8J9F

Structure of STG-hydrolyzing beta-glucosidase 1 (PSTG1)

• PDB DOI: https://doi.org/10.2210/pdb8J9F/pdb

• Classification: HYDROLASE
• Organism(s): Paenibacillus relictisesami
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-05-03 Released: 2024-04-10 
• Deposition Author(s): Yanai, T., Imaizumi, R., Takahashi, Y., Katsumura, E., Yamamoto, M., Nakayama, T., Yamashita, S., Takeshita, K., Sakai, N., Matsuura, H.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Japan Agency for Medical Research and Development (AMED)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 0.282 
• R-Value Work: 0.232 

Literature

Structural insights into a bacterial beta-glucosidase that is capable of degrading sesaminol triglucoside to produce sesaminol

Yanai, T., Imaizumi, R., Nakayama, T., Yamashita, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 4-mer - A4 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 346.8 kDa 
• Atom Count: 23,612 
• Modelled Residue Count: 2,987 
• Deposited Residue Count: 3,120 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-glucosidase	A, B, C, D	780	Paenibacillus relictisesami	Mutation(s): 0  Gene Names: PSTG
UniProt
Find proteins for D6RVX0 (Paenibacillus relictisesami) Explore D6RVX0  Go to UniProtKB:  D6RVX0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth A], F [auth B], G [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 0.282 
• R-Value Work: 0.232 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.3	α = 71.468
b = 113.25	β = 82.684
c = 158.66	γ = 79.83

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-04-10 
Deposition Author(s): Yanai, T., Imaizumi, R., Takahashi, Y., Katsumura, E., Yamamoto, M., Nakayama, T., Yamashita, S., Takeshita, K., Sakai, N., Matsuura, H.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	23H05470
Japan Agency for Medical Research and Development (AMED)	Japan	--

Revision History  

• Version 1.0: 2024-04-10
  Type: Initial release