Download MendeleyCrystal structure of the bacterial A1408U-mutant ribosomal decoding site (C2 form 2)
Kondo, J., Koganei, M.To be published.
4P43 | pdb_00004p43
Crystal structure of the bacterial A1408U-mutant ribosomal decoding site (C2 form 2)
- PDB DOI: https://doi.org/10.2210/pdb4P43/pdb
- NAKB: 4P43
- Classification: RNA
- Organism(s): synthetic construct
- Mutation(s): No
- Deposited: 2014-03-11 Released: 2016-05-04
- Funding Organization(s): MEXT
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.270 (Depositor), 0.270 (DCC)
- R-Value Work: 0.246 (Depositor), 0.250 (DCC)
wwPDB Validation 3D Report Full Report
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 | |
| 5'-R(*UP*UP*GP*CP*GP*UP*CP*UP*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 | |
| CA Query on CA | C [auth A], E [auth B] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |  | ||
| NA Query on NA | D [auth A], F [auth B] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.270 (Depositor), 0.270 (DCC)
- R-Value Work: 0.246 (Depositor), 0.250 (DCC)
Space Group: C 1 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 86.45 | α = 90 |
| b = 31.69 | β = 116.34 |
| c = 49.41 | γ = 90 |
| Software Name | Purpose |
|---|---|
| CrystalClear | data collection |
| PHENIX | phasing |
| CNS | refinement |
| PDB_EXTRACT | data extraction |
| d*TREK | data reduction |
| d*TREK | data scaling |
Entry History & Funding Information
Deposition Data
- Released Date: 2016-05-04 Deposition Author(s): Kondo, J., Koganei, M.
| Funding Organization | Location | Grant Number |
|---|---|---|
| MEXT | Japan | 23790054 |
Revision History (Full details and data files)
- Version 1.0: 2016-05-04
Type: Initial release - Version 1.1: 2023-12-27
Changes: Data collection, Database references, Derived calculations
