[English] 日本語
![](img/lk-miru.gif)
- PDB-1kxk: Crystal Structure of a RNA Molecule Containing Domain 5 and 6 of ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1kxk | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of a RNA Molecule Containing Domain 5 and 6 of the Yeast ai5g Group II Self-splicing Intron | ||||||
![]() | ai5g group II Self-splicing intron | ||||||
![]() | RNA / double helix / tetraloop / tetraloop receptor / two-nucleotide bulge | ||||||
Function / homology | RNA / RNA (> 10)![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhang, L. / Doudna, J.A. | ||||||
![]() | ![]() Title: Structural insights into group II intron catalysis and branch-site selection. Authors: Zhang, L. / Doudna, J.A. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 46.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 34.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 382.3 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 386.8 KB | Display | |
Data in XML | ![]() | 4.4 KB | Display | |
Data in CIF | ![]() | 5.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: RNA chain | Mass: 22620.477 Da / Num. of mol.: 1 / Fragment: domain 5 and 6 / Source method: obtained synthetically Details: THE SEQUENCE IS FROM Saccharomyces cerevisiae (yeast). in vitro transcription. |
---|---|
#2: Chemical |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 6.23 Å3/Da / Density % sol: 80.26 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: HEPES-KOH, magnesium chloride, ammonium sulfate, spermine, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 25 ℃ | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source |
| ||||||||||||||||||
Detector |
| ||||||||||||||||||
Radiation |
| ||||||||||||||||||
Radiation wavelength |
| ||||||||||||||||||
Reflection | Resolution: 3→30 Å / Num. all: 12289 / Num. obs: 10014 / % possible obs: 81.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 15.5 % / Rsym value: 0.054 / Net I/σ(I): 23.4 | ||||||||||||||||||
Reflection shell | Resolution: 3→3.11 Å / Mean I/σ(I) obs: 3 / Rsym value: 0.43 / % possible all: 51.7 | ||||||||||||||||||
Reflection | *PLUS Lowest resolution: 30 Å / % possible obs: 85.8 % / Rmerge(I) obs: 0.054 | ||||||||||||||||||
Reflection shell | *PLUS % possible obs: 51.7 % / Rmerge(I) obs: 0.43 |
-
Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→30 Å
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 3→3.11 Å
| |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 30 Å | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
| |||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor obs: 0.4186 |