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Yorodumi- PDB-263d: ISOHELICITY AND PHASING IN DRUG-DNA SEQUENCE RECOGNITION: CRYSTAL... -
+Open data
-Basic information
Entry | Database: PDB / ID: 263d | ||||||||||||||||||
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Title | ISOHELICITY AND PHASING IN DRUG-DNA SEQUENCE RECOGNITION: CRYSTAL STRUCTURE OF A TRIS(BENZIMIDAZOLE)-OLIGONUCLEOTIDE COMPLEX | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / B-DNA / DOUBLE HELIX / COMPLEXED WITH DRUG | Function / homology | Chem-TBZ / DNA / DNA (> 10) | Function and homology information Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | Authors | Clark, G.R. / Gray, E.J. / Neidle, S. / Li, Y.-H. / Leupin, W. | Citation | Journal: Biochemistry / Year: 1996 Title: Isohelicity and phasing in drug--DNA sequence recognition: crystal structure of a tris(benzimidazole)--oligonucleotide complex. Authors: Clark, G.R. / Gray, E.J. / Neidle, S. / Li, Y.H. / Leupin, W. #1: Journal: Nucleic Acids Res. / Year: 1994 Title: Sequence-Dependent Effects in Drug-DNA Interaction: The Crystal Structure of Hoechst 33258 Bound to the d(CGCAAATTTGCG)2 Duplex Authors: Spink, N. / Skelly, J.V. / Neidle, S. #2: Journal: Eur.J.Biochem. / Year: 1994 Title: Three-Dimensional Crystal Structure of the A-Tract DNA Dodecamer d(CGCAAATTTGCG) Complexed with the Minor-Groove-Binding Drug Hoechst 33258 Authors: Vega, M.C. / Saez, I.G. / Aymami, J. / Eritja, R. / van der Marel, G.A. / van Boom, J.H. / Rich, A. / Coll, M. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 263d.cif.gz | 25 KB | Display | PDBx/mmCIF format |
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PDB format | pdb263d.ent.gz | 16.2 KB | Display | PDB format |
PDBx/mmJSON format | 263d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 263d_validation.pdf.gz | 566.6 KB | Display | wwPDB validaton report |
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Full document | 263d_full_validation.pdf.gz | 568.9 KB | Display | |
Data in XML | 263d_validation.xml.gz | 4.4 KB | Display | |
Data in CIF | 263d_validation.cif.gz | 5.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/63/263d ftp://data.pdbj.org/pub/pdb/validation_reports/63/263d | 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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Unit cell |
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-Components
#1: DNA chain | Mass: 3662.404 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Chemical | ChemComp-TBZ / | #3: 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: 2.23 Å3/Da / Density % sol: 44.93 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 286 K / Method: vapor diffusion, hanging drop / pH: 7 Details: pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 286.00K | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS pH: 7 | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: ROTATING ANODE / Wavelength: 1.5418 |
Detector | Type: XENTRONICS / Detector: AREA DETECTOR / Date: May 15, 1996 |
Radiation | Monochromator: GRAPHITE / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→8 Å / Num. obs: 3594 / % possible obs: 92 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.083 |
Reflection shell | Resolution: 2.2→2.35 Å / % possible all: 57 |
Reflection | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 8 Å / % possible obs: 92 % / Observed criterion σ(I): 2 |
Reflection shell | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 2.35 Å / % possible obs: 57 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: GDL023 Resolution: 2.2→8 Å / σ(F): 2
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Displacement parameters | Biso mean: 24 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine Biso | Class: ALL ATOMS / Details: TR / Treatment: isotropic | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 8 Å / σ(F): 2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |