+Open data
-Basic information
Entry | Database: PDB / ID: 8dcj | ||||||||||||||||||||||||
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Title | [A:T] Self-Assembled 3D DNA Rhombohedral Tensegrity Triangle | ||||||||||||||||||||||||
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: 3.33 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 | 8dcj.cif.gz | 38 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8dcj.ent.gz | 21.9 KB | Display | PDB format |
PDBx/mmJSON format | 8dcj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8dcj_validation.pdf.gz | 394.5 KB | Display | wwPDB validaton report |
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Full document | 8dcj_full_validation.pdf.gz | 397.5 KB | Display | |
Data in XML | 8dcj_validation.xml.gz | 3.7 KB | Display | |
Data in CIF | 8dcj_validation.cif.gz | 4.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dc/8dcj ftp://data.pdbj.org/pub/pdb/validation_reports/dc/8dcj | HTTPS FTP |
-Related structure data
Related structure data | 8cs1C 8cs2C 8cs3C 8cs4C 8cs5C 8cs6C 8cs7C 8cs8C 8cymC 8cynC 8dagC 8dahC 5w6wS 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: DNA chain | Mass: 6441.188 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: 2129.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#4: DNA chain | Mass: 2143.432 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: 8.04 Å3/Da / Density % sol: 84.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5 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: Feb 21, 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: 3.33→66.2 Å / Num. obs: 3608 / % possible obs: 83.2 % / Redundancy: 10.7 % / Biso Wilson estimate: 172.34 Å2 / CC1/2: 1 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 3.33→3.66 Å / Num. unique obs: 194 / CC1/2: 0.34 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5W6W Resolution: 3.33→33.1 Å / SU ML: 0.3913 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 41.5255 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: 148.31 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.33→33.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.33→33.1 Å
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