Download MendeleyCrystal structure of tetrameric pyridoxal 4-dehydrogenase from Mesorhizobium loti
Chu, H.N., Kobayashi, J., Yoshikane, Y., Mikami, B., Yagi, T.To be published.
3NDR
Crystal structure of tetrameric pyridoxal 4-dehydrogenase from Mesorhizobium loti
- PDB DOI: https://doi.org/10.2210/pdb3NDR/pdb
- Classification: OXIDOREDUCTASE
- Organism(s): Mesorhizobium loti
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2010-06-08 Released: 2011-06-08
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.88 Å
- R-Value Free: 0.248
- R-Value Work: 0.185
- R-Value Observed: 0.188
This is version 1.3 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 |
| 3-oxoacyl-(Acyl-carrier protein) reductase | 247 | Mesorhizobium loti | Mutation(s): 0 Gene Names: mlr6807, pldh-t EC: 1.1.1.107 |  | |
UniProt | |||||
Find proteins for Q988B7 (Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099)) Explore Q988B7 Go to UniProtKB: Q988B7 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q988B7 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| NAD Query on NAD | E [auth A], F [auth B], G [auth C], H [auth D] | NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| MSE Query on MSE | A, B, C, D | L-PEPTIDE LINKING | C5 H11 N O2 Se |  | MET |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.88 Å
- R-Value Free: 0.248
- R-Value Work: 0.185
- R-Value Observed: 0.188
- Space Group: P 1 21 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 86.203 | α = 90 |
| b = 51.109 | β = 89.36 |
| c = 91.732 | γ = 90 |
| Software Name | Purpose |
|---|---|
| HKL-2000 | data collection |
| PHENIX | refinement |
Entry History
Deposition Data
- Released Date: 2011-06-08 Deposition Author(s): Chu, H.N.
Revision History (Full details and data files)
- Version 1.0: 2011-06-08
Type: Initial release - Version 1.1: 2011-07-13
Changes: Version format compliance - Version 1.2: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description - Version 1.3: 2023-11-22
Changes: Data collection
