/10.1016/j.bbrc.2011.05.158
• Primary Citation of Related Structures:  
  3AOK


• PubMed Abstract: 
  

  Thaumatin, an intensely sweet-tasting protein, elicits a sweet taste sensation at 50 nM. Here the X-ray crystallographic structure of one of its variants, thaumatin II, was determined at a resolution of 1.27 Å. Overall structure of thaumatin II is similar to thaumatin I, but a slight shift of the Cα atom of G96 in thaumatin II was observed. Furthermore, the side chain of residue 67 in thaumatin II is highly disordered. Since residue 67 is one of two residues critical to the sweetness of thaumatin, the present results suggested that the critical positive charges at positions 67 and 82 are disordered and the flexibility and fluctuation of these side chains would be suitable for interaction of thaumatin molecules with sweet receptors.

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Organizational Affiliation: 

Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 22.98 kDa 
• Atom Count: 2,215 
• Modelled Residue Count: 207 
• Deposited Residue Count: 207 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thaumatin-2	A	207	Thaumatococcus daniellii	Mutation(s): 0
UniProt
Find proteins for P02884 (Thaumatococcus daniellii) Explore P02884  Go to UniProtKB:  P02884

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TLA	B [auth A], C [auth A]	L(+)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-JCYAYHJZSA-N
GOL	D [auth A], E [auth A], F [auth A], G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.27 Å
• R-Value Free:  0.148 (Depositor), 0.110 (DCC) 
• R-Value Work:  0.110 (DCC) 
• R-Value Observed: 0.112 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.769	α = 90
b = 57.769	β = 90
c = 150.126	γ = 90

Software Package:

Software Name	Purpose
SHELX	model building
SHELXL-97	refinement
HKL-2000	data reduction
HKL-2000	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-07-27 
Deposition Author(s): Masuda, T., Mikami, B., Kitabatake, N.

Revision History  

• Version 1.0: 2011-07-27
  Type: Initial release
  
• Version 1.1: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary