9H6H | pdb_00009h6h

Bacteroides ovatus GH98 endoxylanase with Seleno-methionine substituents

PDB DOI: https://doi.org/10.2210/pdb9H6H/pdb

Classification: HYDROLASE
Organism(s): Bacteroides ovatus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.242 (Depositor), 0.249 (DCC)
R-Value Work:
0.192 (Depositor), 0.199 (DCC)

wwPDB Validation 3D Report Full Report

Validation slider image for 9H6H

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

Literature

Seleno-Methionine substituted structure of Bacteriodes ovatus GH98

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

To be published.

Macromolecule Content

Total Structure Weight: 206.22 kDa
Atom Count: 15,585
Modeled Residue Count: 1,791
Deposited Residue Count: 1,812
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycosyl hydrolase family 98	A, B	906	Bacteroides ovatus	Mutation(s): 1 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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain G [auth B] SDF format, chain F [auth B] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain F [auth B] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] F [auth B] G [auth B] H [auth B] C [auth A], D [auth A], F [auth B], G [auth B], H [auth B], I [auth B], J [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain E [auth A] MOL2 format, chain K [auth B] MOL2 format, chain E [auth A] mmCIF format, chain K [auth B] mmCIF format, chain E [auth A]	E [auth A], K [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain K [auth B] Interactions & Density Focus chain E [auth A] Focus chain K [auth B]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET
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: 2.00 Å
R-Value Free: 0.242 (Depositor), 0.249 (DCC)
R-Value Work: 0.192 (Depositor), 0.199 (DCC)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 183.914	α = 90
b = 62.447	β = 118.058
c = 178.713	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

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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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.