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- PDB-6n5p: Structure of Human pir-miRNA-340 Apical Loop and One-base-pair Fu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6n5p | ||||||
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Title | Structure of Human pir-miRNA-340 Apical Loop and One-base-pair Fused to the YdaO Riboswitch Scaffold | ||||||
![]() | RNA (127-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 | ![]()
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![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 155.4 KB | Display | ![]() |
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PDB format | ![]() | 122.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 6.6 KB | Display | |
Data in CIF | ![]() | 8.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6n5kC ![]() 6n5nC ![]() 6n5oC ![]() 6n5qC ![]() 6n5sC ![]() 6n5tC ![]() 6wtlC ![]() 4qk8S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-RNA chain , 1 types, 1 molecules A
#1: RNA chain | Mass: 41183.305 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) |
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-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 / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.34 Å3/Da / Density % sol: 76.96 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 1.89 M (NH4)2SO4, 0.214 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 |
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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: 2.991→75.369 Å / Num. obs: 18192 / % possible obs: 99.9 % / Redundancy: 38.2 % / CC1/2: 1 / Rpim(I) all: 0.016 / Rrim(I) all: 0.101 / Net I/σ(I): 27.1 |
Reflection shell | Resolution: 2.991→3.1 Å / Redundancy: 35.7 % / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1819 / CC1/2: 0.848 / Rpim(I) all: 0.324 / Rrim(I) all: 2.02 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4QK8 Resolution: 2.991→75.369 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.91
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 401.54 Å2 / Biso mean: 113.5714 Å2 / Biso min: 24.29 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.991→75.369 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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