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Yorodumi- PDB-443d: 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'/ BENZIMIDAZOLE DERIV... -
+Open data
-Basic information
Entry | Database: PDB / ID: 443d | ||||||||||||||||||
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Title | 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'/ BENZIMIDAZOLE DERIVATIVE COMPLEX | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / B-DNA / MINOR GROOVE BINDING | Function / homology | Chem-IA / DNA / DNA (> 10) | Function and homology information Method | X-RAY DIFFRACTION / Resolution: 1.6 Å | Authors | Squire, C.J. / Baker, L.J. / Clark, G.R. / Martin, R.F. / White, J. | Citation | Journal: Nucleic Acids Res. / Year: 2000 Title: Structures of m-iodo Hoechst-DNA complexes in crystals with reduced solvent content: implications for minor groove binder drug design. Authors: Squire, C.J. / Baker, L.J. / Clark, G.R. / Martin, R.F. / White, J. #1: Journal: Nucleic Acids Res. / Year: 2000 Title: Intermolecular interactions and water structure in a condensed phase B-DNA crystal Authors: Clark, G.R. / Squire, C.J. / Baker, L.J. / Martin, R.F. / White, J. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 443d.cif.gz | 28.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb443d.ent.gz | 16.9 KB | Display | PDB format |
PDBx/mmJSON format | 443d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 443d_validation.pdf.gz | 599.4 KB | Display | wwPDB validaton report |
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Full document | 443d_full_validation.pdf.gz | 624.1 KB | Display | |
Data in XML | 443d_validation.xml.gz | 7.2 KB | Display | |
Data in CIF | 443d_validation.cif.gz | 8.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/43/443d ftp://data.pdbj.org/pub/pdb/validation_reports/43/443d | HTTPS FTP |
-Related structure data
Related structure data | 442dC 444dC 445dC 447dC 448dC 449dC C: citing same article (ref.) |
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Similar 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-IA / | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.78 Å3/Da / Density % sol: 30.88 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||
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: SIEMENS / Wavelength: 0.7107 |
Detector | Type: BRUKER SMART / Detector: CCD / Date: Dec 28, 1997 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7107 Å / Relative weight: 1 |
Reflection | Highest resolution: 1.6 Å / Num. all: 7321 / Num. obs: 7321 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Redundancy: 5.02 % / Rmerge(I) obs: 0.092 |
Reflection shell | Resolution: 1.6→1.657 Å / Rmerge(I) obs: 0.459 |
Reflection | *PLUS Num. obs: 8269 / Observed criterion σ(F): 2 |
-Processing
Software |
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Refinement | Resolution: 1.6→8 Å / Cross valid method: THROUGHOUT / σ(F): 4
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Refinement step | Cycle: LAST / Resolution: 1.6→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.187 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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