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Yorodumi- PDB-7ozz: The crystal structure of a DNA:RNA hybrid duplex sequence CTTTTCT... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ozz | |||||||||
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Title | The crystal structure of a DNA:RNA hybrid duplex sequence CTTTTCTTTG with LNA-amide modification | |||||||||
Components |
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Keywords | DNA-RNA HYBRID / Amide-LNA / duplex / DNA:RNA / unmodified | |||||||||
Function / homology | : / DNA / RNA Function and homology information | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | |||||||||
Authors | Thorpe, C. / Hardwick, J. / McDonough, M.A. / Hall, J.P. / Baker, Y.R. / El-Sagheer, A.H. / Brown, T. | |||||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Nat Commun / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ozz.cif.gz | 23.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ozz.ent.gz | 13 KB | Display | PDB format |
PDBx/mmJSON format | 7ozz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ozz_validation.pdf.gz | 399.7 KB | Display | wwPDB validaton report |
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Full document | 7ozz_full_validation.pdf.gz | 401.4 KB | Display | |
Data in XML | 7ozz_validation.xml.gz | 3.3 KB | Display | |
Data in CIF | 7ozz_validation.cif.gz | 3.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oz/7ozz ftp://data.pdbj.org/pub/pdb/validation_reports/oz/7ozz | HTTPS FTP |
-Related structure data
Related structure data | 7nrpSC 7oooC 7oosC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-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: 2981.045 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 | ChemComp-K / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.32 Å3/Da / Density % sol: 62.95 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: Drop solution 0.5 mM duplex, 40 mM Sodium chloride, 6.0 mM Potassium chloride, 20 mM Sodium cacodylate trihydrate pH 7.0, 17.5% (v/v) MPD, 6.0 mM Spermine tetrahydrochloride, Well solution, ...Details: Drop solution 0.5 mM duplex, 40 mM Sodium chloride, 6.0 mM Potassium chloride, 20 mM Sodium cacodylate trihydrate pH 7.0, 17.5% (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: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9762 Å |
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: 2.7→27.06 Å / Num. obs: 2283 / % possible obs: 99.9 % / Redundancy: 9.7 % / CC1/2: 0.999 / Net I/σ(I): 23 |
Reflection shell | Resolution: 2.7→2.77 Å / Num. unique obs: 152 / CC1/2: 0.421 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7NRP Resolution: 2.7→27.06 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.12 / 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: 2.7→27.06 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→27.06 Å
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