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- PDB-7oos: The crystal structure of a DNA:RNA hybrid duplex sequence CTTTTCTTTG -
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Open data
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Basic information
Entry | Database: PDB / ID: 7oos | |||||||||
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Title | The crystal structure of a DNA:RNA hybrid duplex sequence CTTTTCTTTG | |||||||||
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![]() | DNA-RNA HYBRID / Amide-LNA / duplex / DNA:RNA / unmodified | |||||||||
Function / homology | STRONTIUM ION / DNA / RNA![]() | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Thorpe, C. / Hardwick, J. / McDonough, M.A. / Hall, J.P. / Baker, Y.R. / El-Sagheer, A.H. / Brown, T. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: An LNA-amide modification that enhances the cell uptake and activity of phosphorothioate exon-skipping oligonucleotides. Authors: Baker, Y.R. / Thorpe, C. / Chen, J. / Poller, L.M. / Cox, L. / Kumar, P. / Lim, W.F. / Lie, L. / McClorey, G. / Epple, S. / Singleton, D. / McDonough, M.A. / Hardwick, J.S. / Christensen, K. ...Authors: Baker, Y.R. / Thorpe, C. / Chen, J. / Poller, L.M. / Cox, L. / Kumar, P. / Lim, W.F. / Lie, L. / McClorey, G. / Epple, S. / Singleton, D. / McDonough, M.A. / Hardwick, J.S. / Christensen, K.E. / Wood, M.J.A. / Hall, J.P. / El-Sagheer, A.H. / Brown, T. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 24.2 KB | Display | ![]() |
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PDB format | ![]() | 13 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 400.5 KB | Display | ![]() |
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Full document | ![]() | 402.2 KB | Display | |
Data in XML | ![]() | 3.3 KB | Display | |
Data in CIF | ![]() | 3.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7nrpSC ![]() 7oooC ![]() 7ozzC S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: RNA chain | Mass: 3255.076 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others) | ||||
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#2: DNA chain | Mass: 2953.035 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others) | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.26 Å3/Da / Density % sol: 62.24 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: Drop solution, 0.5 mM duplex, 20 mM Lithium chloride, 40 mM Strontium chloride hexahydrate, 20 mM Sodium cacodylate trihydrate pH 7.0, 15% (v/v) MPD, 6.0 mM Spermine tetrahydrochloride; Well ...Details: Drop solution, 0.5 mM duplex, 20 mM Lithium chloride, 40 mM Strontium chloride hexahydrate, 20 mM Sodium cacodylate trihydrate pH 7.0, 15% (v/v) MPD, 6.0 mM Spermine tetrahydrochloride; Well solution, Component concentrations are double the concentration of the drop solution and do not contain the oligonucleotide duplex |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 3, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→47.75 Å / Num. obs: 2517 / % possible obs: 99.9 % / Redundancy: 7.5 % / CC1/2: 0.943 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 2.6→2.72 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 308 / CC1/2: 0.645 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7NRP Resolution: 2.6→47.75 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 27.22 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→47.75 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→47.75 Å
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