Download MendeleyCharacterization of the Escherichia coli vitamin B6 salvage enzyme, pyridoxal reductase (PDXI)
Donkor, A.K., Musayev, F.N., Ghatge, M.S., Safo, M.K., Di Salvo, M.L., Contestabile, R.To be published.
8TF1
Crystal Structure of Pyridoxal Reductase (PDXI)in complex with NADPH and Pyridoxal
- PDB DOI: https://doi.org/10.2210/pdb8TF1/pdb
- Classification: OXIDOREDUCTASE
- Organism(s): Escherichia coli
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2023-07-07 Released: 2024-12-18
- Funding Organization(s): National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.237
- R-Value Work: 0.179
- R-Value Observed: 0.181
Starting Model: experimental
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This is version 1.0 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 |
| Pyridoxine 4-dehydrogenase | 306 | Escherichia coli | Mutation(s): 0 Gene Names: pdxI EC: 1.1.1.65 |  | |
UniProt | |||||
Find proteins for P25906 (Escherichia coli (strain K12)) Explore P25906 Go to UniProtKB: P25906 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P25906 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| NAP Query on NAP | B [auth A] | NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N |  | ||
| UEG (Subject of Investigation/LOI) Query on UEG | C [auth A] | 4,5-bis(hydroxymethyl)-2-methyl-pyridin-3-ol C8 H11 N O3 LXNHXLLTXMVWPM-UHFFFAOYSA-N |  | ||
| MG Query on MG | D [auth A] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.237
- R-Value Work: 0.179
- R-Value Observed: 0.181
- Space Group: P 21 21 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 91.952 | α = 90 |
| b = 75.745 | β = 90 |
| c = 43.094 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| Aimless | data scaling |
| PHASER | phasing |
| CrysalisPro | data reduction |
Entry History & Funding Information
Deposition Data
- Released Date: 2024-12-18 Deposition Author(s): Donkor, A.K., Safo, M.K., Musayev, F.N.
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI) | United States | 1R61HL156158 |
Revision History (Full details and data files)
- Version 1.0: 2024-12-18
Type: Initial release
