+Open data
-Basic information
Entry | Database: PDB / ID: 3ggk | ||||||||||||||||||
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Title | Locating monovalent cations in one turn of G/C rich B-DNA | ||||||||||||||||||
Components | 5'-D(*Keywords | DNA / CATIONS / DIVALENT CATIONS / MONOVALENT CATIONS / RUBIDIUM ION | Function / homology | RUBIDIUM ION / DNA | Function and homology information Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.87 Å | Authors | Maehigashi, T. / Moulaei, T. / Watkins, D. / Komeda, S. / Williams, L.D. | Citation | Journal: To be Published | Title: Locating monovalent cations in one turn of G/C rich B-DNA Authors: Maehigashi, T. / Moulaei, T. / Watkins, D. / Komeda, S. / Williams, L.D. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ggk.cif.gz | 34.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ggk.ent.gz | 23.6 KB | Display | PDB format |
PDBx/mmJSON format | 3ggk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ggk_validation.pdf.gz | 366.1 KB | Display | wwPDB validaton report |
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Full document | 3ggk_full_validation.pdf.gz | 366.9 KB | Display | |
Data in XML | 3ggk_validation.xml.gz | 4.8 KB | Display | |
Data in CIF | 3ggk_validation.cif.gz | 6.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gg/3ggk ftp://data.pdbj.org/pub/pdb/validation_reports/gg/3ggk | HTTPS FTP |
-Related structure data
Related structure data | 3ggiC 1bd1S 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 on special symmetry positions |
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-Components
#1: DNA chain | Mass: 3045.992 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic construct | ||||
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#2: Chemical | ChemComp-MG / #3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.41 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: MPD, Magnesium acetate, Rubidium acetate, Rubidium hydroxide, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.81528 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 21, 2004 |
Radiation | Monochromator: Cryogenically cooled Si (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.81528 Å / Relative weight: 1 |
Reflection | Resolution: 0.784→30.6 Å / Num. obs: 19281 / % possible obs: 63.9 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 23 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: DNA coordinates from PDB Entry 1bd1 (Heinemann and Alings) Resolution: 0.87→30.6 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.979 / SU B: 0.377 / SU ML: 0.011 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.02 / ESU R Free: 0.02 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 7.764 Å2
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Refinement step | Cycle: LAST / Resolution: 0.87→30.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 0.865→0.887 Å / Total num. of bins used: 20
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