[English] 日本語
![](img/lk-miru.gif)
- PDB-6n5q: Structure of Human pir-miRNA-378a Apical Loop and One-base-pair F... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6n5q | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of Human pir-miRNA-378a Apical Loop and One-base-pair Fused to the YdaO Riboswitch Scaffold | ||||||
![]() | RNA (128-MER) | ||||||
![]() | RNA / microRNA / RNA processing / Protein-RNA interaction | ||||||
Function / homology | Chem-2BA / : / RNA / RNA (> 10) / RNA (> 100)![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Shoffner, G.M. / Peng, Z. / Guo, F. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Three-dimensional structures of pri-miRNA apical junctions and loops revealed by scaffold-directed crystallography Authors: Shoffner, G.M. / Peng, Z. / Guo, F. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 159.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 125.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 6.4 KB | Display | |
Data in CIF | ![]() | 8.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6n5kC ![]() 6n5nC ![]() 6n5oC ![]() 6n5pC ![]() 6n5sC ![]() 6n5tC ![]() 6wtlC ![]() 4qk8S C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-RNA chain , 1 types, 1 molecules A
#1: RNA chain | Mass: 41541.609 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: in vitro transcription vector pT7-Fluc(deltai) (others) |
---|
-Non-polymers , 5 types, 12 molecules ![](data/chem/img/2BA.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/K.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/K.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-K / | #5: Chemical | ChemComp-SO4 / | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 5.25 Å3/Da / Density % sol: 76.59 % |
---|---|
Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 1.63 M (NH4)2SO4, 0.272 M Li2SO4, and 0.1 M HEPES pH 7.4 Temp details: Room Temperature |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 20, 2017 |
Radiation | Monochromator: Water-cooled flat double Si(111) Khozu monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.116 Å / Relative weight: 1 |
Reflection | Resolution: 2.946→75.131 Å / Num. obs: 18836 / % possible obs: 99.8 % / Redundancy: 19.4 % / CC1/2: 1 / Rpim(I) all: 0.015 / Rrim(I) all: 0.067 / Net I/σ(I): 25.5 |
Reflection shell | Resolution: 2.95→3.05 Å / Redundancy: 18.9 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1884 / CC1/2: 0.84 / Rpim(I) all: 0.346 / Rrim(I) all: 1.54 / % possible all: 97.5 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 4QK8 Resolution: 2.946→75.131 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.85
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 330.83 Å2 / Biso mean: 117.2108 Å2 / Biso min: 51.23 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.946→75.131 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13
|