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Yorodumi- PDB-109d: VARIABILITY IN DNA MINOR GROOVE WIDTH RECOGNISED BY LIGAND BINDIN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 109d | ||||||||||||||||||
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Title | VARIABILITY IN DNA MINOR GROOVE WIDTH RECOGNISED BY LIGAND BINDING: THE CRYSTAL STRUCTURE OF A BIS-BENZIMIDAZOLE COMPOUND BOUND TO THE DNA DUPLEX D(CGCGAATTCGCG)2 | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / B-DNA / DOUBLE HELIX / COMPLEXED WITH DRUG | Function / homology | Chem-IBB / DNA / DNA (> 10) | Function and homology information Method | X-RAY DIFFRACTION / Resolution: 2 Å | Authors | Czarny, A. / Boykin, D.W. / Wood, A.A. / Nunn, C.M. / Neidle, S. / Zhao, M. / Wilson, W.D. | Citation | Journal: Nucleic Acids Res. / Year: 1995 Title: Variability in DNA minor groove width recognised by ligand binding: the crystal structure of a bis-benzimidazole compound bound to the DNA duplex d(CGCGAATTCGCG)2. Authors: Wood, A.A. / Nunn, C.M. / Czarny, A. / Boykin, D.W. / Neidle, S. #1: Journal: J.Am.Chem.Soc. / Year: 1995 Title: Analysis of Van Der Waals and Electrostatic Contributions in the Interactions of Minor Groove Binding Benzimidazoles with DNA Authors: Czarny, A. / Boykin, D.W. / Wood, A.A. / Nunn, C.M. / Neidle, S. / Zhao, M. / Wilson, W.D. #2: 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. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 109d.cif.gz | 27.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb109d.ent.gz | 17.3 KB | Display | PDB format |
PDBx/mmJSON format | 109d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/09/109d ftp://data.pdbj.org/pub/pdb/validation_reports/09/109d | HTTPS FTP |
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-Related structure data
Similar structure data |
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-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-IBB / | #3: Chemical | ChemComp-MG / | #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: 2.23 Å3/Da / Density % sol: 44.88 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 19 ℃ / pH: 7 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS / Wavelength: 1.5418 |
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Detector | Type: XENTRONICS / Detector: AREA DETECTOR |
Radiation | Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | % possible obs: 87 % |
Reflection | *PLUS Highest resolution: 2 Å / Num. all: 5026 / Num. obs: 4365 / % possible obs: 87 % / Num. measured all: 11176 / Rmerge(I) obs: 0.031 |
-Processing
Software | Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2→8 Å / σ(F): 2 /
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Refinement step | Cycle: LAST / Resolution: 2→8 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 8 Å / σ(F): 2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |