+Open data
-Basic information
Entry | Database: PDB / ID: 3tvb | ||||||||||||||||||
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Title | A Highly Symmetric DNA G-4 Quadruplex/drug Complex | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA/antibiotic / G-4 Quadruplex / Daunomycin / DNA-Drug Complex / DNA-antibiotic complex | Function / homology | DAUNOMYCIN / DNA | Function and homology information Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 1.08 Å | Authors | Clark, G.R. / Pytel, P.D. / Squire, C.J. | Citation | Journal: Nucleic Acids Res. / Year: 2012 | Title: The high-resolution crystal structure of a parallel intermolecular DNA G-4 quadruplex/drug complex employing syn glycosyl linkages. Authors: Clark, G.R. / Pytel, P.D. / Squire, C.J. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3tvb.cif.gz | 27.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3tvb.ent.gz | 19.2 KB | Display | PDB format |
PDBx/mmJSON format | 3tvb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tv/3tvb ftp://data.pdbj.org/pub/pdb/validation_reports/tv/3tvb | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: DNA chain | Mass: 1271.866 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic oligomer #2: Chemical | ChemComp-DM1 / #3: Chemical | ChemComp-NA / #4: Chemical | #5: 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: 3.96 Å3/Da / Density % sol: 68.93 % |
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Crystal grow | Temperature: 277 K / Method: sitting drop / pH: 7 Details: NATRIX NR46 droplets 0.005 M Magnesium sulfate, 0.05 M Tris HCl buffer at pH 8.5, 35% w/v 1,6-hexane diol, Sitting drop, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 1.006 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 10, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.006 Å / Relative weight: 1 |
Reflection | Resolution: 1.08→10 Å / Num. all: 21428 / Num. obs: 21428 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Redundancy: 66.9 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 81.79 |
Reflection shell | Resolution: 1.08→1.13 Å / Rmerge(I) obs: 0.273 / Mean I/σ(I) obs: 15.14 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO Starting model: NONE Resolution: 1.08→10 Å / Num. parameters: 2579 / Num. restraintsaints: 2250 / Cross valid method: FREE R / σ(F): 4 / Stereochemistry target values: ENGH AND HUBER
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Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 430.19 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.08→10 Å
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Refine LS restraints |
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