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Yorodumi- PDB-7tga: [T:Ag+/Hg2+:T--(pH8.5-pH11; 30s in metals)] Metal-mediated DNA ba... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7tga | |||||||||||||||||||||
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Title | [T:Ag+/Hg2+:T--(pH8.5-pH11; 30s in metals)] Metal-mediated DNA base pair in tensegrity triangle grown at pH 8.5 and soaked in pH 11 with Ag+ and Hg2+ for 30s | |||||||||||||||||||||
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: 6.61 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: To Be Published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7tga.cif.gz | 67.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7tga.ent.gz | 43.7 KB | Display | PDB format |
PDBx/mmJSON format | 7tga.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7tga_validation.pdf.gz | 370.2 KB | Display | wwPDB validaton report |
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Full document | 7tga_full_validation.pdf.gz | 371.4 KB | Display | |
Data in XML | 7tga_validation.xml.gz | 2.5 KB | Display | |
Data in CIF | 7tga_validation.cif.gz | 3.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tg/7tga ftp://data.pdbj.org/pub/pdb/validation_reports/tg/7tga | HTTPS FTP |
-Related structure data
Related structure data | 7tftC 7tfuC 7tfvC 7tfwC 7tfxC 7tfyC 7tfzC 7tg0C 7tg1C 7tg2C 7tg3C 7tg4C 7tg6C 7tg7C 7tg8C 7tg9C 7tgbC 7tgcC 7tgdC 8dxvC 8dxwC 8dxxC 8dxyC 8dxzC 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) |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 7.07 Å3/Da / Density % sol: 82.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 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: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1.00743 Å |
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Nov 14, 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: 6.61→60.93 Å / Num. obs: 466 / % possible obs: 82.9 % / Redundancy: 7.5 % / Biso Wilson estimate: 211.13 Å2 / CC1/2: 0.988 / Net I/σ(I): 5.1 |
Reflection shell | Resolution: 6.61→9.18 Å / Num. unique obs: 474 / CC1/2: 0.765 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 6.61→60.93 Å / SU ML: 1.0058 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 50.6722 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: 516.01 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 6.61→60.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 6.61→60.93 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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