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Yorodumi- PDB-3gjk: crystal structure of a DNA duplex containing 7,8-dihydropyridol[2... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gjk | ||||||
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Title | crystal structure of a DNA duplex containing 7,8-dihydropyridol[2,3-d]pyrimidin-2-one | ||||||
Components |
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Keywords | DNA / duplex / bicyclic cytosine / 7 / 8-dihydropyridol[2 / 3-d]pyrimidin-2-one | ||||||
Function / homology | : / DNA Function and homology information | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Takenaka, A. / Juan, E.C.M. / Shimizu, S. / Haraguchi, T. / Xiao, M. / Kurose, T. / Ohkubo, A. / Sekine, M. / Shibata, T. / Millington, C.L. / Williams, D.M. | ||||||
Citation | Journal: To be Published Title: Insights into the stabilizing contributions of bicyclic cytosine analogues: crystal structures of DNA duplexes containing 7,8-dihydropyridol[2,3-d]pyrimidin-2-one Authors: Takenaka, A. / Juan, E.C.M. / Shimizu, S. / Haraguchi, T. / Xiao, M. / Kurose, T. / Ohkubo, A. / Sekine, M. / Shibata, T. / Millington, C.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gjk.cif.gz | 17.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gjk.ent.gz | 11.3 KB | Display | PDB format |
PDBx/mmJSON format | 3gjk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gj/3gjk ftp://data.pdbj.org/pub/pdb/validation_reports/gj/3gjk | HTTPS FTP |
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-Related structure data
Related structure data | 3gjhC 3gjjC 3gjlC 1ehvS S: Starting model for refinement C: citing same article (ref.) |
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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: 1818.231 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 1838.251 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Chemical | ChemComp-K / |
#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: 2.69 Å3/Da / Density % sol: 54.23 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 20mM Sodium cacodylate (pH7.0), 6mM Spermine tetrahydrochloride, 6mM NaCl, 40mM KCl, 5% MPD , VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 31, 2006 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 2137 / Num. obs: 2137 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.5 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 70.4 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.307 / Mean I/σ(I) obs: 11.3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ehv Resolution: 2.2→18.7 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.909 / SU B: 10.241 / SU ML: 0.215 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 0 / ESU R: 0.272 / ESU R Free: 0.249 / Stereochemistry target values: Engh & Huber / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.346 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→18.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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