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 | pdb_00005tsd
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 (Depositor), 0.200 (DCC)
- R-Value Work: 0.155 (Depositor), 0.160 (DCC)
- R-Value Observed: 0.157 (Depositor)
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 (Depositor), 0.200 (DCC)
- R-Value Work: 0.155 (Depositor), 0.160 (DCC)
- R-Value Observed: 0.157 (Depositor)
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
