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- PDB-7smb: [U:Ag+/Ag+:U--pH 11] Metal-mediated DNA base pair in tensegrity t... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7smb | |||||||||||||||||||||
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Title | [U:Ag+/Ag+:U--pH 11] Metal-mediated DNA base pair in tensegrity triangle in Ag+ and Hg2+ solution | |||||||||||||||||||||
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![]() | DNA / tensegrity triangle / self-assembling crystal / metal-mediated mismatch | |||||||||||||||||||||
Function / homology | SILVER ION / 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: Heterobimetallic Base Pair Programming in Designer 3D DNA Crystals. Authors: Lu, B. / Ohayon, Y.P. / Woloszyn, K. / Yang, C.F. / Yoder, J.B. / Rothschild, L.J. / Wind, S.J. / Hendrickson, W.A. / Mao, C. / Seeman, N.C. / Canary, J.W. / Sha, R. / 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 | ![]() | 70.9 KB | Display | ![]() |
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PDB format | ![]() | 44.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 759.3 KB | Display | ![]() |
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Full document | ![]() | 765.9 KB | Display | |
Data in XML | ![]() | 3.3 KB | Display | |
Data in CIF | ![]() | 4.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7slbC ![]() 7slcC ![]() 7sldC ![]() 7sleC ![]() 7slfC ![]() 7slgC ![]() 7sljC ![]() 7slkC ![]() 7sllC ![]() 7slmC ![]() 7slnC ![]() 7sloC ![]() 7sm0C ![]() 7sm1C ![]() 7sm2C ![]() 7sm3C ![]() 7sm4C ![]() 7sm5C ![]() 7sm6C ![]() 7sm7C ![]() 7sm8C ![]() 7sm9C ![]() 7smaC ![]() 7ti3C ![]() 7ujzC ![]() 7uk0C ![]() 8dx1C ![]() 8dx5C ![]() 8dx6C ![]() 8dx7C ![]() 8dx9C ![]() 8dxaC ![]() 8dxcC ![]() 8dxdC ![]() 8dxfC 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: 6449.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||
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#2: DNA chain | Mass: 2052.375 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: 8.41 Å3/Da / Density % sol: 83.97 % / Description: Rhombohedral |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 11 Details: Tris, magnesium sulfate, silver nitrate, mercury chloride 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: Oct 17, 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: 4.63→64.22 Å / Num. obs: 1427 / % possible obs: 84.9 % / Redundancy: 10.6 % / Biso Wilson estimate: 259.8 Å2 / CC1/2: 1 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 4.63→5.34 Å / Num. unique obs: 203 / CC1/2: 0.46 |
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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: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 359.54 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 4.63→32.54 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 4.63→32.54 Å
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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