9FKJ | pdb_00009fkj

The structure of glycosynthase IXT6 (E241G mutant), the intracellular xylanase of G.proteiniphilus T-6 in complex with two xylobiose-F molecules

• PDB DOI: https://doi.org/10.2210/pdb9FKJ/pdb

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


• Deposited: 2024-06-03 Released: 2025-06-18 
• Deposition Author(s): Hadad, N., Chmelnik, O., Dessau, M., Shoham, Y., Shoham, G.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.198 (Depositor), 0.198 (DCC) 
• R-Value Work: 
  0.163 (Depositor), 0.164 (DCC) 
• R-Value Observed: 
  0.165 (Depositor) 

Starting Model: experimental

Literature

The structure of glycosynthase IXT6 (E241G mutant), the intracellular xylanase of G.proteiniphilus T-6 in complex with two xylobiose-F molecules

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

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 78.37 kDa 
• Atom Count: 6,268 
• Modeled Residue Count: 657 
• Deposited Residue Count: 662 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-xylanase	A, B	331	Geobacillus proteiniphilus	Mutation(s): 1  Gene Names: xynA2 EC: 3.2.1.8
UniProt
Find proteins for P45703 (Geobacillus stearothermophilus) Explore P45703  Go to UniProtKB:  P45703

Oligosaccharides

Help

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	F [auth A], G [auth A], H [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.198 (Depositor), 0.198 (DCC) 
• R-Value Work:  0.163 (Depositor), 0.164 (DCC) 
• R-Value Observed: 0.165 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 169.165	α = 90
b = 80.602	β = 92.218
c = 79.307	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-06-18 
Deposition Author(s): Hadad, N., Chmelnik, O., Dessau, M., Shoham, Y., Shoham, G.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-06-18
  Type: Initial release