Download MendeleyInsights into product binding in sucrose isomerases from crystal structures of MutB from Rhizobium sp.
Lipski, A., Watzlawick, H., Ravaud, S., Robert, X., Haser, R., Mattes, R., Aghajari, N.To be published.
4H8U
MUTB inactive double mutant D200A-D415N soaked with sucrose and having as bound ligands sucrose in molecule A and the reaction product trehalulose in molecule B
- PDB DOI: 10.2210/pdb4H8U/pdb
- Classification: ISOMERASE
- Organism(s): Rhizobium sp. MX-45
- Expression System: Escherichia coli
- Mutation(s): Yes
- Deposited: 2012-09-24 Released: 2013-09-25
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.257
- R-Value Work: 0.189
- R-Value Observed: 0.192
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 |
| Sucrose isomerase | A, B | 557 | Rhizobium sp. MX-45 | Mutation(s): 2 Gene Names: mutB |  |
UniProt | |||||
Find proteins for M1E1F6 (Rhizobium sp. MX-45) Explore M1E1F6 Go to UniProtKB: M1E1F6 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | M1E1F6 | ||||
Protein Feature ViewExpand | |||||
| |||||
Oligosaccharides
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Chain Length | 2D Diagram | Glycosylation | 3D Interactions |
| beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose | C | 2 |  | N/A | Oligosaccharides Interaction |
Glycosylation Resources | |||||
GlyTouCan: G05551OP GlyCosmos: G05551OP | |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| TEU Query on TEU | F [auth B] | 1-O-alpha-D-glucopyranosyl-D-fructose C12 H22 O11 NMELTECMHKKXLF-DGQJZECASA-N |  | Ligand Interaction | |
| GOL Query on GOL | D [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | Ligand Interaction | |
| CA Query on CA | E [auth A], G [auth B] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |  | Ligand Interaction | |
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| ID | Chains | Name | Type/Class | 2D Diagram | 3D Interactions |
| PRD_900003 Query on PRD_900003 | C | sucrose | Oligosaccharide / Nutrient |  | Ligand Interaction |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.257
- R-Value Work: 0.189
- R-Value Observed: 0.192
- Space Group: P 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 64.37 | α = 66.15 |
| b = 73.68 | β = 74.29 |
| c = 82.67 | γ = 72.42 |
| Software Name | Purpose |
|---|---|
| ADSC | data collection |
| REFMAC | refinement |
| XDS | data reduction |
| XSCALE | data scaling |
| REFMAC | phasing |
Entry History
Deposition Data
- Released Date: 2013-09-25 Deposition Author(s): Lipski, A., Haser, R., Aghajari, N.
Revision History (Full details and data files)
- Version 1.0: 2013-09-25
Type: Initial release - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
