Download MendeleyCrystal structure of the eukaryotic ribosomal decoding site in complex with G418 and Hg(II)
Kondo, J., Suzuki, C.To be published.
7EDM | pdb_00007edm
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 (Depositor), 0.240 (DCC)
- R-Value Work: 0.164 (Depositor), 0.170 (DCC)
- R-Value Observed: 0.170 (Depositor)
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 (Depositor), 0.240 (DCC)
- R-Value Work: 0.164 (Depositor), 0.170 (DCC)
- R-Value Observed: 0.170 (Depositor)
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
