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), 0.245 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.192 (DCC) 

Starting Model: experimental

Literature

Bacteroides ovatus GH98 endoxylanase in complex with arabino-xylooligosaccharide

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

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly Evidence: gel filtration

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

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

Oligosaccharides

Help

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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XYP (Subject of Investigation/LOI)	F [auth B]	beta-D-xylopyranose C5 H10 O5 SRBFZHDQGSBBOR-KKQCNMDGSA-N
AHR (Subject of Investigation/LOI)	D [auth A], G [auth B]	alpha-L-arabinofuranose C5 H10 O5 HMFHBZSHGGEWLO-QMKXCQHVSA-N
CA	E [auth A], H [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
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), 0.245 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.192 (DCC) 

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

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-05 
Deposition Author(s): Tomlinson, C.W.E., Cartmell, A., Bolam, D.

---

Funding Organization	Location	Grant Number
Not funded		--

Revision History  

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