8BDP | pdb_00008bdp

A GH20 family sulfoglycosidase Bt4394 in complex with NAG-thiazoline and sulfite

PDB DOI: https://doi.org/10.2210/pdb8BDP/pdb

Classification: HYDROLASE
Organism(s): Bacteroides thetaiotaomicron VPI-5482
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-10-19 Released: 2023-01-11
Deposition Author(s): Zhang, Z., He, Y., Jin, Y.
Funding Organization(s): Wellcome Trust

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.47 Å
R-Value Free:
0.182 (Depositor), 0.182 (DCC)
R-Value Work:
0.130 (Depositor), 0.129 (DCC)

Starting Model: experimental
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This is version 1.1 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.

(2022) ACS Catal

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

Macromolecule Content

Total Structure Weight: 61.79 kDa
Atom Count: 4,735
Modeled Residue Count: 523
Deposited Residue Count: 534
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-N-acetylhexosaminidase	A	534	Bacteroides thetaiotaomicron VPI-5482	Mutation(s): 0 Gene Names: BT_4394 EC: 3.2.1.52
UniProt
Find proteins for Q89ZI3 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)) Explore Q89ZI3 Go to UniProtKB: Q89ZI3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q89ZI3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.47 Å
R-Value Free: 0.182 (Depositor), 0.182 (DCC)
R-Value Work: 0.130 (Depositor), 0.129 (DCC)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.832	α = 90
b = 60.785	β = 107.905
c = 74.223	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data scaling
MOLREP	phasing
xia2	data reduction

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-01-11

Deposition Author(s):

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	209057/Z/17/Z

Revision History (Full details and data files)

Version 1.0: 2023-01-11
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.