[English] 日本語
![](img/lk-miru.gif)
- PDB-5ueg: RNA primer-template complex with guanosine dinucleotide G(5')pppp... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5ueg | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | RNA primer-template complex with guanosine dinucleotide G(5')pppp(5')G ligand | ||||||||||||||||||||
![]() | RNA (5'-R(*![]() RNA / dinucleotide | Function / homology | Chem-86P / RNA / RNA (> 10) | ![]() Biological species | synthetic construct (others) | Method | ![]() ![]() ![]() ![]() Zhang, W. / Tam, C.P. / Szostak, J.W. | ![]() ![]() Title: Insight into the mechanism of nonenzymatic RNA primer extension from the structure of an RNA-GpppG complex. Authors: Zhang, W. / Tam, C.P. / Walton, T. / Fahrenbach, A.C. / Birrane, G. / Szostak, J.W. History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 53.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 43 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.8 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 3.8 MB | Display | |
Data in XML | ![]() | 11.7 KB | Display | |
Data in CIF | ![]() | 13.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5uedC ![]() 5ueeC ![]() 5uefC ![]() 5dhcS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: RNA chain | Mass: 4500.794 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Chemical | ChemComp-86P / [[( |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.08 Å3/Da / Density % sol: 60.08 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.05 M Magnesium chloride, 1.2 M Lithium sulfate, 50 mM MES pH 6.5, 2 mM Cobalt (II) chloride |
-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: 0.995 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 6425 / % possible obs: 96.6 % / Redundancy: 5.1 % / CC1/2: 0.978 / Rmerge(I) obs: 0.1 / Net I/σ(I): 15.14 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.554 / Mean I/σ(I) obs: 1.26 / CC1/2: 0.916 / % possible all: 74.8 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 5dhc Resolution: 2.6→50 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.912 / SU B: 18.124 / SU ML: 0.337 / Cross valid method: THROUGHOUT / ESU R Free: 0.418 / 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: 84.063 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.6→50 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|