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Yorodumi- PDB-1d46: DNA DODECAMER C-G-C-G-A-A-T-T-C-G-C-G/HOECHST 33258 COMPLEX:-100 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1d46 | ||||||||||||||||||
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Title | DNA DODECAMER C-G-C-G-A-A-T-T-C-G-C-G/HOECHST 33258 COMPLEX:-100 DEGREES C, PIPERAZINE DOWN | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / B-DNA / DOUBLE HELIX / COMPLEXED WITH DRUG | Function / homology | Chem-HT / DNA / DNA (> 10) | Function and homology information Method | X-RAY DIFFRACTION / Resolution: 2 Å | Authors | Quintana, J.R. / Lipanov, A.A. / Dickerson, R.E. | Citation | Journal: Biochemistry / Year: 1991 Title: Low-temperature crystallographic analyses of the binding of Hoechst 33258 to the double-helical DNA dodecamer C-G-C-G-A-A-T-T-C-G-C-G. Authors: Quintana, J.R. / Lipanov, A.A. / Dickerson, R.E. #1: Journal: Nucleic Acids Res. / Year: 1988 Title: The Molecular Structure of the Complex of Hoechst 33258 and the DNA Dodecamer d(CGCGAATTCGCG) Authors: Teng, M. / Usman, N. / Frederick, C.A. / Wang, A.H.-J. #2: Journal: J.Mol.Biol. / Year: 1987 Title: Binding of Hoechst 33258 to the Minor Groove of B-DNA Authors: Pjura, P.E. / Grzeskowiak, K. / Dickerson, R.E. #3: Journal: J.Med.Chem. / Year: 1986 Title: Isohelical Analysis of DNA Groove-Binding Drugs Authors: Goodsell, D. / Dickerson, R.E. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1d46.cif.gz | 27.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1d46.ent.gz | 17.4 KB | Display | PDB format |
PDBx/mmJSON format | 1d46.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d4/1d46 ftp://data.pdbj.org/pub/pdb/validation_reports/d4/1d46 | HTTPS FTP |
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-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: 3663.392 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Chemical | ChemComp-MG / | #3: Chemical | ChemComp-HT / | #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: 2.08 Å3/Da / Density % sol: 40.79 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.9 Details: pH 6.90, VAPOR DIFFUSION, SITTING DROP, temperature 277.00K | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, sitting drop / pH: 6.9 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 173 K |
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Diffraction source | Source: ROTATING ANODE |
Detector | Type: RIGAKU AFC-5R / Detector: DIFFRACTOMETER |
Radiation | Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2 Å / Lowest resolution: 8 Å / Num. obs: 2072 / Rmerge(I) obs: 0.187 |
-Processing
Software | Name: NUCLSQ / Classification: refinement | ||||||||||||
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Refinement | Resolution: 2→8 Å / σ(F): 2 /
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Refine Biso |
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Refinement step | Cycle: LAST / Resolution: 2→8 Å
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Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 8 Å / σ(F): 2 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS |