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Yorodumi- PDB-8cyn: [2T7+20bp Linker] Self-Assembled 3D DNA Hexagonal Tensegrity Tria... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8cyn | ||||||||||||||||||||||||
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Title | [2T7+20bp Linker] Self-Assembled 3D DNA Hexagonal Tensegrity Triangle with 20 bp Sticky-End Linker | ||||||||||||||||||||||||
Components |
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Keywords | DNA / tensegrity triangle / synthetic construct / self-assembly | ||||||||||||||||||||||||
Function / homology | DNA / DNA (> 10) Function and homology information | ||||||||||||||||||||||||
Biological species | synthetic construct (others) | ||||||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 9.45 Å | ||||||||||||||||||||||||
Authors | Lu, B. / Vecchioni, S. / Ohayon, Y.P. / Seeman, N.C. / Mao, C. / Sha, R. | ||||||||||||||||||||||||
Funding support | United States, 7items
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Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2023 Title: Programmable 3D Hexagonal Geometry of DNA Tensegrity Triangles. Authors: Lu, B. / Woloszyn, K. / Ohayon, Y.P. / Yang, B. / Zhang, C. / Mao, C. / Seeman, N.C. / Vecchioni, S. / Sha, R. | ||||||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8cyn.cif.gz | 107.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8cyn.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8cyn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8cyn_validation.pdf.gz | 376.8 KB | Display | wwPDB validaton report |
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Full document | 8cyn_full_validation.pdf.gz | 378.3 KB | Display | |
Data in XML | 8cyn_validation.xml.gz | 2.6 KB | Display | |
Data in CIF | 8cyn_validation.cif.gz | 3.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cy/8cyn ftp://data.pdbj.org/pub/pdb/validation_reports/cy/8cyn | HTTPS FTP |
-Related structure data
Related structure data | 8cs1C 8cs2C 8cs3C 8cs4C 8cs5C 8cs6C 8cs7C 8cs8C 8cymC 8dagC 8dahC 8dcjC 7r96S 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
-DNA chain , 6 types, 6 molecules ABCDXY
#1: DNA chain | Mass: 6433.163 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#2: DNA chain | Mass: 2082.400 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: DNA chain | Mass: 1825.216 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#4: DNA chain | Mass: 2432.614 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#5: DNA chain | Mass: 6223.042 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#6: DNA chain | Mass: 6069.930 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 31 Å3/Da / Density % sol: 96.03 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 1.75 M ammonium sulfate, 120 mM Tris, 120 mM Acetic Acid, 6 mM EDTA Temp details: 338-293 at 0.4/hr |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1.00743 Å |
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jun 13, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00743 Å / Relative weight: 1 |
Reflection | Resolution: 9.45→90.06 Å / Num. obs: 1358 / % possible obs: 86.1 % / Redundancy: 18 % / Biso Wilson estimate: 505.6 Å2 / CC1/2: 0.999 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 9.45→10.85 Å / Num. unique obs: 194 / CC1/2: 0.672 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7R96 Resolution: 9.45→50.02 Å / SU ML: 0.3214 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.9185 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 977.02 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 9.45→50.02 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 9.45→50.02 Å
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