Download MendeleyCrystal structure of Catechol 1,2-dioxygenase from Burkholderia vietnamiensis
Conrady, D.G., Dranow, D.M., Lorimer, D., Edwards, T.E.To be published.
5TD3
Crystal structure of Catechol 1,2-dioxygenase from Burkholderia vietnamiensis
- PDB DOI: https://doi.org/10.2210/pdb5TD3/pdb
- Classification: OXIDOREDUCTASE
- Organism(s): Burkholderia vietnamiensis G4
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2016-09-16 Released: 2016-11-02
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.75 Å
- R-Value Free: 0.210
- R-Value Work: 0.177
- R-Value Observed: 0.178
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 |
| Catechol 1,2-dioxygenase | 322 | Burkholderia vietnamiensis G4 | Mutation(s): 0 Gene Names: Bcep1808_5824 EC: 1.13.11.1 |  | |
UniProt | |||||
Find proteins for A4JR51 (Burkholderia vietnamiensis (strain G4 / LMG 22486)) Explore A4JR51 Go to UniProtKB: A4JR51 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A4JR51 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 5 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| PTY Query on PTY | G [auth A], J [auth B] | PHOSPHATIDYLETHANOLAMINE C40 H80 N O8 P NJGIRBISCGPRPF-KXQOOQHDSA-N |  | ||
| ZN Query on ZN | C [auth A], K [auth B] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | ||
| EDO Query on EDO | E [auth A], H [auth A] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | ||
| CL Query on CL | F [auth A], I [auth A] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
| MG Query on MG | D [auth A] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.75 Å
- R-Value Free: 0.210
- R-Value Work: 0.177
- R-Value Observed: 0.178
- Space Group: C 1 2 1
- Diffraction Data: https://doi.org/10.18430/M35TD3
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 169.41 | α = 90 |
| b = 55.86 | β = 116.3 |
| c = 85.69 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| XSCALE | data scaling |
| PDB_EXTRACT | data extraction |
| MOLREP | phasing |
| XDS | data reduction |
Entry History
Deposition Data
- Released Date: 2016-11-02 Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Revision History (Full details and data files)
- Version 1.0: 2016-11-02
Type: Initial release - Version 1.1: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description
