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Yorodumi- PDB-1d10: STRUCTURAL COMPARISON OF ANTICANCER DRUG-DNA COMPLEXES. ADRIAMYCI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1d10 | ||||||||||||||||||
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Title | STRUCTURAL COMPARISON OF ANTICANCER DRUG-DNA COMPLEXES. ADRIAMYCIN AND DAUNOMYCIN | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / RIGHT HANDED DNA / DOUBLE HELIX / COMPLEXED WITH DRUG | Function / homology | DAUNOMYCIN / SPERMINE / DNA | Function and homology information Method | X-RAY DIFFRACTION / Resolution: 1.5 Å | Authors | Frederick, C.A. / Williams, L.D. / Ughetto, G. / Van Der Marel, G.A. / Van Boom, J.H. / Rich, A. / Wang, A.H.-J. | Citation | Journal: Biochemistry / Year: 1990 | Title: Structural comparison of anticancer drug-DNA complexes: adriamycin and daunomycin. Authors: Frederick, C.A. / Williams, L.D. / Ughetto, G. / van der Marel, G.A. / van Boom, J.H. / Rich, A. / Wang, A.H. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1d10.cif.gz | 17.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1d10.ent.gz | 9.5 KB | Display | PDB format |
PDBx/mmJSON format | 1d10.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1d10_validation.pdf.gz | 428.3 KB | Display | wwPDB validaton report |
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Full document | 1d10_full_validation.pdf.gz | 439.8 KB | Display | |
Data in XML | 1d10_validation.xml.gz | 3.7 KB | Display | |
Data in CIF | 1d10_validation.cif.gz | 4.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d1/1d10 ftp://data.pdbj.org/pub/pdb/validation_reports/d1/1d10 | HTTPS FTP |
-Related structure data
-Links
-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-DM1 / |
#3: Chemical | ChemComp-SPM / |
#4: Chemical | ChemComp-NA / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.55 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion / Details: VAPOR DIFFUSION / Temp details: ROOM TEMPERATURE | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS pH: 6.5 / Method: vapor diffusion, sitting drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS Crystal-ID: 1
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-Data collection
Diffraction | Mean temperature: 288 K |
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Detector | Detector: DIFFRACTOMETER |
Radiation | Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Highest resolution: 1.5 Å / Observed criterion σ(F): 2 |
Reflection | *PLUS Highest resolution: 1.5 Å / Observed criterion σ(F): 2 |
-Processing
Software | Name: NUCLSQ / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 1.5→10 Å / σ(F): 2 /
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Refine Biso |
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Refinement step | Cycle: LAST / Resolution: 1.5→10 Å
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Refine LS restraints |
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Refinement | *PLUS σ(F): 2 / Highest resolution: 1.5 Å / Lowest resolution: 10 Å / Num. reflection obs: 2731 / Rfactor obs: 0.175 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: n_bond_d / Dev ideal: 0.036 |