Download MendeleyHierarchical Engineering of meso-Diaminopimelate Dehydrogenase for Efficient Synthesis of Bulky d-Amino Acids
Wei, Y., Geng, Q., Liu, H.P., Wang, Y.Q., Zhang, G.F., Qian, X.L., Yu, H.L., Xu, J.H., Zhang, Z.J.(2024) ACS Catal 14: 11447-11456
8ZMX | pdb_00008zmx
Crystal Structures of meso-diaminopimelate dehydrogenase from Bacillus thermozeamaize
- PDB DOI: https://doi.org/10.2210/pdb8ZMX/pdb
- Classification: OXIDOREDUCTASE
- Organism(s): Bacillus thermozeamaize
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): Yes
- Deposited: 2024-05-24 Released: 2024-11-13
- Funding Organization(s): National Natural Science Foundation of China (NSFC)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.46 Å
- R-Value Free: 0.275 (Depositor), 0.274 (DCC)
- R-Value Work: 0.225 (Depositor), 0.231 (DCC)
- R-Value Observed: 0.228 (Depositor)
Starting Model: experimental
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This is version 1.0 of the entry. See complete history.
Literature
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Meso-diaminopimelate D-dehydrogenase | 313 | Bacillus thermozeamaize | Mutation(s): 5 Gene Names: BAA01_00405 EC: 1.4.1.16 |  | |
UniProt | |||||
Find proteins for A0A1Y3PXT7 (Bacillus thermozeamaize) Explore A0A1Y3PXT7 Go to UniProtKB: A0A1Y3PXT7 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A0A1Y3PXT7 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| NAP Query on NAP | D [auth A], E [auth B], F [auth C] | NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.46 Å
- R-Value Free: 0.275 (Depositor), 0.274 (DCC)
- R-Value Work: 0.225 (Depositor), 0.231 (DCC)
- R-Value Observed: 0.228 (Depositor)
Space Group: P 43 21 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 157.09 | α = 90 |
| b = 157.09 | β = 90 |
| c = 111.45 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| XDS | data reduction |
| XDS | data scaling |
| PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2024-11-13 Deposition Author(s): Geng, Q., Wei, Y., Zhang, Z.J.
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Natural Science Foundation of China (NSFC) | China | 32071475 |
Revision History (Full details and data files)
- Version 1.0: 2024-11-13
Type: Initial release
