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Yorodumi- PDB-1d63: CRYSTAL STRUCTURE OF A BERENIL-D(CGCAAATTTGCG) COMPLEX; AN EXAMPL... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1d63 | ||||||||||||||||||
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Title | CRYSTAL STRUCTURE OF A BERENIL-D(CGCAAATTTGCG) COMPLEX; AN EXAMPLE OF DRUG-DNA RECOGNITION BASED ON SEQUENCE-DEPENDENT STRUCTURAL FEATURES | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / B-DNA / DOUBLE HELIX / COMPLEXED WITH DRUG | Function / homology | BERENIL / DNA / DNA (> 10) | Function and homology information Method | X-RAY DIFFRACTION / Resolution: 2 Å | Authors | Brown, D.G. / Sanderson, M.R. / Garman, E. / Neidle, S. | Citation | Journal: J.Mol.Biol. / Year: 1992 Title: Crystal structure of a berenil-d(CGCAAATTTGCG) complex. An example of drug-DNA recognition based on sequence-dependent structural features. Authors: Brown, D.G. / Sanderson, M.R. / Garman, E. / Neidle, S. #1: Journal: Embo J. / Year: 1990 Title: Crystal Structure of a Berenil-Dodecanucleotide Complex: The Role of Water in Sequence-Specific Ligand Binding Authors: Brown, D.G. / Sanderson, M.R. / Skelly, J.V. / Jenkins, T.C. / Brown, T. / Garman, E. / Stuart, D.I. / Neidle, S. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1d63.cif.gz | 26.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1d63.ent.gz | 16.6 KB | Display | PDB format |
PDBx/mmJSON format | 1d63.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1d63_validation.pdf.gz | 606.7 KB | Display | wwPDB validaton report |
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Full document | 1d63_full_validation.pdf.gz | 613.5 KB | Display | |
Data in XML | 1d63_validation.xml.gz | 5 KB | Display | |
Data in CIF | 1d63_validation.cif.gz | 6.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d6/1d63 ftp://data.pdbj.org/pub/pdb/validation_reports/d6/1d63 | 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-MG / | #3: Chemical | ChemComp-BRN / | #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: 2.22 Å3/Da / Density % sol: 44.65 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7 / Details: pH 7.00, VAPOR DIFFUSION, HANGING DROP / Temp details: ROOM TEMPERATURE | ||||||||||||||||||||||||||||||||||||||||||||||||
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: 291 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 |
Detector | Type: XENTRONICS / Detector: AREA DETECTOR |
Radiation | Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Highest resolution: 2 Å / Num. all: 12415 / Num. obs: 4067 / Rmerge(I) obs: 0.062 |
Reflection | *PLUS Highest resolution: 2 Å / Num. all: 4530 / Num. measured all: 14737 |
-Processing
Software | Name: NUCLSQ / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2→7 Å / σ(F): 2 /
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Refine Biso |
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Refinement step | Cycle: LAST / Resolution: 2→7 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 7 Å / σ(F): 2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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