Download MendeleyCrystal Structure of Beta-glucosidase from the Indigo-producing Plant Polygonum tinctorium
Yoneda, K., Himeno, M., Sakuraba, H., Ohshima, T.To be published.
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
- Funding Organization(s): Not funded
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
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This is version 1.0 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Beta-glucosidase | 478 | Persicaria tinctoria | Mutation(s): 0 EC: 3.2.1.21 |  | |
UniProt | |||||
Find proteins for Q9XJ67 (Persicaria tinctoria) Explore Q9XJ67 Go to UniProtKB: Q9XJ67 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9XJ67 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| 1PG (Subject of Investigation/LOI) Query on 1PG | 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) Query on TRS | 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) Query on EDO | 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 Name | Purpose |
|---|---|
| REFMAC | refinement |
| XDS | data reduction |
| XDS | data scaling |
| MOLREP | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2025-08-20 Deposition Author(s): Yoneda, K., Himeno, M., Sakuraba, H., Ohshima, T.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Not funded | -- |
Revision History (Full details and data files)
- Version 1.0: 2025-08-20
Type: Initial release
