9H6F | pdb_00009h6f

Bacteroides ovatus GH98 endoxylanase in complex with arabino-xylooligosaccharide

PDB DOI: https://doi.org/10.2210/pdb9H6F/pdb

Classification: HYDROLASE
Organism(s): Bacteroides ovatus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-10-24 Released: 2025-11-05
Deposition Author(s): Tomlinson, C.W.E., Cartmell, A., Bolam, D.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.245 (Depositor), 0.242 (DCC)
R-Value Work:
0.192 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Bacteroides ovatus GH98 endoxylanase in complex with arabino-xylooligosaccharide

Tomlinson, C.W.E., Cartmell, A., Bolam, D.

To be published.

Macromolecule Content

Total Structure Weight: 202.93 kDa
Atom Count: 14,893
Modeled Residue Count: 1,790
Deposited Residue Count: 1,790
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycosyl hydrolase family 98	A, B	895	Bacteroides ovatus	Mutation(s): 0 Gene Names: F3F51_01075, HUV13_02585
UniProt
Find proteins for A0A6N3VET1 (Bacteroides ovatus) Explore A0A6N3VET1 Go to UniProtKB: A0A6N3VET1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A6N3VET1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-xylopyranose-(1-3)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose	C	4		N/A	Interactions Focus chain C Interactions & Density Focus chain C

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AHR (Subject of Investigation/LOI) Query on AHR Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain D [auth A] mmCIF format, chain G [auth B] mmCIF format, chain D [auth A]	D [auth A], G [auth B]	alpha-L-arabinofuranose C₅ H₁₀ O₅ HMFHBZSHGGEWLO-QMKXCQHVSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]
XYP (Subject of Investigation/LOI) Query on XYP Download:Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B] mmCIF format, chain F [auth B]	F [auth B]	beta-D-xylopyranose C₅ H₁₀ O₅ SRBFZHDQGSBBOR-KKQCNMDGSA-N		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A]	E [auth A], H [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PHD Query on PHD	A, B	L-PEPTIDE LINKING	C₄ H₈ N O₇ P		ASP

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.245 (Depositor), 0.242 (DCC)
R-Value Work: 0.192 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 186.05	α = 90
b = 63.85	β = 118.69
c = 180.49	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
REFMAC	refinement
XDS	data reduction
Coot	model building
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-11-05

Deposition Author(s):

Tomlinson, C.W.E.

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-11-05
Type: Initial release

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