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Yorodumi- PDB-198d: A TRIGONAL FORM OF THE IDARUBICIN-D(CGATCG) COMPLEX: CRYSTAL AND ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 198d | ||||||||||||||||||
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Title | A TRIGONAL FORM OF THE IDARUBICIN-D(CGATCG) COMPLEX: CRYSTAL AND MOLECULAR STRUCTURE AT 2.0 ANGSTROMS RESOLUTION | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / RIGHT HANDED DNA / DOUBLE HELIX / COMPLEXED WITH DRUG | Function / homology | IDARUBICIN / SPERMINE / DNA | Function and homology information Method | X-RAY DIFFRACTION / Resolution: 1.97 Å | Authors | Dautant, A. / Langlois D'Estaintot, B. / Gallois, B. / Brown, T. / Hunter, W.N. | Citation | Journal: Nucleic Acids Res. / Year: 1995 Title: A trigonal form of the idarubicin:d(CGATCG) complex; crystal and molecular structure at 2.0 A resolution. Authors: Dautant, A. / Langlois d'Estaintot, B. / Gallois, B. / Brown, T. / Hunter, W.N. #1: Journal: Anti-Cancer Drug Des. / Year: 1991 Title: Influence of Aglycone Modifications on the Binding of Anthracycline Drugs to DNA: The Molecular Structure of Idarubicin and 4-O-Demethyl-11-Deoxydoxorubicin Complexed to d(CGATCG) Authors: Gao, Y.-G. / Wang, A.H.-J. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 198d.cif.gz | 31.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb198d.ent.gz | 20.8 KB | Display | PDB format |
PDBx/mmJSON format | 198d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 198d_validation.pdf.gz | 623.8 KB | Display | wwPDB validaton report |
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Full document | 198d_full_validation.pdf.gz | 648.8 KB | Display | |
Data in XML | 198d_validation.xml.gz | 5.9 KB | Display | |
Data in CIF | 198d_validation.cif.gz | 7.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/98/198d ftp://data.pdbj.org/pub/pdb/validation_reports/98/198d | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 1809.217 Da / Num. of mol.: 4 / Source method: obtained synthetically #2: Chemical | ChemComp-DM5 / #3: Chemical | ChemComp-SPM / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.7 Å3/Da / Density % sol: 66.8 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 277.00K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 277 K / pH: 6.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 |
Detector | Type: RIGAKU AFC-5 / Detector: DIFFRACTOMETER |
Radiation | Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Highest resolution: 2 Å / Num. all: 7276 / Observed criterion σ(F): 2 |
Reflection | *PLUS Highest resolution: 2 Å / Lowest resolution: 10 Å / Num. obs: 3768 / Observed criterion σ(F): 2 / Rmerge(I) obs: 0.061 |
-Processing
Software | Name: NUCLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 1.97→18 Å / σ(F): 2 /
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Refine Biso |
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Refinement step | Cycle: LAST / Resolution: 1.97→18 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 10 Å / σ(F): 2 / Rfactor obs: 0.19 / Rfactor Rwork: 0.19 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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