7DVA

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.184
R-Value Work: 0.142

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0P0FIE8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NGS (Subject of Investigation/LOI) Query on NGS Download Ideal Coordinates CCD File SDF format, chain C [auth B] SDF format, chain F [auth A] MOL2 format, chain C [auth B] MOL2 format, chain F [auth A] mmCIF format, chain C [auth B] mmCIF format, chain F [auth A]	C [auth B], F [auth A]	2-acetamido-2-deoxy-6-O-sulfo-beta-D-glucopyranose C₈ H₁₅ N O₉ S WJFVEEAIYIOATH-FMDGEEDCSA-N		Interactions Focus chain C [auth B] Focus chain F [auth A] Interactions & Density Focus chain C [auth B] Focus chain F [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain E [auth B] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] MOL2 format, chain D [auth B] MOL2 format, chain E [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] mmCIF format, chain D [auth B] mmCIF format, chain E [auth B] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A]	D [auth B], E [auth B], G [auth A], H [auth A], I [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Focus chain E [auth B] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain D [auth B] Focus chain E [auth B] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.184
R-Value Work: 0.142
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

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2022-01-19

Deposition Author(s):

Zhang, Z.

He, Y.

Jin, Y.

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

Revision History (Full details and data files)

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

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Help and Resources

7DVA

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

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)