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Yorodumi- PDB-5xuv: Crystal structure of DNA duplex containing 4-thiothymine-2Ag(I)-4... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xuv | ||||||||||||||||||||||||||||
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Title | Crystal structure of DNA duplex containing 4-thiothymine-2Ag(I)-4-thiothymine base pairs | ||||||||||||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / metallo-base pair / silver | Function / homology | SILVER ION / : / DNA / DNA (> 10) | Function and homology information Biological species | synthetic construct (others) | Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å | Authors | Kondo, J. / Sugawara, T. / Saneyoshi, H. / Ono, A. | Funding support | Japan, 1items |
Citation | Journal: Chem. Commun. (Camb.) / Year: 2017 | Title: Crystal structure of a DNA duplex containing four Ag(i) ions in consecutive dinuclear Ag(i)-mediated base pairs: 4-thiothymine-2Ag(i)-4-thiothymine Authors: Kondo, J. / Sugawara, T. / Saneyoshi, H. / Ono, A. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xuv.cif.gz | 27.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xuv.ent.gz | 16.4 KB | Display | PDB format |
PDBx/mmJSON format | 5xuv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5xuv_validation.pdf.gz | 2.7 MB | Display | wwPDB validaton report |
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Full document | 5xuv_full_validation.pdf.gz | 2.7 MB | Display | |
Data in XML | 5xuv_validation.xml.gz | 3.5 KB | Display | |
Data in CIF | 5xuv_validation.cif.gz | 4.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xu/5xuv ftp://data.pdbj.org/pub/pdb/validation_reports/xu/5xuv | HTTPS FTP |
-Related structure data
Related structure data | 4l24S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: DNA chain | Mass: 3654.512 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Chemical | ChemComp-AG / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 46.97 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: sodium cacodylate, silver nitrate, spermine, 2-methyl-2,4-pentanediol |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 0.98 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 9, 2016 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→33.216 Å / Num. obs: 10314 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 6.703 % / Biso Wilson estimate: 31.83 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.045 / Rrim(I) all: 0.049 / Χ2: 1.315 / Net I/σ(I): 20.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4L24 Resolution: 1.9→33.216 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 23.84
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 64.98 Å2 / Biso mean: 41.1742 Å2 / Biso min: 30.96 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.9→33.216 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7
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