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- PDB-5ns4: Crystal structures of Cy3 cyanine fluorophores stacked onto the e... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ns4 | ||||||
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Title | Crystal structures of Cy3 cyanine fluorophores stacked onto the end of double-stranded RNA | ||||||
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![]() | RNA BINDING PROTEIN / Cy3 / fluorophores / RNA | ||||||
Function / homology | ![]() cytosolic large ribosomal subunit / tRNA binding / rRNA binding / structural constituent of ribosome / translation Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Liu, Y.J. / Lilley, D.M.J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal Structures of Cyanine Fluorophores Stacked onto the End of Double-Stranded RNA. Authors: Liu, Y. / Lilley, D.M.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 110.2 KB | Display | ![]() |
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PDB format | ![]() | 79.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 797.9 KB | Display | ![]() |
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Full document | ![]() | 803.2 KB | Display | |
Data in XML | ![]() | 15.8 KB | Display | |
Data in CIF | ![]() | 22 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ns3C ![]() 1mjiS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 20590.947 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: RNA chain | Mass: 10527.345 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-96T / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.73 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop Details: 50 mM sodium cacodylate at pH 6.5, 100 mM Mg(CH3COO)2, 50 mM KF, 15% PEG 8000 drop |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 22, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979601 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→46.88 Å / Num. obs: 23654 / % possible obs: 100 % / Redundancy: 4.4 % / Biso Wilson estimate: 48.88 Å2 / Rmerge(I) obs: 0.09978 / Rrim(I) all: 0.1141 / Net I/σ(I): 12.48 |
Reflection shell | Resolution: 2.4→2.486 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.162 / Mean I/σ(I) obs: 6.26 / Num. unique obs: 2309 / Rrim(I) all: 0.1834 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1MJI Resolution: 2.4→46.88 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 112.67 Å2 / Biso mean: 37.1008 Å2 / Biso min: 20 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.4→46.88 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: 9
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