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- PDB-109d: VARIABILITY IN DNA MINOR GROOVE WIDTH RECOGNISED BY LIGAND BINDIN... -
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Open data
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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 | ||||||||||||||||||
![]() | DNA (5'-D(*![]() DNA / B-DNA / DOUBLE HELIX / COMPLEXED WITH DRUG | Function / homology | Chem-IBB / DNA / DNA (> 10) | ![]() Method | ![]() ![]() Czarny, A. / Boykin, D.W. / Wood, A.A. / Nunn, C.M. / Neidle, S. / Zhao, M. / Wilson, W.D. | ![]() ![]() 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: ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 27.4 KB | Display | ![]() |
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PDB format | ![]() | 17.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 574.2 KB | Display | ![]() |
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Full document | ![]() | 585 KB | Display | |
Data in XML | ![]() | 6.2 KB | Display | |
Data in CIF | ![]() | 7.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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: ![]() |
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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: ![]() |
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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 |
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Processing
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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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Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 8 Å / σ(F): 2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |