9FKL | pdb_00009fkl

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

PDB DOI: https://doi.org/10.2210/pdb9FKL/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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.206 (Depositor), 0.206 (DCC)
R-Value Work:
0.153 (Depositor), 0.154 (DCC)
R-Value Observed:
0.156 (Depositor)

Starting Model: experimental
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Literature

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

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

To be published.

Macromolecule Content

Total Structure Weight: 78.34 kDa
Atom Count: 6,026
Modeled Residue Count: 657
Deposited Residue Count: 662
Unique protein chains: 1

Macromolecules

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P45703
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-1-fluoro-D-xylopyranose	D	6	N/A	N/A	Interactions Focus chain D Interactions & Density Focus chain D

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.206 (Depositor), 0.206 (DCC)
R-Value Work: 0.153 (Depositor), 0.154 (DCC)
R-Value Observed: 0.156 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 169.014	α = 90
b = 80.526	β = 91.993
c = 79.074	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-06-18

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-06-18
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.