Download MendeleyCRYSTAL STRUCTURE OF L-RHAMNONATE DEHYDRATASE FROM AZOTOBACTER VINELANDII complexed with Mg and L-TARTRATE
Fedorov, A.A., Fedorov, E.V., Sauder, J.M., Burley, S.K., Gerlt, J.A., Almo, S.C.To be published.
3EKG
CRYSTAL STRUCTURE OF L-RHAMNONATE DEHYDRATASE FROM AZOTOBACTER VINELANDII complexed with Mg and L-TARTRATE
- PDB DOI: https://doi.org/10.2210/pdb3EKG/pdb
- Classification: LYASE
- Organism(s): Azotobacter vinelandii DJ
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2008-09-19 Released: 2008-09-30
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.60 Å
- R-Value Free: 0.214
- R-Value Work: 0.196
- R-Value Observed: 0.196
wwPDB Validation 3D Report Full Report
This is version 1.5 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 |
| Mandelate racemase/muconate lactonizing enzyme | 404 | Azotobacter vinelandii DJ | Mutation(s): 0 Gene Names: AvinDRAFT_6446 |  | |
UniProt | |||||
Find proteins for C1DMY1 (Azotobacter vinelandii (strain DJ / ATCC BAA-1303)) Explore C1DMY1 Go to UniProtKB: C1DMY1 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | C1DMY1 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| TLA Query on TLA | C [auth A], E [auth B] | L(+)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-JCYAYHJZSA-N |  | ||
| MG Query on MG | D [auth A], F [auth B] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| MSE Query on MSE | A, B | L-PEPTIDE LINKING | C5 H11 N O2 Se |  | MET |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.60 Å
- R-Value Free: 0.214
- R-Value Work: 0.196
- R-Value Observed: 0.196
- Space Group: I 4
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 119.326 | α = 90 |
| b = 119.326 | β = 90 |
| c = 116.696 | γ = 90 |
| Software Name | Purpose |
|---|---|
| ADSC | data collection |
| BALBES | phasing |
| CNS | refinement |
| DENZO | data reduction |
| SCALEPACK | data scaling |
Entry History
Deposition Data
- Released Date: 2008-09-30 Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Sauder, J.M., Burley, S.K., Gerlt, J.A., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)
Revision History (Full details and data files)
- Version 1.0: 2008-09-30
Type: Initial release - Version 1.1: 2011-07-13
Changes: Version format compliance - Version 1.2: 2018-11-14
Changes: Data collection, Structure summary - Version 1.3: 2021-02-10
Changes: Database references, Derived calculations, Structure summary - Version 1.4: 2023-08-30
Changes: Data collection, Database references, Refinement description - Version 1.5: 2023-11-15
Changes: Data collection
