Download MendeleyCrystal structure of putative mandelate racemase from Bordetella bronchiseptica RB50 complexed with 2-oxoglutarate/phosphate
Malashkevich, V.N., Patskovsky, Y., Ramagopal, U., Toro, R., Sauder, J.M., Burley, S.K., Almo, S.C.To be published.
3OP2
Crystal structure of putative mandelate racemase from Bordetella bronchiseptica RB50 complexed with 2-oxoglutarate/phosphate
- PDB DOI: https://doi.org/10.2210/pdb3OP2/pdb
- Classification: ISOMERASE
- Organism(s): Bordetella bronchiseptica
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2010-08-31 Released: 2010-09-15
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.222
- R-Value Work: 0.183
- R-Value Observed: 0.185
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 |
| Putative mandelate racemase | 397 | Bordetella bronchiseptica | Mutation(s): 0 Gene Names: BB4687 |  | |
UniProt | |||||
Find proteins for A0A0H3LT39 (Bordetella bronchiseptica (strain ATCC BAA-588 / NCTC 13252 / RB50)) Explore A0A0H3LT39 Go to UniProtKB: A0A0H3LT39 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A0A0H3LT39 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| AKG Query on AKG | D [auth A] | 2-OXOGLUTARIC ACID C5 H6 O5 KPGXRSRHYNQIFN-UHFFFAOYSA-N |  | ||
| PO4 Query on PO4 | F [auth B] | PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K |  | ||
| MG Query on MG | C [auth A], E [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: 2.00 Å
- R-Value Free: 0.222
- R-Value Work: 0.183
- R-Value Observed: 0.185
- Space Group: I 4
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 117.55 | α = 90 |
| b = 117.55 | β = 90 |
| c = 123.21 | γ = 90 |
| Software Name | Purpose |
|---|---|
| SCALEPACK | data scaling |
| PHASER | phasing |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| CBASS | data collection |
| HKL-2000 | data reduction |
Entry History
Deposition Data
- Released Date: 2010-09-15 Deposition Author(s): Malashkevich, V.N., Patskovsky, Y., Ramagopal, U., Toro, R., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)
Revision History (Full details and data files)
- Version 1.0: 2010-09-15
Type: Initial release - Version 1.1: 2011-07-13
Changes: Version format compliance - Version 1.2: 2018-11-21
Changes: Data collection, Structure summary - Version 1.3: 2021-02-10
Changes: Database references, Derived calculations, Structure summary - Version 1.4: 2023-09-06
Changes: Data collection, Database references, Refinement description - Version 1.5: 2023-12-06
Changes: Data collection
