7DVA | pdb_00007dva

Structure of wild type Bt4394, a GH20 family sulfoglycosidase, in complex with 6S-GlcNAc

• PDB DOI: https://doi.org/10.2210/pdb7DVA/pdb

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


• Deposited: 2021-01-13 Released: 2022-01-19 
• Deposition Author(s): Zhang, Z., He, Y., Jin, Y.
• Funding Organization(s): Wellcome Trust, National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.184 (Depositor), 0.183 (DCC) 
• R-Value Work: 
  0.142 (Depositor), 0.140 (DCC) 

Starting Model: experimental

Literature

Mechanistic and Structural Insights into the Specificity and Biological Functions of Bacterial Sulfoglycosidases

Zhang, Z., Dong, M., Zallot, R., Blackburn, G.M., Wang, N., Wang, C., Chen, L., Baumann, P., Wu, Z., Wang, Z., Fan, H., Roth, C., Jin, Y., He, Y.

(2023) ACS Catal 13: 824-836

• DOI: https://doi.org/10.1021/acscatal.2c05405

Biological Assembly 1  

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

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

Biological Assembly 2  

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

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

Macromolecule Content 

• Total Structure Weight: 124.57 kDa 
• Atom Count: 9,198 
• Modeled Residue Count: 1,045 
• Deposited Residue Count: 1,068 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-N-acetylhexosaminidase	A [auth B], B [auth A]	534	Bacteroides thetaiotaomicron	Mutation(s): 0  EC: 3.2.1.52
UniProt
Find proteins for A0A0P0FIE8 (Bacteroides thetaiotaomicron) Explore A0A0P0FIE8  Go to UniProtKB:  A0A0P0FIE8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NGS (Subject of Investigation/LOI)	C [auth B], F [auth A]	2-acetamido-2-deoxy-6-O-sulfo-beta-D-glucopyranose C8 H15 N O9 S WJFVEEAIYIOATH-FMDGEEDCSA-N
GOL	D [auth B], E [auth B], G [auth A], H [auth A], I [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.184 (Depositor), 0.183 (DCC) 
• R-Value Work:  0.142 (Depositor), 0.140 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.5	α = 90
b = 125.596	β = 90.631
c = 84.64	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-01-19 
Deposition Author(s): Zhang, Z., He, Y., Jin, Y.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	209057/Z/17/Z
National Natural Science Foundation of China (NSFC)	China	31400663

Revision History  

• Version 1.0: 2022-01-19
  Type: Initial release
  
• Version 1.1: 2023-01-18
  Changes: Database references, Derived calculations, Structure summary
• Version 1.2: 2023-11-29
  Changes: Data collection, Refinement description