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Yorodumi- PDB-3cdm: Structural adaptation and conservation in quadruplex-drug recognition -
+Open data
-Basic information
Entry | Database: PDB / ID: 3cdm | ||||||||||||||||||
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Title | Structural adaptation and conservation in quadruplex-drug recognition | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / QUADRUPLEX / PROPELLER / INTRAMOLECULAR / HUMAN TELOMERE PARALLEL STRANDED / LIGAND / COMPLEX | Function / homology | : / Chem-NII / DNA / DNA (> 10) | Function and homology information Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | Authors | Parkinson, G.N. / Neidle, S. | Citation | Journal: J.Mol.Biol. / Year: 2008 | Title: Topology conservation and loop flexibility in quadruplex-drug recognition: crystal structures of inter- and intramolecular telomeric DNA quadruplex-drug complexes Authors: Parkinson, G.N. / Cuenca, F. / Neidle, S. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3cdm.cif.gz | 48.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cdm.ent.gz | 35.1 KB | Display | PDB format |
PDBx/mmJSON format | 3cdm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cd/3cdm ftp://data.pdbj.org/pub/pdb/validation_reports/cd/3cdm | HTTPS FTP |
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-Related structure data
Related structure data | 3ccoC 1kf1S 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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2 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 7287.690 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans #2: Chemical | ChemComp-NII / #3: Chemical | ChemComp-K / #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: 3.24 Å3/Da / Density % sol: 62 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 333mM ammonium sulfate, 10mM magnesium chloride, 50mM sodium chloride, 50mM potassium chloride, 50mM potassium cacodylate pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K | ||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9785 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 7, 2007 / Details: Monochromator |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→28.69 Å / Num. all: 10055 / Num. obs: 10055 / % possible obs: 91 % / Observed criterion σ(I): 0 / Redundancy: 2.86 % / Biso Wilson estimate: 46 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 17.9 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 2.94 % / Rmerge(I) obs: 0.116 / Mean I/σ(I) obs: 6.4 / Num. unique all: 1041 / % possible all: 95.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1KF1 Resolution: 2.1→10 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.886 / SU B: 5.422 / SU ML: 0.152 / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.295 / ESU R Free: 0.246 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Displacement parameters | Biso mean: 26.776 Å2
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Refine analyze | Luzzati coordinate error obs: 0.267 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.152 Å / Total num. of bins used: 20
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