8BAL | pdb_00008bal

Niako3494, a bacterial protein structure in glycoside hydrolase family 20

PDB DOI: https://doi.org/10.2210/pdb8BAL/pdb

Classification: HYDROLASE
Organism(s): Niastella koreensis GR20-10
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-10-11 Released: 2023-01-11
Deposition Author(s): Dong, M.D., Roth, C.R., Jin, Y.J.
Funding Organization(s): Wellcome Trust, Royal Society

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.27 Å
R-Value Free:
0.356 (Depositor), 0.310 (DCC)
R-Value Work:
0.283 (Depositor), 0.248 (DCC)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 8BAL

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: 218.04 kDa
Atom Count: 13,749
Modeled Residue Count: 1,701
Deposited Residue Count: 1,900
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-N-acetylhexosaminidase	A, B [auth C], C [auth D], D [auth E], E [auth F]	380	Niastella koreensis GR20-10	Mutation(s): 0 Gene Names: Niako_3494 EC: 3.2.1.52
UniProt
Find proteins for G8TKW6 (Niastella koreensis (strain DSM 17620 / KACC 11465 / NBRC 106392 / GR20-10)) Explore G8TKW6 Go to UniProtKB: G8TKW6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G8TKW6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth C] SDF format, chain H [auth D] SDF format, chain I [auth E] SDF format, chain J [auth F] MOL2 format, chain F [auth A] MOL2 format, chain G [auth C] MOL2 format, chain H [auth D] MOL2 format, chain I [auth E] MOL2 format, chain J [auth F] mmCIF format, chain F [auth A] mmCIF format, chain G [auth C] mmCIF format, chain H [auth D] mmCIF format, chain I [auth E] mmCIF format, chain J [auth F]	F [auth A], G [auth C], H [auth D], I [auth E], J [auth F]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth C] Focus chain H [auth D] Focus chain I [auth E] Focus chain J [auth F] Interactions & Density Focus chain F [auth A] Focus chain G [auth C] Focus chain H [auth D] Focus chain I [auth E] Focus chain J [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.27 Å
R-Value Free: 0.356 (Depositor), 0.310 (DCC)
R-Value Work: 0.283 (Depositor), 0.248 (DCC)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 146.987	α = 90
b = 254.589	β = 90
c = 139.58	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-01-11

Deposition Author(s):

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	218568/Z/19/Z
Royal Society	United Kingdom	RG170406
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: 2024-05-01
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.