Download MendeleyCrystal Structure of Glycosyltransferase VinC Involved in the Biosynthesis of Vicenistatin
Nango, E., Minami, A., Kumasaka, T., Eguchi, T.To be published.
3WAG | pdb_00003wag
Crystal structure of glycosyltransferase VinC in complex with DTDP
- PDB DOI: https://doi.org/10.2210/pdb3WAG/pdb
- Classification: TRANSFERASE
- Organism(s): Streptomyces halstedii
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2013-05-02 Released: 2014-06-04
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.10 Å
- R-Value Free: 0.256 (Depositor), 0.260 (DCC)
- R-Value Work: 0.191 (Depositor), 0.190 (DCC)
- R-Value Observed: 0.194 (Depositor)
Starting Model: experimental
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This is version 1.1 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 |
| Glycosyltransferase | 419 | Streptomyces halstedii | Mutation(s): 0 Gene Names: vinC |  | |
UniProt | |||||
Find proteins for Q76KZ6 (Streptomyces halstedii) Explore Q76KZ6 Go to UniProtKB: Q76KZ6 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q76KZ6 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| TYD Query on TYD | C [auth A], F [auth B] | THYMIDINE-5'-DIPHOSPHATE C10 H16 N2 O11 P2 UJLXYODCHAELLY-XLPZGREQSA-N |  | ||
| PO4 Query on PO4 | D [auth A], G [auth B], H [auth B] | PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K |  | ||
| MG Query on MG | E [auth A] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.10 Å
- R-Value Free: 0.256 (Depositor), 0.260 (DCC)
- R-Value Work: 0.191 (Depositor), 0.190 (DCC)
- R-Value Observed: 0.194 (Depositor)
Space Group: I 2 2 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 98.829 | α = 90 |
| b = 130.162 | β = 90 |
| c = 139.787 | γ = 90 |
| Software Name | Purpose |
|---|---|
| BSS | data collection |
| REFMAC | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| REFMAC | phasing |
Entry History
Deposition Data
- Released Date: 2014-06-04 Deposition Author(s): Nango, E., Minami, A., Kumasaka, T., Eguchi, T.
Revision History (Full details and data files)
- Version 1.0: 2014-06-04
Type: Initial release - Version 1.1: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description
