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- PDB-9clu: [Q:(Au+)3:F_pH11] Metal-mediated DNA base pair in a self-assembli... -
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Open data
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Basic information
Entry | Database: PDB / ID: 9clu | |||||||||||||||
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Title | [Q:(Au+)3:F_pH11] Metal-mediated DNA base pair in a self-assembling rhombohedral lattice | |||||||||||||||
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![]() | DNA / Tensegrity triangle / mmDNA / thiopurine / Au | |||||||||||||||
Function / homology | : / DNA / DNA (> 10)![]() | |||||||||||||||
Biological species | synthetic construct (others) | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Imstepf, L. / Vecchioni, S. / Sha, R. / Ohayon, Y.P. / Woloszyn, K. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Thioguanine metal base pairs Authors: Imstepf, L. / 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 | ![]() | 65.4 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 4.6 KB | Display | |
Data in CIF | ![]() | 5.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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: 6504.264 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||||
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#2: DNA chain | Mass: 2082.467 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 | Has protein modification | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 8.25 Å3/Da / Density % sol: 85.1 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 100 mM MOPS, 1.25 M magnesium sulfate / Temp details: 338-293 degrees C at 0.4 degrees C/hour |
-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: Mar 23, 2024 | ||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength | Wavelength: 0.9201 Å / Relative weight: 1 | ||||||||||||
Reflection | Resolution: 5.747→67.172 Å / Num. obs: 2656 / % possible obs: 83.8 % / Redundancy: 2.9 % / Biso Wilson estimate: 163.13 Å2 / CC1/2: 0.97 / Net I/σ(I): 3.8 | ||||||||||||
Reflection shell |
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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: 327.67 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 5.75→52.68 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 5.75→52.68 Å
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