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- PDB-385d: FORMATION OF A NEW COMPOUND IN THE CRYSTAL STRUCTURE OF CYANOMORP... -
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Open data
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Basic information
Entry | Database: PDB / ID: 385d | ||||||||||||||||||
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Title | FORMATION OF A NEW COMPOUND IN THE CRYSTAL STRUCTURE OF CYANOMORPHOLINODOXORUBICIN COMPLEXED WITH D(CGATCG) | ||||||||||||||||||
![]() | DNA (5'-D(*![]() DNA / RIGHT HANDED DNA / DOUBLE HELIX / COMPLEXED WITH DRUG | Function / homology | N-ETHYLHYDROXY-DOXORUBICIN / DNA | ![]() Method | ![]() ![]() Ettorre, A. / Cirilli, M. / Ughetto, G. | ![]() ![]() Title: Degradation of the morpholino ring in the crystal structure of cyanomorpholinodoxorubicin complexed with d(CGATCG). Authors: Ettorre, A. / Cirilli, M. / 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 | ![]() | 15.2 KB | Display | ![]() |
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PDB format | ![]() | 8.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 720.5 KB | Display | ![]() |
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Full document | ![]() | 728.3 KB | Display | |
Data in XML | ![]() | 4 KB | Display | |
Data in CIF | ![]() | 4.5 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-NOD / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.93 Å3/Da / Density % sol: 57.99 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 5.5 / Details: pH 5.50, VAPOR DIFFUSION, SITTING DROP | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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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: Oct 1, 1995 |
Radiation | Monochromator: GRAPHITE / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.6→8 Å / Num. obs: 3509 / Biso Wilson estimate: 9.18 Å2 / Rmerge(I) obs: 0.121 |
Reflection | *PLUS Highest resolution: 1.6 Å / Lowest resolution: 8 Å |
Reflection shell | *PLUS Highest resolution: 1.6 Å / Lowest resolution: 1.67 Å / % possible obs: 88.9 % |
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Processing
Software |
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Refinement | Resolution: 1.6→8 Å / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 1.6→8 Å
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Refine LS restraints |
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Software | *PLUS Name: NUCLSQ / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.6 Å / Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor obs: 0.206 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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