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- PDB-8dxx: [T:Au+:T--(pH11-pH7; 45s)] Metal-mediated DNA base pair in tenseg... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8dxx | |||||||||||||||||||||
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Title | [T:Au+:T--(pH11-pH7; 45s)] Metal-mediated DNA base pair in tensegrity triangle grown at pH 11 and soaked in pH 7 for 45s | |||||||||||||||||||||
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![]() | DNA / tensegrity triangle / self-assembling crystal / metal-mediated mismatch | |||||||||||||||||||||
Function / homology | : / DNA / DNA (> 10)![]() | |||||||||||||||||||||
Biological species | synthetic construct (others) | |||||||||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||||||||
![]() | Lu, B. / Vecchioni, S. / Seeman, N.C. / Sha, R. / Ohayon, Y.P. | |||||||||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Crystallographic pH Titration of Silver and Mercury Mediated DNA Base Pairs Authors: Lu, B. / Ohayon, Y.P. / Sha, R. / Woloszyn, K. / Rothschild, L. / Wind, S. / Hendrickson, W. / Mao, C. / Seeman, N.C. / Vecchioni, S. | |||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 36.3 KB | Display | ![]() |
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PDB format | ![]() | 21.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7tftC ![]() 7tfuC ![]() 7tfvC ![]() 7tfwC ![]() 7tfxC ![]() 7tfyC ![]() 7tfzC ![]() 7tg0C ![]() 7tg1C ![]() 7tg2C ![]() 7tg3C ![]() 7tg4C ![]() 7tg6C ![]() 7tg7C ![]() 7tg8C ![]() 7tg9C ![]() 7tgaC ![]() 7tgbC ![]() 7tgcC ![]() 7tgdC ![]() 8dxvC ![]() 8dxwC ![]() 8dxyC ![]() 8dxzC 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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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: ![]() |
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Sample preparation
Crystal | Density Matthews: 7.9 Å3/Da / Density % sol: 84.44 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 11 Details: 40 mM Tris, 125 mM magnesium sulfate, 12 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: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Dec 12, 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: 4.07→65.28 Å / Num. obs: 3992 / % possible obs: 86.7 % / Redundancy: 9.2 % / Biso Wilson estimate: 203.43 Å2 / CC1/2: 1 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 4.07→4.53 Å / Num. unique obs: 408 / CC1/2: 0.281 |
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Processing
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Refinement | Method to determine structure: ![]() 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: 202.45 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 4.07→32.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 4.07→32.67 Å
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