9Z13 | pdb_00009z13

GH95 alpha-fucosidase from Bacteroides fragilis

PDB DOI: https://doi.org/10.2210/pdb9Z13/pdb

Classification: HYDROLASE
Organism(s): Bacteroides fragilis
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2025-11-03 Released: 2026-11-11
Deposition Author(s): Kowalewski, M.E., Redinbo, M.R.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.36 Å
R-Value Free:
0.269 (Depositor), 0.270 (DCC)
R-Value Work:
0.218 (Depositor), 0.218 (DCC)
R-Value Observed:
0.221 (Depositor)

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

Validation slider image for 9Z13

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

Literature

Gut Microbial Fucosidases Contribute to Colitis by Differentially Processing Mucin Glycans

Kowalewski, M.E., Redinbo, M.R.

To be published.

Macromolecule Content

Total Structure Weight: 93.44 kDa
Atom Count: 6,695
Modeled Residue Count: 808
Deposited Residue Count: 829
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycoside hydrolase family 95 protein	A	829	Bacteroides fragilis	Mutation(s): 0 Gene Names: DWW08_08420
UniProt
Find proteins for A0A412YEK4 (Bacteroides fragilis) Explore A0A412YEK4 Go to UniProtKB: A0A412YEK4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A412YEK4
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.36 Å
R-Value Free: 0.269 (Depositor), 0.270 (DCC)
R-Value Work: 0.218 (Depositor), 0.218 (DCC)
R-Value Observed: 0.221 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.802	α = 90
b = 86.802	β = 90
c = 258.19	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing
autoPROC	data processing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-11-11

Deposition Author(s):

Kowalewski, M.E.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35 GM152079

Revision History (Full details and data files)

Version 1.0: 2026-11-11
Type: Initial release