Download MendeleyCrystal structure of 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase from Legionella pneumophila Philadelphia 1
Abendroth, J., Allaire, M., Mayclin, S.J., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.To be published.
6CKT
Crystal structure of 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase from Legionella pneumophila Philadelphia 1
- PDB DOI: https://doi.org/10.2210/pdb6CKT/pdb
- Classification: TRANSFERASE
- Organism(s): Legionella pneumophila subsp. pneumophila str. Philadelphia 1
- Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
- Mutation(s): No
- Deposited: 2018-02-28 Released: 2018-03-21
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 Å
- R-Value Free: 0.188
- R-Value Work: 0.157
- R-Value Observed: 0.160
wwPDB Validation 3D Report Full Report
This is version 1.2 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 |
| 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase | 284 | Legionella pneumophila subsp. pneumophila str. Philadelphia 1 | Mutation(s): 0 Gene Names: dapD, lpg0888 EC: 2.3.1.117 |  | |
UniProt | |||||
Find proteins for Q5ZX45 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)) Explore Q5ZX45 Go to UniProtKB: Q5ZX45 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q5ZX45 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| EDO Query on EDO | B [auth A], C [auth A], D [auth A] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 Å
- R-Value Free: 0.188
- R-Value Work: 0.157
- R-Value Observed: 0.160
- Space Group: H 3
- Diffraction Data: https://doi.org/10.18430/M36CKT
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 101.73 | α = 90 |
| b = 101.73 | β = 90 |
| c = 70.98 | γ = 120 |
| Software Name | Purpose |
|---|---|
| XDS | data reduction |
| XSCALE | data scaling |
| PHENIX | refinement |
| PDB_EXTRACT | data extraction |
| MoRDa | phasing |
| Coot | model building |
Entry History
Deposition Data
- Released Date: 2018-03-21 Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Revision History (Full details and data files)
- Version 1.0: 2018-03-21
Type: Initial release - Version 1.1: 2020-01-15
Changes: Data collection - Version 1.2: 2023-10-04
Changes: Data collection, Database references, Refinement description
