8Z48

Beta-galactosidase from Bacteroides xylanisolvens (complex with methyl beta-galactopyranose)

PDB DOI: https://doi.org/10.2210/pdb8Z48/pdb

Classification: HYDROLASE
Organism(s): Bacteroides xylanisolvens XB1A
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-04-16 Released: 2025-01-01
Deposition Author(s): Nakajima, M., Motouchi, S., Kobayashi, K.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free:
0.251 (Depositor), 0.256 (DCC)
R-Value Work:
0.211 (Depositor), 0.220 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

A beta-Galactosidase acting on unique galactosides: the structure and function of a beta-1,2-galactosidase from Bacteroides xylanisolvens, an intestinal bacterium

Nakazawa, Y., Kageyama, M., Matsuzawa, T., Liang, Z., Kobayashi, K., Shimizu, H., Masuhiro, M., Motouchi, S., Kumano, S., Tanaka, N., Kuranochi, K., Nakai, H., Taguchi, H., Nakajima, M.

To be published.

Macromolecule Content

Total Structure Weight: 251.16 kDa
Atom Count: 17,479
Modelled Residue Count: 2,018
Deposited Residue Count: 2,204
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-galactosidase	A, B, C, D	551	Bacteroides xylanisolvens XB1A	Mutation(s): 0 Gene Names: BXY_22780
UniProt
Find proteins for D6CYU7 (Bacteroides xylanisolvens XB1A) Explore D6CYU7 Go to UniProtKB: D6CYU7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D6CYU7
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MBG (Subject of Investigation/LOI) Query on MBG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth C] SDF format, chain H [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth C] MOL2 format, chain H [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth C] mmCIF format, chain H [auth D]	E [auth A], F [auth B], G [auth C], H [auth D]	methyl beta-D-galactopyranoside C₇ H₁₄ O₆ HOVAGTYPODGVJG-VOQCIKJUSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free: 0.251 (Depositor), 0.256 (DCC)
R-Value Work: 0.211 (Depositor), 0.220 (DCC)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 231.765	α = 90
b = 50.839	β = 96.099
c = 229.445	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-01-01

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-01-01
Type: Initial release

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.