Download MendeleyEnzyme-Substrate interactions of IXT6, the intracellular xylanase of G. stearothermophilus.
Solomon, V., Zolotnitsky, G., Alhadeff, R., Shoham, Y., Shoham, G.To be published.
3MSD
Enzyme-Substrate interactions of IXT6, the intracellular xylanase of G. stearothermophilus.
- PDB DOI: 10.2210/pdb3MSD/pdb
- Classification: HYDROLASE
- Organism(s): Geobacillus stearothermophilus
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2010-04-29 Released: 2011-05-11
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.58 Å
- R-Value Free: 0.209
- R-Value Work: 0.197
wwPDB Validation 3D Report Full Report
This is version 2.0 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 |
| Intra-cellular xylanase ixt6 | A, B | 331 | Geobacillus stearothermophilus | Mutation(s): 0 Gene Names: xynA2 EC: 3.2.1.8 |  |
UniProt | |||||
Find proteins for Q09LY9 (Geobacillus stearothermophilus) Explore Q09LY9 Go to UniProtKB: Q09LY9 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q09LY9 | ||||
Protein Feature ViewExpand | |||||
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Oligosaccharides
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Chain Length | 2D Diagram | Glycosylation | 3D Interactions |
| beta-D-xylopyranose-(1-4)-beta-D-xylopyranose | C, D | 2 |  | N/A | Oligosaccharides Interaction |
Glycosylation Resources | |||||
GlyTouCan: G87728WL GlyCosmos: G87728WL | |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| GOL Query on GOL | E [auth A], H [auth B] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | Ligand Interaction | |
| ACT Query on ACT | G [auth A] | ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M |  | Ligand Interaction | |
| NA Query on NA | F [auth A], I [auth B] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |  | Ligand Interaction | |
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| ID | Chains | Name | Type/Class | 2D Diagram | 3D Interactions |
| PRD_900116 Query on PRD_900116 | C, D | 4beta-beta-xylobiose | Oligosaccharide / Metabolism |  | Ligand Interaction |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.58 Å
- R-Value Free: 0.209
- R-Value Work: 0.197
- Space Group: C 1 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 169.265 | α = 90 |
| b = 80.993 | β = 91.95 |
| c = 79.277 | γ = 90 |
| Software Name | Purpose |
|---|---|
| DENZO | data reduction |
| CNS | refinement |
| SCALEPACK | data scaling |
| CNS | phasing |
Entry History
Deposition Data
- Released Date: 2011-05-11 Deposition Author(s): Solomon, V., Zolotnitsky, G., Alhadeff, R., Shoham, Y., Shoham, G.
Revision History (Full details and data files)
- Version 1.0: 2011-05-11
Type: Initial release - Version 1.1: 2011-07-13
Changes: Version format compliance - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
