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

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:

(by identity cutoff) | 3D Structure

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% Identity50% Identity70% Identity90% Identity95% Identity100% 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 C [auth A] SDF format, chain D [auth A] SDF format, chain F [auth B] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B]	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 E [auth A] SDF format, chain K [auth B] MOL2 format, chain E [auth A] MOL2 format, chain K [auth B] mmCIF format, chain E [auth A] mmCIF format, chain K [auth B]	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