5WR8

Thaumatin structure determined by SACLA at 1.55 Angstrom

• PDB DOI: https://doi.org/10.2210/pdb5WR8/pdb

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


• Deposited: 2016-12-01 Released: 2017-11-29 
• Deposition Author(s): Masuda, T., Suzuki, M., Inoue, S., Sugahara, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.150 
• R-Value Work: 0.127 
• R-Value Observed: 0.128 

Literature

Hydroxyethyl cellulose matrix applied to serial crystallography

Sugahara, M., Nakane, T., Masuda, T., Suzuki, M., Inoue, S., Song, C., Tanaka, R., Nakatsu, T., Mizohata, E., Yumoto, F., Tono, K., Joti, Y., Kameshima, T., Hatsui, T., Yabashi, M., Nureki, O., Numata, K., Nango, E., Iwata, S.

(2017) Sci Rep 7: 703-703

• PubMed: 28386083 
• DOI: https://doi.org/10.1038/s41598-017-00761-0
• Primary Citation of Related Structures:  
  5WR8, 5WR9, 5WRA, 5WRB, 5WRC


• PubMed Abstract: 
  

  Serial femtosecond crystallography (SFX) allows structures of proteins to be determined at room temperature with minimal radiation damage. A highly viscous matrix acts as a crystal carrier for serial sample loading at a low flow rate that enables the determination of the structure, while requiring consumption of less than 1 mg of the sample. However, a reliable and versatile carrier matrix for a wide variety of protein samples is still elusive. Here we introduce a hydroxyethyl cellulose-matrix carrier, to determine the structure of three proteins. The de novo structure determination of proteinase K from single-wavelength anomalous diffraction (SAD) by utilizing the anomalous signal of the praseodymium atom was demonstrated using 3,000 diffraction images.

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Organizational Affiliation: 

RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, 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: 22.38 kDa 
• Atom Count: 1,836 
• 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: 1.55 Å
• R-Value Free: 0.150 
• R-Value Work: 0.127 
• R-Value Observed: 0.128 
• Space Group: P 4₁ 2₁ 2
• Diffraction Data: https://doi.org/10.11577/1350028
• Diffraction Data: https://doi.org/10.11577/1350029
• Diffraction Data: https://doi.org/10.11577/1350030
• Diffraction Data: https://doi.org/10.11577/1350031

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.459	α = 90
b = 58.459	β = 90
c = 151.639	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CrystFEL	data reduction
CrystFEL	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-11-29 
Deposition Author(s): Masuda, T., Suzuki, M., Inoue, S., Sugahara, M.

Revision History  

• Version 1.0: 2017-11-29
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Data collection
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references