+Open data
-Basic information
Entry | Database: PDB / ID: 3nx5 | ||||||||||||||||||
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Title | The crystal structure of Sanguinarine bound to DNA d(CGTACG) | ||||||||||||||||||
Components | 5'-D(*Keywords | DNA / DRUG-DNA COMPLEX / DOUBLE HELIX | Function / homology | Chem-SAU / DNA | Function and homology information Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.31 Å | Authors | Ferraroni, M. / Bazzicalupi, C. / Gratteri, P. / Bilia, A.R. | Citation | Journal: Chem.Commun.(Camb.) / Year: 2011 | Title: X-Ray diffraction analyses of the natural isoquinoline alkaloids Berberine and Sanguinarine complexed with double helix DNA d(CGTACG) Authors: Ferraroni, M. / Bazzicalupi, C. / Bilia, A.R. / Gratteri, P. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3nx5.cif.gz | 23.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3nx5.ent.gz | 14.7 KB | Display | PDB format |
PDBx/mmJSON format | 3nx5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nx/3nx5 ftp://data.pdbj.org/pub/pdb/validation_reports/nx/3nx5 | HTTPS FTP |
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-Related structure data
Related structure data | 3np6SC 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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2 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 1809.217 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: Synthetic DNA #2: Chemical | ChemComp-SAU / | #3: Chemical | ChemComp-CA / | #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: 2.14 Å3/Da / Density % sol: 42.42 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion / pH: 6.5 Details: MPD, MgCl2, NaCl, pH 6.5, vapor diffusion, temperature 296K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9763 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 8, 2010 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.29→39.69 Å / Num. obs: 3006 / % possible obs: 96.3 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Biso Wilson estimate: 47.698 Å2 / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Net I/σ(I): 20.99 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3NP6 Resolution: 2.31→39.69 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.892 / WRfactor Rfree: 0.3248 / WRfactor Rwork: 0.2852 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.5756 / SU B: 14.156 / SU ML: 0.294 / SU R Cruickshank DPI: 0.0981 / SU Rfree: 0.0596 / Cross valid method: THROUGHOUT / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES: REFINED INDIVIDUALLY
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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 max: 60.94 Å2 / Biso mean: 33.9258 Å2 / Biso min: 13.33 Å2
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Refinement step | Cycle: LAST / Resolution: 2.31→39.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.305→2.365 Å / Total num. of bins used: 20
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