8WNA | pdb_00008wna

Crystal structure of GH1 beta-glucosidase Td2F2 E352Q laminaribiose complex

• PDB DOI: https://doi.org/10.2210/pdb8WNA/pdb

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


• Deposited: 2023-10-05 Released: 2025-01-15 
• Deposition Author(s): Lin, C.C., Lu, T.J., Fushinobu, S.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.16 Å
• R-Value Free: 
  0.164 (Depositor), 0.164 (DCC) 
• R-Value Work: 
  0.151 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.151 (Depositor) 

Starting Model: experimental

Literature

Structural insights into glycoside hydrolase family 1 beta-glucosidase: Selective oligosaccharide hydrolysis, synthesis, and product profiling.

Lin, C.-C., Uno, H., Yamada, C., Terada, T., Lu, T.-J., Fushinobu, S.

(2026) J Biological Chem 

• DOI: https://doi.org/10.1016/j.jbc.2026.111293

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 53 kDa 
• Atom Count: 3,991 
• Modeled Residue Count: 443 
• Deposited Residue Count: 465 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
beta-glucosidase Td2F2	A	465	metagenomes	Mutation(s): 0  EC: 3.2.1.21

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-glucopyranose-(1-3)-beta-D-glucopyranose	B [auth C], D	2		N/A
Glycosylation Resources
GlyTouCan: G36535HU GlyCosmos: G36535HU

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-glucopyranose-(1-3)-alpha-D-glucopyranose	C [auth B]	2		N/A
Glycosylation Resources
GlyTouCan: G89266VM GlyCosmos: G89266VM

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NHE	F [auth A]	2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID C8 H17 N O3 S MKWKNSIESPFAQN-UHFFFAOYSA-N
MLA	E [auth A]	MALONIC ACID C3 H4 O4 OFOBLEOULBTSOW-UHFFFAOYSA-N
SO4	G [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900024	B [auth C], D	beta-laminaribiose	Oligosaccharide / Antimicrobial

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.16 Å
• R-Value Free:  0.164 (Depositor), 0.164 (DCC) 
• R-Value Work:  0.151 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.151 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.41	α = 90
b = 68.416	β = 90
c = 95.988	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-01-15 
Deposition Author(s): Lin, C.C., Lu, T.J., Fushinobu, S.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-01-15
  Type: Initial release
  
• Version 1.1: 2026-02-25
  Changes: Database references