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Yorodumi- PDB-7ul8: [T:Au+:T--pH 11] Metal-mediated DNA base pair in tensegrity triangle -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ul8 | |||||||||||||||||||||
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Title | [T:Au+:T--pH 11] Metal-mediated DNA base pair in tensegrity triangle | |||||||||||||||||||||
Components |
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Keywords | DNA / Tensegrity triangle / self-assembling crystal / metal-mediated mismatch | |||||||||||||||||||||
Function / homology | : / DNA / DNA (> 10) Function and homology information | |||||||||||||||||||||
Biological species | synthetic construct (others) | |||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 4.22 Å | |||||||||||||||||||||
Authors | Lu, B. / Vecchioni, S. / Seeman, N.C. / Sha, R. / Ohayon, Y.P. | |||||||||||||||||||||
Funding support | United States, 6items
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Citation | Journal: Adv Mater / Year: 2023 Title: Metal-Mediated DNA Nanotechnology in 3D: Structural Library by Templated Diffraction. Authors: Vecchioni, S. / Lu, B. / Livernois, W. / Ohayon, Y.P. / Yoder, J.B. / Yang, C.F. / Woloszyn, K. / Bernfeld, W. / Anantram, M.P. / Canary, J.W. / Hendrickson, W.A. / Rothschild, L.J. / Mao, C. ...Authors: Vecchioni, S. / Lu, B. / Livernois, W. / Ohayon, Y.P. / Yoder, J.B. / Yang, C.F. / Woloszyn, K. / Bernfeld, W. / Anantram, M.P. / Canary, J.W. / Hendrickson, W.A. / Rothschild, L.J. / Mao, C. / Wind, S.J. / Seeman, N.C. / Sha, R. #1: Journal: Adv Mater / Year: 2023 Title: Metal-Mediated DNA Nanotechnology in 3D: Structural Library by Templated Diffraction. Authors: Vecchioni, S. / Lu, B. / Livernois, W. / Ohayon, Y.P. / Yoder, J.B. / Yang, C.F. / Woloszyn, K. / Bernfeld, W. / Anantram, M.P. / Canary, J.W. / Hendrickson, W.A. / Rothschild, L.J. / Mao, C. ...Authors: Vecchioni, S. / Lu, B. / Livernois, W. / Ohayon, Y.P. / Yoder, J.B. / Yang, C.F. / Woloszyn, K. / Bernfeld, W. / Anantram, M.P. / Canary, J.W. / Hendrickson, W.A. / Rothschild, L.J. / Mao, C. / Wind, S.J. / Seeman, N.C. / Sha, R. | |||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ul8.cif.gz | 38.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ul8.ent.gz | 22.3 KB | Display | PDB format |
PDBx/mmJSON format | 7ul8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ul/7ul8 ftp://data.pdbj.org/pub/pdb/validation_reports/ul/7ul8 | HTTPS FTP |
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-Related structure data
Related structure data | 8e4dC 8e4eC 8eg4C 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: 6463.185 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||
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#2: DNA chain | Mass: 2066.401 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: 2128.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||
#5: Chemical | 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: 7.78 Å3/Da / Density % sol: 84.19 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 11 Details: 400 mM Tris, 1.25 M magnesium sulfate, 36 uM gold(I) phosphine 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: 19-ID / Wavelength: 1.02466 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 25, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.02466 Å / Relative weight: 1 |
Reflection | Resolution: 4.21→64.76 Å / Num. obs: 4138 / % possible obs: 87.5 % / Redundancy: 8.5 % / Biso Wilson estimate: 269.6 Å2 / CC1/2: 0.998 / Net I/σ(I): 8 |
Reflection shell | Resolution: 4.21→4.66 Å / Rmerge(I) obs: 3.873 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 422 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 4.22→41.18 Å / SU ML: 0.5282 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 45.1012 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: 191.52 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 4.22→41.18 Å
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Refine LS restraints |
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LS refinement shell |
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