9FX5

Crystal structure of Cryo2RT Thaumatin at 296K

• PDB DOI: https://doi.org/10.2210/pdb9FX5/pdb

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


• Deposited: 2024-07-01 Released: 2024-07-31 
• Deposition Author(s): Huang, C.Y., Aumonier, S., Olieric, V., Wang, M.
• Funding Organization(s): Swiss National Science Foundation, H2020 Marie Curie Actions of the European Commission

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.59 Å
• R-Value Free: 0.221 
• R-Value Work: 0.193 
• R-Value Observed: 0.194 

Starting Model: experimental

Literature

Cryo2RT: a high-throughput method for room-temperature macromolecular crystallography from cryo-cooled crystals.

Huang, C.Y., Aumonier, S., Olieric, V., Wang, M.

(2024) Acta Crystallogr D Struct Biol 80: 620-628

• PubMed: 39052318 
• DOI: https://doi.org/10.1107/S2059798324006697
• Primary Citation of Related Structures:  
  7H56, 7H57, 7H58, 7H59, 7H5A, 7H5B, 7H5C, 7H5D, 7H5E, 7H5F, 7H5G, 7H5H, 7H5I, 7H5J, 7H5K, 7H5L, 7H5M, 7H5N, 7H5O, 7H5P, 7H5Q, 7H5R, 7H5S, 7H5T, 7H5U, 7H5V, 7H5W, 7H5X, 7H5Y, 7H5Z, 9FX4, 9FX5, 9FX6, 9FX7


• PubMed Abstract: 
  

  Advances in structural biology have relied heavily on synchrotron cryo-crystallography and cryogenic electron microscopy to elucidate biological processes and for drug discovery. However, disparities between cryogenic and room-temperature (RT) crystal structures pose challenges. Here, Cryo2RT, a high-throughput RT data-collection method from frozen crystals that leverages the cryo-crystallography workflow, is introduced. Tested on endothiapepsin crystals with four soaked fragments, thaumatin and SARS-CoV-2 3CL ^pro , Cryo2RT reveals unique ligand-binding poses, offers a comparable throughput to cryo-crystallography and eases the exploration of structural dynamics at various temperatures.

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Organizational Affiliation: 

Swiss Light Source, Center for Photon Science, Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen PSI, Switzerland.

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: 25.61 kDa 
• Atom Count: 1,828 
• Modelled Residue Count: 207 
• Deposited Residue Count: 235 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thaumatin I	A	235	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: 1.59 Å
• R-Value Free: 0.221 
• R-Value Work: 0.193 
• R-Value Observed: 0.194 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.449	α = 90
b = 58.449	β = 90
c = 151.499	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-31 
Deposition Author(s): Huang, C.Y., Aumonier, S., Olieric, V., Wang, M.

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Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	182369
H2020 Marie Curie Actions of the European Commission	European Union	884104 PSI-FELLOW-III-3i

Revision History  

• Version 1.0: 2024-07-31
  Type: Initial release
  
• Version 1.1: 2024-08-07
  Changes: Database references
• Version 1.2: 2024-08-14
  Changes: Database references
• Version 1.3: 2024-11-20
  Changes: Structure summary