7WXT | pdb_00007wxt

Thaumatin protected by polyacrylamide gel

• PDB DOI: https://doi.org/10.2210/pdb7WXT/pdb

• Classification: HYDROLASE
• Organism(s): Thaumatococcus daniellii
• Mutation(s): No 


• Deposited: 2022-02-15 Released: 2023-02-22 
• Deposition Author(s): Muroyama, H., Tomoike, F., Nagae, T., Okada, T.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.215 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Starting Model: experimental

Literature

Post-crystallization protection of protein crystals by polyacrylamide

Muroyama, H., Kato, S., Itabashi, T., Nagae, T., Okada, T., Tomoike, F.

To be published.

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: 22.73 kDa 
• Atom Count: 1,763 
• Modeled Residue Count: 206 
• Deposited Residue Count: 206 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thaumatin I	A	206	Thaumatococcus daniellii	Mutation(s): 0
UniProt
Find proteins for P02883 (Thaumatococcus daniellii) Explore P02883  Go to UniProtKB:  P02883

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]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.215 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.013	α = 90
b = 58.013	β = 90
c = 150.419	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-02-22 
Deposition Author(s): Muroyama, H., Tomoike, F., Nagae, T., Okada, T.

---

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	19K15713

Revision History  

• Version 1.0: 2023-02-22
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary