Download MendeleyCrystal structure of AtoDA complex
Arbing, M.A., Koo, C.W., Shin, A., Medrano-Soto, A., Eisenberg, D.To be published.
5DBN
Crystal structure of AtoDA complex
- PDB DOI: https://doi.org/10.2210/pdb5DBN/pdb
- Classification: TRANSFERASE
- Organism(s): Escherichia coli DH5[alpha]
- Expression System: Escherichia coli BL21(DE3), Escherichia coli BL21
- Mutation(s): No
- Deposited: 2015-08-21 Released: 2016-08-24
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.55 Å
- R-Value Free: 0.221
- R-Value Work: 0.188
- R-Value Observed: 0.189
wwPDB Validation 3D Report Full Report
This is version 1.2 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 |
| Acetate CoA-transferase subunit alpha | 221 | Escherichia coli DH5[alpha] | Mutation(s): 0 Gene Names: atoD, b2221, JW2215 EC: 2.8.3.8 |  | |
UniProt | |||||
Find proteins for P76458 (Escherichia coli (strain K12)) Explore P76458 Go to UniProtKB: P76458 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P76458 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Acetate CoA-transferase subunit beta | 223 | Escherichia coli DH5[alpha] | Mutation(s): 0 Gene Names: atoA, b2222, JW2216 EC: 2.8.3.8 |  | |
UniProt | |||||
Find proteins for P76459 (Escherichia coli (strain K12)) Explore P76459 Go to UniProtKB: P76459 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P76459 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| PEG Query on PEG | J [auth B], K [auth B], M [auth C], P [auth F], S [auth H] | DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N |  | ||
| PO4 Query on PO4 | I [auth A], L [auth B], O [auth E], R [auth G], T [auth H] | PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K |  | ||
| GOL Query on GOL | Q [auth F] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| CL Query on CL | N [auth E] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.55 Å
- R-Value Free: 0.221
- R-Value Work: 0.188
- R-Value Observed: 0.189
- Space Group: P 1 21 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 73.68 | α = 90 |
| b = 175.68 | β = 113.01 |
| c = 76.16 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| XDS | data reduction |
| XSCALE | data scaling |
| PHASER | phasing |
| PDB_EXTRACT | data extraction |
Entry History
Deposition Data
- Released Date: 2016-08-24 Deposition Author(s): Arbing, M.A., Koo, C.W., Shin, A., Medrano-Soto, A., Eisenberg, D.
Revision History (Full details and data files)
- Version 1.0: 2016-08-24
Type: Initial release - Version 1.1: 2019-11-27
Changes: Author supporting evidence, Derived calculations - Version 1.2: 2023-09-27
Changes: Data collection, Database references, Refinement description
