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Yorodumi- PDB-276d: SUBSTITUTIONS AT C2' OF DAUNOSAMINE IN THE ANTICANCER DAUNORUBICI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 276d | ||||||||||||||||||
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Title | SUBSTITUTIONS AT C2' OF DAUNOSAMINE IN THE ANTICANCER DAUNORUBICIN ALTER ITS DNA-BINDING SEQUENCE SPECIFICITY | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / RIGHT HANDED DNA / DOUBLE HELIX / COMPLEXED WITH DRUG | Function / homology | 2'-BROMO-4'-EPIDAUNORUBICIN / DNA | Function and homology information Method | X-RAY DIFFRACTION / Resolution: 1.8 Å | Authors | Gao, Y.-G. / Priebe, W. / Wang, A.H.-J. | Citation | Journal: Eur.J.Biochem. / Year: 1996 | Title: Substitutions at C2' of daunosamine in the anticancer drug daunorubicin alter its DNA-binding sequence specificity. Authors: Gao, Y.G. / Priebe, W. / 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 | 276d.cif.gz | 15.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb276d.ent.gz | 8.4 KB | Display | PDB format |
PDBx/mmJSON format | 276d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 276d_validation.pdf.gz | 423.7 KB | Display | wwPDB validaton report |
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Full document | 276d_full_validation.pdf.gz | 430.8 KB | Display | |
Data in XML | 276d_validation.xml.gz | 2.8 KB | Display | |
Data in CIF | 276d_validation.cif.gz | 3.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/76/276d ftp://data.pdbj.org/pub/pdb/validation_reports/76/276d | 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-DM8 / Mass: 606.416 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H28BrNO10 Details: 2'-BROMO-4'-EPIDAUNORUBICIN IS A DAUNORUBICIN DERIVATIVE WHICH HAS ALPHA-MANNO CONFIGURATION. IT HAS SIMILAR ACTIVITY TO DAUNORUBICIN AND EXHIBITS PROMISING ACTIVITY TOWARD MULTIDRUG RESISTANT CELLS. |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.86 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 6 / Details: pH 6.00, VAPOR DIFFUSION, temperature 298.00K / Temp details: ROOM TEMPERATURE | ||||||||||||||||||||||||||||||||||||||||||||||||
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: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jul 12, 1995 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Redundancy: 4 % / Rmerge(I) obs: 0.044 |
Reflection | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 8 Å |
Reflection shell | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 1.89 Å / % possible obs: 86.1 % |
-Processing
Software |
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Refinement | Resolution: 1.8→10 Å / σ(F): 4 /
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Refinement step | Cycle: LAST / Resolution: 1.8→10 Å
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Refine LS restraints |
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Software | *PLUS Name: NUCLSQ / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 10 Å / σ(F): 4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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