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- PDB-1r68: Role of the amino sugar in DNA binding of disaccharide anthracycl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1r68 | ||||||||||||||||||
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Title | Role of the amino sugar in DNA binding of disaccharide anthracyclines: crystal structure of MAR70/d(CGATCG) complex | ||||||||||||||||||
![]() | 5'-D(*![]() DNA / right handed DNA / double helix / drug-DNA complex | Function / homology | 4'-EPI-4'-(2-DEOXYFUCOSE)DAUNOMYCIN / DNA | ![]() Method | ![]() ![]() ![]() Temperini, C. / Cirilli, M. / Aschi, M. / Ughetto, G. | ![]() ![]() Title: Role of the amino sugar in DNA binding of disaccharide anthracyclines: crystal structure of the complex MAR70/d(CGATCG). Authors: Temperini, C. / Cirilli, M. / Aschi, M. / Ughetto, G. #1: ![]() Title: The crystal structure of the complex between a disaccharide anthracycline and the DNA hexamer d(CGATCG) reveals two different binding sites involving two DNA duplexes Authors: Temperini, C. / Messori, L. / Orioli, P. / Di Bugno, C. / Animati, F. / Ughetto, G. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 17.2 KB | Display | ![]() |
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PDB format | ![]() | 9.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 700.1 KB | Display | ![]() |
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Full document | ![]() | 714.2 KB | Display | |
Data in XML | ![]() | 4.7 KB | Display | |
Data in CIF | ![]() | 5.3 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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Components
#1: DNA chain | Mass: 1809.217 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: Chemical | ChemComp-MAR / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.92 Å3/Da / Density % sol: 57.93 % | ||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / pH: 6 Details: Magnesium chloride, cacodylate, spermine, MPD, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K, pH 6.00 | ||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU AFC-5R / Detector: DIFFRACTOMETER / Date: Feb 15, 2003 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→15 Å / Num. obs: 6369 / % possible obs: 97.8 % / Biso Wilson estimate: 15.34 Å2 / Rmerge(I) obs: 0.114 / Net I/σ(I): 4.3 |
Reflection shell | Resolution: 1.2→1.3 Å / % possible all: 87 |
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Processing
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Refinement | Method to determine structure: ![]()
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Refinement step | Cycle: LAST / Resolution: 1.2→10 Å
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Refine LS restraints |
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