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- PDB-7u3v: [F224] Self-assembling tensegrity triangle with two turns, two tu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7u3v | ||||||||||||||||||
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Title | [F224] Self-assembling tensegrity triangle with two turns, two turns and four turns of DNA per axis by extension with P1 symmetry | ||||||||||||||||||
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![]() | DNA / Tensegrity triangle / self-assembling crystal | ||||||||||||||||||
Function / homology | DNA / DNA (> 10)![]() | ||||||||||||||||||
Biological species | synthetic construct (others) | ||||||||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||||||||
![]() | Woloszyn, K. / Vecchioni, S. / Seeman, N.C. / Sha, R. / Ohayon, Y.P. | ||||||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Augmented DNA Nanoarchitectures: A Structural Library of 3D Self-Assembling Tensegrity Triangle Variants. Authors: Woloszyn, K. / Vecchioni, S. / Ohayon, Y.P. / Lu, B. / Ma, Y. / Huang, Q. / Zhu, E. / Chernovolenko, D. / Markus, T. / Jonoska, N. / Mao, C. / Seeman, N.C. / Sha, R. | ||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 219.3 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 414.8 KB | Display | ![]() |
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Full document | ![]() | 423.8 KB | Display | |
Data in XML | ![]() | 7.8 KB | Display | |
Data in CIF | ![]() | 10.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7u3oC ![]() 7u3pC ![]() 7u3qC ![]() 7u3rC ![]() 7u3sC ![]() 7u3tC ![]() 7u3uC ![]() 7u3wC ![]() 7u3xC ![]() 7u3yC ![]() 7u3zC ![]() 7u40C ![]() 7u41C ![]() 7u42C ![]() 7u43C ![]() 7u44C ![]() 7u45C ![]() 3gbiS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-DNA chain , 7 types, 7 molecules AEDBFCM
#1: DNA chain | Mass: 12805.232 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#2: DNA chain | Mass: 4366.837 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: DNA chain | Mass: 10890.979 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#4: DNA chain | Mass: 6466.202 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#5: DNA chain | Mass: 4293.773 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#6: DNA chain | Mass: 6457.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#7: DNA chain | Mass: 6313.090 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: MOPS, Magnesium sulfate, Sodium hydroxide / Temp details: 338-293 at 0.4/hr, 293-277 at 0.1/hr |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jul 18, 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: 5.13→67.093 Å / Num. obs: 5031 / % possible obs: 82.6 % / Redundancy: 3.6 % / Biso Wilson estimate: 380.48 Å2 / CC1/2: 1 / Net I/σ(I): 11.4 | |||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3GBI Resolution: 5.14→42.33 Å / SU ML: 0.7257 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 29.6494 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: 489.65 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 5.14→42.33 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -7.149 Å / Origin y: -3.806 Å / Origin z: 20.871 Å
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Refinement TLS group |
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