Download MendeleyCrystal structure of the eukaryotic ribosomal decoding site in complex with G418 and Hg(II)
Kondo, J., Suzuki, C.To be published.
7EDM
Crystal structure of the eukaryotic ribosomal decoding site in complex with G418 and Hg(II)
- PDB DOI: https://doi.org/10.2210/pdb7EDM/pdb
- NAKB: 7EDM
- Classification: RNA
- Organism(s): synthetic construct
- Mutation(s): No
- Deposited: 2021-03-16 Released: 2022-03-16
- Funding Organization(s): Ministry of Education, Culture, Sports, Science and Technology (Japan)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.81 Å
- R-Value Free: 0.229
- R-Value Work: 0.164
- R-Value Observed: 0.170
Starting Model: experimental
View more details
This is version 1.1 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| RNA (5'-R(P*UP*GP*CP*GP*UP*CP*GP*CP*GP*UP*CP*GP*AP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3') | 23 | synthetic construct |  | ||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| GET (Subject of Investigation/LOI) Query on GET | E [auth B], F [auth B] | GENETICIN C20 H40 N4 O10 BRZYSWJRSDMWLG-DJWUNRQOSA-N |  | ||
| HG (Subject of Investigation/LOI) Query on HG | C [auth A], D [auth A] | MERCURY (II) ION Hg BQPIGGFYSBELGY-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.81 Å
- R-Value Free: 0.229
- R-Value Work: 0.164
- R-Value Observed: 0.170
- Space Group: P 21 21 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 31.429 | α = 90 |
| b = 97.487 | β = 90 |
| c = 47.548 | γ = 90 |
| Software Name | Purpose |
|---|---|
| XSCALE | data scaling |
| PHENIX | refinement |
| XDS | data reduction |
| PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2022-03-16 Deposition Author(s): Kondo, J., Suzuki, C.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Ministry of Education, Culture, Sports, Science and Technology (Japan) | Japan | 24245037 |
Revision History (Full details and data files)
- Version 1.0: 2022-03-16
Type: Initial release - Version 1.1: 2023-11-29
Changes: Data collection, Refinement description
