3WXS

Thaumatin structure determined by SPring-8 Angstrom Compact free electron Laser (SACLA)

• PDB DOI: https://doi.org/10.2210/pdb3WXS/pdb

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


• Deposited: 2014-08-07 Released: 2014-11-05 
• Deposition Author(s): Masuda, T., Nango, E., Sugahara, M., Mizohata, E., Tanaka, T., Tanaka, R., Suzuki, M., Mikami, B., Iwata, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.200 
• R-Value Work: 0.157 
• R-Value Observed: 0.159 

Literature

Grease matrix as a versatile carrier of proteins for serial crystallography

Sugahara, M., Mizohata, E., Nango, E., Suzuki, M., Tanaka, T., Masuda, T., Tanaka, R., Shimamura, T., Tanaka, Y., Suno, C., Ihara, K., Pan, D., Kakinouchi, K., Sugiyama, S., Murata, M., Inoue, T., Tono, K., Song, C., Park, J., Kameshima, T., Hatsui, T., Joti, Y., Yabashi, M., Iwata, S.

(2015) Nat Methods 12: 61-63

• PubMed: 25384243 
• DOI: https://doi.org/10.1038/nmeth.3172
• Primary Citation of Related Structures:  
  3WUL, 3WUM, 3WXQ, 3WXS, 3WXT, 3WXU, 4W4Q


• PubMed Abstract: 
  

  Serial femtosecond X-ray crystallography (SFX) has revolutionized atomic-resolution structural investigation by expanding applicability to micrometer-sized protein crystals, even at room temperature, and by enabling dynamics studies. However, reliable crystal-carrying media for SFX are lacking. Here we introduce a grease-matrix carrier for protein microcrystals and obtain the structures of lysozyme, glucose isomerase, thaumatin and fatty acid-binding protein type 3 under ambient conditions at a resolution of or finer than 2 Å.

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Organizational Affiliation: 

RIKEN SPring-8 Center, Sayo, Japan.

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: 22.38 kDa 
• Atom Count: 1,821 
• Modelled Residue Count: 207 
• 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	B [auth A]	L(+)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-JCYAYHJZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.200 
• R-Value Work: 0.157 
• R-Value Observed: 0.159 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.699	α = 90
b = 57.699	β = 90
c = 149.776	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CrystFEL	data reduction
CrystFEL	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-11-05 
Deposition Author(s): Masuda, T., Nango, E., Sugahara, M., Mizohata, E., Tanaka, T., Tanaka, R., Suzuki, M., Mikami, B., Iwata, S.

Revision History  

• Version 1.0: 2014-11-05
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Data collection, Database references
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description