[English] 日本語
![](img/lk-miru.gif)
- PDB-8olv: Structure of Oceanobacillus iheyensis group II intron in the pres... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8olv | |||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Mg2+ and ARN25850 | |||||||||||||||||||||||||||
![]() | Group IIC intron | |||||||||||||||||||||||||||
![]() | RNA / RIBOZYME / METALLOENZYME / SELF-SPLICING / RETROTRANSPOSITION | |||||||||||||||||||||||||||
Function / homology | : / SPERMINE / : / RNA / RNA (> 10) / RNA (> 100)![]() | |||||||||||||||||||||||||||
Biological species | ![]() | |||||||||||||||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||||||||||||||
![]() | Silvestri, I. / Marcia, M. | |||||||||||||||||||||||||||
Funding support | ![]() ![]()
| |||||||||||||||||||||||||||
![]() | ![]() Title: Targeting the conserved active site of splicing machines with specific and selective small molecule modulators Authors: Silvestri, I. / Manigrasso, J. / Andreani, A. / Brindani, N. / Mas, C. / Reiser, J.B. / Vidossich, P. / Martino, G. / McCarthy, A. / De Vivo, M. / Marcia, M. | |||||||||||||||||||||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 236.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 175.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 787.4 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 816.5 KB | Display | |
Data in XML | ![]() | 16.7 KB | Display | |
Data in CIF | ![]() | 24.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8olsC ![]() 8olwC ![]() 8olyC ![]() 8olzC ![]() 8om0C ![]() 8ruhC ![]() 8ruiC ![]() 8rujC ![]() 8rukC ![]() 8rulC ![]() 8rumC ![]() 8runC C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-RNA chain , 1 types, 1 molecules A
#1: RNA chain | Mass: 127991.789 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
---|
-Non-polymers , 6 types, 54 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/K.gif)
![](data/chem/img/SPM.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/K.gif)
![](data/chem/img/SPM.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-K / #4: Chemical | ChemComp-SPM / | #5: Chemical | #6: Chemical | ChemComp-VTR / | Mass: 568.212 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H20Br2N2O6 / Feature type: SUBJECT OF INVESTIGATION #7: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.75 Å3/Da / Density % sol: 67.18 % |
---|---|
Crystal grow | Temperature: 303.15 K / Method: vapor diffusion, hanging drop Details: 100 mM magnesium acetate, 100 mM potassium chloride, 10 mM lithium chloride, 50 mM HEPES sodium, pH 7.0, 3.5% PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: May 9, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→48.42 Å / Num. obs: 46958 / % possible obs: 97.9 % / Redundancy: 12.4 % / CC1/2: 1 / Rmerge(I) obs: 0.11 / Net I/σ(I): 11.97 |
Reflection shell | Resolution: 2.8→2.9 Å / Num. unique obs: 4256 / CC1/2: 0.083 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.81→48.42 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.811→2.884 Å / Total num. of bins used: 20
|