Download MendeleyThe 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.
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
- Funding Organization(s): Not funded
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
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wwPDB Validation 3D Report Full Report
This is version 1.0 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Beta-xylanase | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P45703 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Oligosaccharides
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 | 3D Interactions | |
| GOL Query on 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 Name | Purpose |
|---|---|
| PHENIX | refinement |
| PHENIX | refinement |
| XDS | data reduction |
| Aimless | data scaling |
| PHENIX | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2025-06-18 Deposition Author(s): Hadad, N., Chmelnik, O., Dessau, M., Shoham, Y., Shoham, G.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Not funded | -- |
Revision History (Full details and data files)
- Version 1.0: 2025-06-18
Type: Initial release
