8YK3

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


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 

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Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


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) 


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alpha-galactosidase
A, B
673Bifidobacterium bifidum JCM 1254Mutation(s): 0 
Gene Names: agabbGBA83_07165
EC: 3.2.1
UniProt
Find proteins for L8B3G2 (Bifidobacterium bifidum)
Explore L8B3G2 
Go to UniProtKB:  L8B3G2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupL8B3G2
Sequence Annotations
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  • Reference Sequence
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 = 63.34α = 90
b = 73.154β = 91.38
c = 177.968γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan24380053
Japan Society for the Promotion of Science (JSPS)Japan23H00322

Revision History  (Full details and data files)

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