[English] 日本語
![](img/lk-miru.gif)
- PDB-5vci: RNA hairpin structure containing tetraloop/receptor motif, comple... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5vci | ||||||
---|---|---|---|---|---|---|---|
Title | RNA hairpin structure containing tetraloop/receptor motif, complexed with 2-MeImpG analogue | ||||||
![]() |
| ||||||
![]() | ![]() | ||||||
Function / homology | Chem-8OS / ![]() ![]() | ||||||
Biological species | synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Szostak, J.W. / Zhang, W. | ||||||
![]() | ![]() Title: Structural Rationale for the Enhanced Catalysis of Nonenzymatic RNA Primer Extension by a Downstream Oligonucleotide. Authors: Zhang, W. / Tam, C.P. / Zhou, L. / Oh, S.S. / Wang, J. / Szostak, J.W. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 31.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 19.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 5ux3C ![]() 5uz6C ![]() 5v0hC ![]() 5v0jC ![]() 5v0oC ![]() 5v9zC ![]() 5vcfC ![]() 5vgwC ![]() 6az4C ![]() 6bmdC ![]() 4fnjS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: RNA chain | Mass: 7112.306 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
---|---|
#2: RNA chain | Mass: 3765.256 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: Chemical | ChemComp-8OS / |
#4: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 61.5 % |
---|---|
Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 50 mM MgCl2, 0.2 M Lithium sulfate monohydrate, 0.1 M BIS-TRIS pH 7.0, 25% w/v Polyethylene glycol 3,350 |
-Data collection
Diffraction | Mean temperature: 99 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 28, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.6→50 Å / Num. obs: 3864 / % possible obs: 97.8 % / Redundancy: 3.2 % / CC1/2: 0.944 / Rmerge(I) obs: 0.054 / Rsym value: 0.052 / Χ2: 1.138 / Net I/σ(I): 18.45 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.526 / Mean I/σ(I) obs: 1.81 / Num. unique obs: 338 / CC1/2: 0.523 / Rsym value: 0.81 / Χ2: 1.09 / % possible all: 87.8 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() ![]() Starting model: 4FNJ Resolution: 2.6→45.91 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.968 / SU B: 12.887 / SU ML: 0.237 / Cross valid method: THROUGHOUT / ESU R: 0.47 / ESU R Free: 0.257 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 75.432 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.6→45.91 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|