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- PDB-6xcl: Crystal Structure of human telomeric DNA G-quadruplex in complex ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6xcl | ||||||||||||||||||||||||||||
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Title | Crystal Structure of human telomeric DNA G-quadruplex in complex with a novel platinum(II) complex. | ||||||||||||||||||||||||||||
![]() | DNA (5'-D(*![]() DNA / guanine quadruplex / Ligand Complex | Function / homology | : / Chem-V4A / DNA / DNA (> 10) | ![]() Biological species | ![]() Method | ![]() ![]() ![]() ![]() Miron, C.E. / van Staalduinen, L.M. / Jia, Z. / Petitjean, A. | Funding support | | ![]()
![]() ![]() Title: Going Platinum to the Tune of a Remarkable Guanine Quadruplex Binder: Solution- and Solid-State Investigations. Authors: Miron, C.E. / van Staalduinen, L. / Rangaswamy, A.M. / Chen, M. / Liang, Y. / Jia, Z. / Mergny, J.L. / Petitjean, A. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 45.7 KB | Display | ![]() |
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PDB format | ![]() | 26.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 4.1 KB | Display | |
Data in CIF | ![]() | 5.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3t5eS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: DNA chain | Mass: 6983.497 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-K / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.58 Å3/Da / Density % sol: 65.63 % |
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 100 mM KCl, 10 mM MgCl2, 50 mM MES (pH 6.0), 10% PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 7, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→35 Å / Num. obs: 10637 / % possible obs: 99.8 % / Redundancy: 5.8 % / Biso Wilson estimate: 55.79 Å2 / Rsym value: 0.097 / Net I/σ(I): 14.28 |
Reflection shell | Resolution: 2.7→2.9 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 2.51 / Num. unique obs: 2054 / Rsym value: 0.816 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3t5e Resolution: 2.7→33.6 Å / SU ML: 0.3274 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 27.956 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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: 41.07 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→33.6 Å
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Refine LS restraints |
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LS refinement shell |
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