Download MendeleyCrystal structure of NADPH-dependent 2-hydroxyacid dehydrogenase from Rhizobium etli CFN 42 in complex with NADPH and oxalate
Matelska, D., Shabalin, I.G., Kutner, J., Handing, K.B., Gasiorowska, O.A., Cooper, D.R., Minor, W.To be published.
5TSD
Crystal structure of NADPH-dependent 2-hydroxyacid dehydrogenase from Rhizobium etli CFN 42 in complex with NADPH and oxalate
- PDB DOI: https://doi.org/10.2210/pdb5TSD/pdb
- Classification: OXIDOREDUCTASE
- Organism(s): Rhizobium etli CFN 42
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2016-10-28 Released: 2016-11-16
- Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.90 Å
- R-Value Free: 0.198
- R-Value Work: 0.155
- R-Value Observed: 0.157
Starting Model: experimental
View more details
This is version 1.4 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 |
| Probable hydroxyacid dehydrogenase protein | 322 | Rhizobium etli CFN 42 | Mutation(s): 0 Gene Names: RHE_CH00179 |  | |
UniProt | |||||
Find proteins for Q2KDT2 (Rhizobium etli (strain ATCC 51251 / DSM 11541 / JCM 21823 / NBRC 15573 / CFN 42)) Explore Q2KDT2 Go to UniProtKB: Q2KDT2 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q2KDT2 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| NDP Query on NDP | C [auth A], E [auth B] | NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H30 N7 O17 P3 ACFIXJIJDZMPPO-NNYOXOHSSA-N |  | ||
| OXD Query on OXD | D [auth A], F [auth B] | OXALIC ACID C2 H2 O4 MUBZPKHOEPUJKR-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.90 Å
- R-Value Free: 0.198
- R-Value Work: 0.155
- R-Value Observed: 0.157
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 68.945 | α = 90 |
| b = 70.124 | β = 90 |
| c = 126.615 | γ = 90 |
| Software Name | Purpose |
|---|---|
| MD2 | data collection |
| HKL-3000 | phasing |
| HKL-3000 | data scaling |
| MOLREP | phasing |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| DENZO | data reduction |
| SCALEPACK | data scaling |
Entry History & Funding Information
Deposition Data
- Released Date: 2016-11-16 Deposition Author(s): Matelska, D., Shabalin, I.G., Kutner, J., Handing, K.B., Gasiorowska, O.A., Cooper, D.R., Minor, W., New York Structural Genomics Research Consortium (NYSGRC)
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | United States | -- |
Revision History (Full details and data files)
- Version 1.0: 2016-11-16
Type: Initial release - Version 1.1: 2017-09-20
Changes: Author supporting evidence, Derived calculations, Refinement description - Version 1.2: 2020-01-01
Changes: Author supporting evidence - Version 1.3: 2022-04-13
Changes: Database references, Structure summary - Version 1.4: 2023-10-04
Changes: Data collection, Refinement description
