8YK3

Blood group B alpha-1,3-galactosidase AgaBb from Bifidobacterium bifidum, construct T7-tag_24-673

• PDB DOI: https://doi.org/10.2210/pdb8YK3/pdb

• Classification: HYDROLASE
• Organism(s): Bifidobacterium bifidum JCM 1254
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-03-04 Released: 2024-07-10 
• Deposition Author(s): Kashima, T., Ashida, H., Fushinobu, S.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 0.285 
• R-Value Work: 0.203 
• R-Value Observed: 0.207 

Starting Model: experimental

Literature

Crystal Structure of Bifidobacterium bifidum Glycoside Hydrolase Family 110 alpha-Galactosidase Specific for Blood Group B Antigen

Kashima, T., Akama, M., Wakinaka, T., Arakawa, T., Ashida, H., Fushinobu, S.

(2024) J Appl Glycosci (1999) 

• DOI: https://doi.org/10.5458/jag.jag.JAG-2024_0005

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 145.92 kDa 
• Atom Count: 9,480 
• Modelled Residue Count: 1,239 
• Deposited Residue Count: 1,346 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-galactosidase	A, B	673	Bifidobacterium bifidum JCM 1254	Mutation(s): 0  Gene Names: agabb, GBA83_07165 EC: 3.2.1
UniProt
Find proteins for L8B3G2 (Bifidobacterium bifidum) Explore L8B3G2  Go to UniProtKB:  L8B3G2

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MES	G [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
GLA (Subject of Investigation/LOI)	C [auth A], H [auth B]	alpha-D-galactopyranose C6 H12 O6 WQZGKKKJIJFFOK-PHYPRBDBSA-N
EDO	D [auth A], E [auth A], F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 0.285 
• R-Value Work: 0.203 
• R-Value Observed: 0.207 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.34	α = 90
b = 73.154	β = 91.38
c = 177.968	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-10 
Deposition Author(s): Kashima, T., Ashida, H., Fushinobu, S.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	24380053
Japan Society for the Promotion of Science (JSPS)	Japan	23H00322

Revision History  

• Version 1.0: 2024-07-10
  Type: Initial release