3WXS | pdb_00003wxs

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 (Depositor), 0.205 (DCC) 
• R-Value Work: 
  0.157 (Depositor), 0.162 (DCC) 
• R-Value Observed: 
  0.159 (Depositor) 

Starting Model: experimental

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 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.
Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, Japan.
1] RIKEN SPring-8 Center, Sayo, Japan. [2] Laboratory of Supramolecular Crystallography, Research Center for Structural and Functional Proteomics, Institute for Protein Research, Osaka University, Suita, Japan.
1] RIKEN SPring-8 Center, Sayo, Japan. [2] Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Japan.
Department of Cell Biology, Graduate School of Medicine, Kyoto University, Sakyo, Japan.
Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Japan.
Japan Science and Technology Agency (JST)-Exploratory Research for Advanced Technology (ERATO), Lipid Active Structure Project, Toyonaka, Japan.
Japan Synchrotron Radiation Research Institute, Sayo, Japan.
1] RIKEN SPring-8 Center, Sayo, Japan. [2] Department of Cell Biology, Graduate School of Medicine, Kyoto University, Sakyo, 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 
• Modeled 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 (Depositor), 0.205 (DCC) 
• R-Value Work:  0.157 (Depositor), 0.162 (DCC) 
• R-Value Observed: 0.159 (Depositor) 

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
• Version 1.3: 2024-11-20
  Changes: Structure summary