Crystal structure of BvGH123

Experimental Data Snapshot

  • Resolution: 1.85 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.180 

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Structural and mechanistic insights into a Bacteroides vulgatus retaining N-acetyl-beta-galactosaminidase that uses neighbouring group participation.

Roth, C.Petricevic, M.John, A.Goddard-Borger, E.D.Davies, G.J.Williams, S.J.

(2016) Chem Commun (Camb) 52: 11096-11099

  • DOI: https://doi.org/10.1039/c6cc04649e
  • Primary Citation of Related Structures:  
    5L7R, 5L7U, 5L7V

  • PubMed Abstract: 

    Bacteroides vulgatus is a member of the human microbiota whose abundance is increased in patients with Crohn's disease. We show that a B. vulgatus glycoside hydrolase from the carbohydrate active enzyme family GH123, BvGH123, is an N-acetyl-β-galactosaminidase that acts with retention of stereochemistry, and, through a 3-D structure in complex with Gal-thiazoline, provide evidence in support of a neighbouring group participation mechanism.

  • Organizational Affiliation

    Department of Chemistry, University of York, Heslington, York, UK. gideon.davies@york.ac.uk.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
glycoside hydrolase
A, B
578Phocaeicola vulgatus ATCC 8482Mutation(s): 0 
Gene Names: BVU_2198
Find proteins for A6L2E5 (Phocaeicola vulgatus (strain ATCC 8482 / DSM 1447 / JCM 5826 / CCUG 4940 / NBRC 14291 / NCTC 11154))
Explore A6L2E5 
Go to UniProtKB:  A6L2E5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA6L2E5
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.85 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.180 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.269α = 90
b = 147.794β = 90
c = 150.5γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/K003836/1

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-22
    Type: Initial release
  • Version 2.0: 2017-08-30
    Changes: Atomic model, Author supporting evidence