5L7U | pdb_00005l7u

Crystal structure of BvGH123 with bound GalNAc

• PDB DOI: https://doi.org/10.2210/pdb5L7U/pdb

• Classification: HYDROLASE
• Organism(s): Phocaeicola vulgatus ATCC 8482
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2016-06-03 Released: 2017-03-22 
• Deposition Author(s): Roth, C., Petricevic, M., John, A., Goddard-Borger, E.D., Davies, G.J., Williams, S.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.227 (Depositor), 0.205 (DCC) 
• R-Value Work: 
  0.193 (Depositor) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: experimental

Literature

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

• PubMed: 27546776 
• DOI: https://doi.org/10.1039/c6cc04649e
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Chemistry, University of York, Heslington, York, UK. [e-mail].

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 133.13 kDa 
• Atom Count: 9,250 
• Modeled Residue Count: 1,115 
• Deposited Residue Count: 1,156 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycoside hydrolase	A, B	578	Phocaeicola vulgatus ATCC 8482	Mutation(s): 0  Gene Names: BVU_2198
UniProt
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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NGA	C [auth A], D [auth B]	2-acetamido-2-deoxy-beta-D-galactopyranose C8 H15 N O6 OVRNDRQMDRJTHS-JAJWTYFOSA-N
CL	E [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.227 (Depositor), 0.205 (DCC) 
• R-Value Work:  0.193 (Depositor) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.345	α = 90
b = 142.207	β = 90
c = 145.806	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-03-22 
Deposition Author(s): Roth, C., Petricevic, M., John, A., Goddard-Borger, E.D., Davies, G.J., Williams, S.J.

Revision History  

• Version 1.0: 2017-03-22
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.3: 2024-10-23
  Changes: Structure summary