7DVB | pdb_00007dvb

D335N variant of Bt4394 in complex with 6SO3-NAG-oxazoline intermediate

• PDB DOI: https://doi.org/10.2210/pdb7DVB/pdb

• Classification: HYDROLASE
• Organism(s): Bacteroides thetaiotaomicron
• Expression System: Escherichia coli
• Mutation(s): Yes 


• 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: 2.05 Å
• R-Value Free: 
  0.259 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.229 (Depositor), 0.230 (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.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 248.44 kDa 
• Atom Count: 17,255 
• Modelled Residue Count: 2,052 
• Deposited Residue Count: 2,136 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-N-acetylhexosaminidase	A, B, C, D	534	Bacteroides thetaiotaomicron	Mutation(s): 1  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)	I [auth D]	2-acetamido-2-deoxy-6-O-sulfo-beta-D-glucopyranose C8 H15 N O9 S WJFVEEAIYIOATH-FMDGEEDCSA-N
Q4Z (Subject of Investigation/LOI)	E [auth A], F [auth B], G [auth C], H [auth D]	[(3~{a}~{R},5~{R},6~{S},7~{R},7~{a}~{R})-2-methyl-6,7-bis(oxidanyl)-5,6,7,7~{a}-tetrahydro-3~{a}~{H}-pyrano[3,2-d][1,3]oxazol-1-ium-5-yl]methyl sulfate C8 H13 N O8 S JTXHTZSXIURMTP-PVFLNQBWSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.259 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.229 (Depositor), 0.230 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.026	α = 90
b = 67.002	β = 94.673
c = 192.803	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	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