Download MendeleyCrystal structure of catechol 1,2-dioxygenase from Burkholderia ambifaria
Phan, J.N., Dranow, D.M., Lorimer, D., Edwards, T.E.To be published.
5VXT
Crystal structure of catechol 1,2-dioxygenase from Burkholderia ambifaria
- PDB DOI: https://doi.org/10.2210/pdb5VXT/pdb
- Classification: OXIDOREDUCTASE
- Organism(s): Burkholderia ambifaria MC40-6
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2017-05-24 Released: 2017-06-14
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.75 Å
- R-Value Free: 0.224
- R-Value Work: 0.186
- R-Value Observed: 0.187
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 | 325 | Burkholderia ambifaria MC40-6 | Mutation(s): 0 Gene Names: BamMC406_6300 |  | |
UniProt | |||||
Find proteins for B1Z4S0 (Burkholderia ambifaria (strain MC40-6)) Explore B1Z4S0 Go to UniProtKB: B1Z4S0 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | B1Z4S0 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 5 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| PTY Query on PTY | C [auth A], I [auth B] | PHOSPHATIDYLETHANOLAMINE C40 H80 N O8 P NJGIRBISCGPRPF-KXQOOQHDSA-N |  | ||
| CAQ Query on CAQ | E [auth A], K [auth B] | CATECHOL C6 H6 O2 YCIMNLLNPGFGHC-UHFFFAOYSA-N |  | ||
| EDO Query on EDO | F [auth A], G [auth A], L [auth B], M [auth B] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | ||
| FE Query on FE | D [auth A], J [auth B] | FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N |  | ||
| CL Query on CL | H [auth A] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.75 Å
- R-Value Free: 0.224
- R-Value Work: 0.186
- R-Value Observed: 0.187
- Space Group: P 1 21 1
- Diffraction Data: https://doi.org/10.18430/M35VXT
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 66.08 | α = 90 |
| b = 52.2 | β = 106.62 |
| c = 105.19 | γ = 90 |
| Software Name | Purpose |
|---|---|
| XSCALE | data scaling |
| MOLREP | phasing |
| PHENIX | refinement |
| PDB_EXTRACT | data extraction |
| XDS | data reduction |
| Coot | model building |
Entry History
Deposition Data
- Released Date: 2017-06-14 Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Revision History (Full details and data files)
- Version 1.0: 2017-06-14
Type: Initial release - Version 1.1: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description
