Download MendeleyCrystal structure of the adenylation domain from an epsilon-poly-l-lysine synthetase provides molecular mechanism for substrate specificity
Okamoto, T., Yamanaka, K., Hamano, Y., Nagano, S., Hino, T.(2022) Biochem Biophys Res Commun 596: 43-48
7WEW
Structure of adenylation domain of epsilon-poly-L-lysine synthase
- PDB DOI: https://doi.org/10.2210/pdb7WEW/pdb
- Classification: LIGASE
- Organism(s): Streptomyces noursei
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2021-12-24 Released: 2022-02-09
- Funding Organization(s): Japan Society for the Promotion of Science (JSPS)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.30 Å
- R-Value Free: 0.220
- R-Value Work: 0.187
- R-Value Observed: 0.189
This is version 1.1 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 |
| Epsilon-poly-L-lysine synthase | 509 | Streptomyces noursei | Mutation(s): 0 Gene Names: pls |  | |
UniProt | |||||
Find proteins for B5BR95 (Streptomyces noursei) Explore B5BR95 Go to UniProtKB: B5BR95 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | B5BR95 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| LAD (Subject of Investigation/LOI) Query on LAD | K [auth A] | ADENOSINE-5'-[LYSYL-PHOSPHATE] C16 H26 N7 O8 P RZWIOOBQBMRZTQ-OPYVMVOTSA-N |  | ||
| SO4 Query on SO4 | B [auth A] C [auth A] D [auth A] E [auth A] F [auth A] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
| GOL Query on GOL | H [auth A], I [auth A], J [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.30 Å
- R-Value Free: 0.220
- R-Value Work: 0.187
- R-Value Observed: 0.189
- Space Group: P 3 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 152.511 | α = 90 |
| b = 152.511 | β = 90 |
| c = 48.202 | γ = 120 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| XDS | data reduction |
| Aimless | data scaling |
| PHASER | phasing |
| Coot | model building |
Entry History & Funding Information
Deposition Data
- Released Date: 2022-02-09 Deposition Author(s): Okamoto, T., Yamanaka, K., Hamano, Y., Nagano, S., Hino, T.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Japan Society for the Promotion of Science (JSPS) | Japan | 20H02918 |
| Japan Society for the Promotion of Science (JSPS) | Japan | 16H06445 |
| Japan Society for the Promotion of Science (JSPS) | Japan | 19K06551 |
Revision History (Full details and data files)
- Version 1.0: 2022-02-09
Type: Initial release - Version 1.1: 2023-11-29
Changes: Data collection, Refinement description
