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Yorodumi- PDB-4l25: Crystal structure of DNA duplex containing consecutive T-T mispairs -
+Open data
-Basic information
Entry | Database: PDB / ID: 4l25 | ||||||||||||||||||
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Title | Crystal structure of DNA duplex containing consecutive T-T mispairs | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / T-T mispair / A-T-T triplet / non-helical DNA duplex | Function / homology | DNA / DNA (> 10) | Function and homology information Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å | Authors | Kondo, J. / Yamada, T. / Hirose, C. / Tanaka, Y. / Ono, A. | Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2014 | Title: Crystal Structure of Metallo DNA Duplex Containing Consecutive Watson-Crick-like T-Hg(II) -T Base Pairs Authors: Kondo, J. / Yamada, T. / Hirose, C. / Okamoto, I. / Tanaka, Y. / Ono, A. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4l25.cif.gz | 25.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4l25.ent.gz | 16.4 KB | Display | PDB format |
PDBx/mmJSON format | 4l25.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l2/4l25 ftp://data.pdbj.org/pub/pdb/validation_reports/l2/4l25 | HTTPS FTP |
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-Related structure data
Related structure data | 4l24C 4l26SC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 3654.378 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemically synthesized #2: 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: 2.23 Å3/Da / Density % sol: 44.92 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Sodium Cacodylate, Spermine tetrahydrochloride, 2-methyl-2,4-pentanediol, ammonium chloride , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1 Å |
Detector | Date: Oct 16, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→19.1 Å / Num. obs: 24441 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4L26 Resolution: 1.1→19.08 Å / Occupancy max: 1 / Occupancy min: 0.5 / σ(F): 0
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Solvent computation | Bsol: 50.0215 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 51.24 Å2 / Biso mean: 15.1144 Å2 / Biso min: 6.3 Å2
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Refinement step | Cycle: LAST / Resolution: 1.1→19.08 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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Xplor file |
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