9FK3 | pdb_00009fk3

The structure of glycosynthase XT6 (E265G mutant), the extracellular xylanase of G.proteiniphilus T-6 in complex with xylobiose-F and xylotetraose-F molecules

PDB DOI: https://doi.org/10.2210/pdb9FK3/pdb

Classification: HYDROLASE
Organism(s): Geobacillus proteiniphilus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2024-06-01 Released: 2025-06-11
Deposition Author(s): Hadad, N., Chmelnik, O., Dessau, M., Shoham, Y., Shoham, G.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.200 (Depositor), 0.200 (DCC)
R-Value Work:
0.154 (Depositor), 0.155 (DCC)
R-Value Observed:
0.157 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

The structure of glycosynthase XT6 (E265G mutant), the extracellular xylanase of G.proteiniphilus T-6 in complex with xylobiose-F and xylotetraose-F molecules

Hadad, N., Chmelnik, O., Dessau, M., Shoham, Y., Shoham, G.

To be published.

Macromolecule Content

Total Structure Weight: 45.1 kDa
Atom Count: 3,532
Modeled Residue Count: 375
Deposited Residue Count: 379
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endo-1,4-beta-xylanase	A	379	Geobacillus proteiniphilus	Mutation(s): 1 EC: 3.2.1.8
UniProt
Find proteins for P40943 (Geobacillus stearothermophilus) Explore P40943 Go to UniProtKB: P40943
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P40943
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A]	J [auth A], K [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain J [auth A] Focus chain K [auth A]