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Yorodumi- PDB-5axe: Crystal Structure Analysis of DNA Duplexes containing sulfoamide-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5axe | ||||||||||||||||||||
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Title | Crystal Structure Analysis of DNA Duplexes containing sulfoamide-bridged nucleic acid (SuNA-NH) | ||||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / A-FORM DNA / SULFONAMIDE-BRIDGED NUCLEIC ACID / SuNA[NH] / ANTISENSE | Function / homology | DNA | Function and homology information Biological species | synthetic construct (others) | Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 0.95 Å | Authors | Mitsuoka, Y. / Aoyama, H. / Kugimiya, A. / Fujimura, Y. / Yamamoto, T. / Waki, R. / Wada, F. / Tahara, S. / Sawamura, M. / Noda, M. ...Mitsuoka, Y. / Aoyama, H. / Kugimiya, A. / Fujimura, Y. / Yamamoto, T. / Waki, R. / Wada, F. / Tahara, S. / Sawamura, M. / Noda, M. / Hari, Y. / Obika, S. | Citation | Journal: Org.Biomol.Chem. / Year: 2016 | Title: Effect of an N-substituent in sulfonamide-bridged nucleic acid (SuNA) on hybridization ability and duplex structure. Authors: Mitsuoka, Y. / Aoyama, H. / Kugimiya, A. / Fujimura, Y. / Yamamoto, T. / Waki, R. / Wada, F. / Tahara, S. / Sawamura, M. / Noda, M. / Hari, Y. / Obika, S. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5axe.cif.gz | 44.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5axe.ent.gz | 33 KB | Display | PDB format |
PDBx/mmJSON format | 5axe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5axe_validation.pdf.gz | 378.9 KB | Display | wwPDB validaton report |
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Full document | 5axe_full_validation.pdf.gz | 379.8 KB | Display | |
Data in XML | 5axe_validation.xml.gz | 5.1 KB | Display | |
Data in CIF | 5axe_validation.cif.gz | 6.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ax/5axe ftp://data.pdbj.org/pub/pdb/validation_reports/ax/5axe | HTTPS FTP |
-Related structure data
Related structure data | 5axfC 1i5wS 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: 3136.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #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: 1.83 Å3/Da / Density % sol: 32.82 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS AND I_PLUS/MINUS COLUMNS |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: May 14, 2014 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 0.95→23.68 Å / Num. obs: 29154 / % possible obs: 98.8 % / Redundancy: 13.7 % / Biso Wilson estimate: 4.93 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 27.6 |
Reflection shell | Resolution: 0.95→0.97 Å / Redundancy: 12.5 % / Rmerge(I) obs: 0.241 / Mean I/σ(I) obs: 7 / % possible all: 97.1 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1I5W Resolution: 0.95→16.35 Å / SU ML: 0.05 / Cross valid method: NONE / σ(F): 1.08 / Phase error: 10.76 / Stereochemistry target values: ML Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS AND I_PLUS/MINUS COLUMNS
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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: 11.5 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.95→16.35 Å
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Refine LS restraints |
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LS refinement shell |
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