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Yorodumi- PDB-7nrp: The crystal structure of a DNA:RNA hybrid duplex sequence CTTTTCTTTG -
+Open data
-Basic information
Entry | Database: PDB / ID: 7nrp | ||||||
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Title | The crystal structure of a DNA:RNA hybrid duplex sequence CTTTTCTTTG | ||||||
Components |
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Keywords | DNA-RNA HYBRID / Amide-LNA / duplex / DNA:RNA / unmodified | ||||||
Function / homology | CACODYLATE ION / DNA / RNA Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 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 | 7nrp.cif.gz | 25.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7nrp.ent.gz | 12.9 KB | Display | PDB format |
PDBx/mmJSON format | 7nrp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7nrp_validation.pdf.gz | 384.1 KB | Display | wwPDB validaton report |
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Full document | 7nrp_full_validation.pdf.gz | 384.1 KB | Display | |
Data in XML | 7nrp_validation.xml.gz | 2 KB | Display | |
Data in CIF | 7nrp_validation.cif.gz | 2.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nr/7nrp ftp://data.pdbj.org/pub/pdb/validation_reports/nr/7nrp | HTTPS FTP |
-Related structure data
Related structure data | 7oooC 7oosC 7ozzC 1pjoS 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: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#2: DNA chain | Mass: 2991.961 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: Chemical | ChemComp-CAC / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.13 Å3/Da / Density % sol: 60.7 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.8 Details: 0.5 mM duplex, 12 mM Mg(OAc)2, 0.6 mM Spermidine.HCl, 0.075% b-Octylglucoside, 12 mM Sodium cacodylate, 12 % (v/v) 2-Methyl-2,4-pentanediol (MPD); equilibrated against 50% MPD in H2O |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.97862 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 15, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97862 Å / Relative weight: 1 |
Reflection | Resolution: 2.67→27.17 Å / Num. obs: 2243 / % possible obs: 98.8 % / Redundancy: 19.3 % / Biso Wilson estimate: 84.71 Å2 / CC1/2: 0.996 / Net I/σ(I): 25.2 |
Reflection shell | Resolution: 2.67→2.8 Å / Num. unique obs: 275 / CC1/2: 0.646 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1PJO Resolution: 2.67→27.17 Å / SU ML: 0.1955 / Cross valid method: FREE R-VALUE / σ(F): 0.82 / Phase error: 23.6638 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 75.06 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.67→27.17 Å
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Refine LS restraints |
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LS refinement shell |
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