9FK9 | pdb_00009fk9

The structure of XT6 from G.proteiniphilus T-6: The E265G/Q238A/W241A mutant

• PDB DOI: https://doi.org/10.2210/pdb9FK9/pdb

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


• Deposited: 2024-06-02 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: 2.70 Å
• R-Value Free: 
  0.264 (Depositor), 0.264 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

Literature

The structure of XT6 from G.proteiniphilus T-6: The E265G/Q238A/W241A mutant

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.

Macromolecule Content 

• Total Structure Weight: 44.25 kDa 
• Atom Count: 3,187 
• Modeled Residue Count: 374 
• Deposited Residue Count: 379 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endo-1,4-beta-xylanase	A	379	Geobacillus proteiniphilus	Mutation(s): 3  EC: 3.2.1.8
UniProt
Find proteins for P40943 (Geobacillus stearothermophilus) Explore P40943  Go to UniProtKB:  P40943

Oligosaccharides

Help  

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	E [auth A], F [auth A], G [auth A], H [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	C [auth A], D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.264 (Depositor), 0.264 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.263	α = 90
b = 61.817	β = 105.244
c = 110.576	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