[English] 日本語
![](img/lk-miru.gif)
- PDB-6laz: the wildtype SAM-VI riboswitch bound to a N-mustard SAM analog M1 -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6laz | ||||||
---|---|---|---|---|---|---|---|
Title | the wildtype SAM-VI riboswitch bound to a N-mustard SAM analog M1 | ||||||
![]() |
| ||||||
![]() | RNA / Riboswitch / SAM / SAM-VI | ||||||
Function / homology | ![]() U1 snRNP binding / U1 snRNP / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / mRNA Splicing - Major Pathway / spliceosomal complex / mRNA splicing, via spliceosome / DNA binding / RNA binding / nucleoplasm ...U1 snRNP binding / U1 snRNP / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / mRNA Splicing - Major Pathway / spliceosomal complex / mRNA splicing, via spliceosome / DNA binding / RNA binding / nucleoplasm / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ren, A. / Sun, A. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: SAM-VI riboswitch structure and signature for ligand discrimination. Authors: Sun, A. / Gasser, C. / Li, F. / Chen, H. / Mair, S. / Krasheninina, O. / Micura, R. / Ren, A. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 132.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 98 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 16.4 KB | Display | |
Data in CIF | ![]() | 23 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6lasSC ![]() 6lauC ![]() 6laxC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
3 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: RNA chain | Mass: 17896.502 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() #2: Protein | Mass: 10796.682 Da / Num. of mol.: 3 / Mutation: Y31H, Q36R, S46K Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Chemical | ChemComp-MG / | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.17 Å3/Da / Density % sol: 61.19 % |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 0.1 M sodium acetate trihydrate pH 4.6, 10% w/v polyethylene glycol 4,000 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 22, 2019 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.102 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.76→42.67 Å / Num. obs: 20968 / % possible obs: 94.8 % / Redundancy: 6.9 % / Biso Wilson estimate: 73.11 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.031 / Rrim(I) all: 0.081 / Net I/σ(I): 15.9 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 6LAS Resolution: 2.76→42.67 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 26.38
| ||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 167.21 Å2 / Biso mean: 79.1927 Å2 / Biso min: 42.83 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.76→42.67 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
|