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- PDB-1p20: Surprising Roles of Electrostatic Interactions in DNA-Ligand Complexes -
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Open data
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Basic information
Entry | Database: PDB / ID: 1p20 | ||||||||||||||||||
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Title | Surprising Roles of Electrostatic Interactions in DNA-Ligand Complexes | ||||||||||||||||||
![]() | 5'-D(*![]() DNA / adriamycin / intercalation / electrostatics / thallium | Function / homology | DOXORUBICIN / THALLIUM (I) ION / DNA | ![]() Method | ![]() ![]() ![]() Howerton, S.B. / Nagpal, A. / Williams, L.D. | ![]() ![]() Title: Surprising Roles of Electrostatic Interactions in DNA-Ligand Complexes Authors: Howerton, S.B. / Nagpal, A. / Williams, L.D. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 15.9 KB | Display | ![]() |
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PDB format | ![]() | 9.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 407.9 KB | Display | ![]() |
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Full document | ![]() | 412.2 KB | Display | |
Data in XML | ![]() | 2.2 KB | Display | |
Data in CIF | ![]() | 2.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Details | The second part of the biological assembly is generated by the two fold axis: -Y,-X,1/2-Z |
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Components
#1: DNA chain | Mass: 1809.217 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
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#2: Chemical | ChemComp-DM2 / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.29 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: d(CGATCG), Tl acetate, Mg acetate, MPD, spermine acetate, adriamycin, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 3, 2001 / Details: Osmic blue multilayer confocal |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.26→100 Å |
Reflection | *PLUS Lowest resolution: 100 Å / Num. obs: 5559 / % possible obs: 99.9 % / Num. measured all: 31250 |
Reflection shell | *PLUS Highest resolution: 1.34 Å / % possible obs: 99.9 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: NDB Entry DDF044 Resolution: 1.34→35 Å / Isotropic thermal model: isotropic Cross valid method: throughout refinement except final round σ(F): 2 / Stereochemistry target values: Parkinson & Berman, 1996
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Displacement parameters | Biso mean: 13.8 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.34→35 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 35 Å | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |