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Yorodumi- PDB-6s15: Pyridine derivative of the natural alkaloid Berberine as Human Te... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6s15 | ||||||
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Title | Pyridine derivative of the natural alkaloid Berberine as Human Telomeric G-quadruplex Binder | ||||||
Components | DNA TAGGGTTAGGGT | ||||||
Keywords | DNA / DRUG-DNA COMPLEX / telomeric G-quadruplex | ||||||
Function / homology | : / Berberine / DNA / DNA (> 10) Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å | ||||||
Authors | Ferraroni, M. / Bazzicalupi, C. / Gratteri, P. / Papi, F. | ||||||
Citation | Journal: Acs Med.Chem.Lett. / Year: 2020 Title: Pyridine Derivative of the Natural Alkaloid Berberine as Human Telomeric G4-DNA Binder: A Solution and Solid-State Study. Authors: Papi, F. / Bazzicalupi, C. / Ferraroni, M. / Ciolli, G. / Lombardi, P. / Khan, A.Y. / Kumar, G.S. / Gratteri, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6s15.cif.gz | 27.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6s15.ent.gz | 17.4 KB | Display | PDB format |
PDBx/mmJSON format | 6s15.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6s15_validation.pdf.gz | 724 KB | Display | wwPDB validaton report |
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Full document | 6s15_full_validation.pdf.gz | 728.9 KB | Display | |
Data in XML | 6s15_validation.xml.gz | 4.1 KB | Display | |
Data in CIF | 6s15_validation.cif.gz | 5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s1/6s15 ftp://data.pdbj.org/pub/pdb/validation_reports/s1/6s15 | HTTPS FTP |
-Related structure data
Related structure data | 5cdbS 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: 3773.462 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: quadruplex structure / Source: (synth.) synthetic construct (others) #2: Chemical | #3: Chemical | ChemComp-KQT / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 1.93 Å3/Da / Density % sol: 36.38 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Potassium Cacodylate, Lithium Sulfate, Magnesium Sulfate, Iso-propanol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 24, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→35.35 Å / Num. obs: 6173 / % possible obs: 99.1 % / Redundancy: 22.9 % / Biso Wilson estimate: 32.91 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.078 / Rrim(I) all: 0.081 / Χ2: 0.97 / Net I/σ(I): 21.74 |
Reflection shell | Resolution: 1.7→1.74 Å / Redundancy: 20 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3.54 / Num. unique obs: 418 / CC1/2: 0.99 / Rrim(I) all: 0.33 / % possible all: 96.35 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5CDB Resolution: 1.7→35.35 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.904 / SU B: 3.242 / SU ML: 0.108 / SU R Cruickshank DPI: 0.1758 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.176 / ESU R Free: 0.156 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 70.22 Å2 / Biso mean: 32.915 Å2 / Biso min: 18.76 Å2
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Refinement step | Cycle: final / Resolution: 1.7→35.35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.703→1.747 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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