9JTT | pdb_00009jtt

Crystal Structure of Beta-glucosidase from the Indigo-producing Plant Polygonum tinctorium

• PDB DOI: https://doi.org/10.2210/pdb9JTT/pdb

• Classification: HYDROLASE
• Organism(s): Persicaria tinctoria
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-10-07 Released: 2025-08-20 
• Deposition Author(s): Yoneda, K., Himeno, M., Sakuraba, H., Ohshima, T.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free: 
  0.252 (Depositor), 0.254 (DCC) 
• R-Value Work: 
  0.213 (Depositor), 0.221 (DCC) 
• R-Value Observed: 
  0.215 (Depositor) 

Starting Model: in silico

Literature

Crystal Structure of Beta-glucosidase from the Indigo-producing Plant Polygonum tinctorium

Yoneda, K., Himeno, M., Sakuraba, H., Ohshima, T.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 109.91 kDa 
• Atom Count: 8,226 
• Modeled Residue Count: 933 
• Deposited Residue Count: 956 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-glucosidase	A, B	478	Persicaria tinctoria	Mutation(s): 0  EC: 3.2.1.21
UniProt
Find proteins for Q9XJ67 (Persicaria tinctoria) Explore Q9XJ67  Go to UniProtKB:  Q9XJ67

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1PG (Subject of Investigation/LOI)	E [auth B]	2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL C11 H24 O6 SLNYBUIEAMRFSZ-UHFFFAOYSA-N
TRS (Subject of Investigation/LOI)	C [auth A], D [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
EDO (Subject of Investigation/LOI)	F [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free:  0.252 (Depositor), 0.254 (DCC) 
• R-Value Work:  0.213 (Depositor), 0.221 (DCC) 
• R-Value Observed: 0.215 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.435	α = 90
b = 104.059	β = 103.55
c = 99.474	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-08-20 
Deposition Author(s): Yoneda, K., Himeno, M., Sakuraba, H., Ohshima, T.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-08-20
  Type: Initial release