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Yorodumi- PDB-298d: TARGETING THE MINOR GROOVE OF DNA: CRYSTAL STRUCTURES OF TWO COMP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 298d | ||||||||||||||||||
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Title | TARGETING THE MINOR GROOVE OF DNA: CRYSTAL STRUCTURES OF TWO COMPLEXES BETWEEN FURAN DERIVATIVES OF BERENIL AND THE DNA DODECAMER D(CGCGAATTCGCG)2 | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / B-DNA / DOUBLE HELIX / COMPLEXED WITH DRUG | Function / homology | Chem-D18 / DNA / DNA (> 10) | Function and homology information Method | X-RAY DIFFRACTION / Resolution: 2.2 Å | Authors | Trent, J.O. / Clark, G.R. / Kumar, A. / Wilson, W.D. / Boykin, D.W. / Hall, J.E. / Tidwell, R.R. / Blagburn, B.L. / Neidle, S. | Citation | Journal: J.Med.Chem. / Year: 1996 Title: Targeting the minor groove of DNA: crystal structures of two complexes between furan derivatives of berenil and the DNA dodecamer d(CGCGAATTCGCG)2. Authors: Trent, J.O. / Clark, G.R. / Kumar, A. / Wilson, W.D. / Boykin, D.W. / Hall, J.E. / Tidwell, R.R. / Blagburn, B.L. / Neidle, S. #1: Journal: Biochemistry / Year: 1996 Title: A Crystallographic and Spectroscopic Study of the Complex Between d(CGCGAATTCGCG)2 and 2,5-Bis(4-guanylphenyl)furan, an Analogue of Berenil. Structural Origins of Enhanced DNA-binding Affinity Authors: Laughton, C.A. / Tanious, F. / Nunn, C.M. / Boykin, D.W. / Wilson, W.D. / Neidle, S. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 298d.cif.gz | 25.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb298d.ent.gz | 16.1 KB | Display | PDB format |
PDBx/mmJSON format | 298d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 298d_validation.pdf.gz | 556.6 KB | Display | wwPDB validaton report |
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Full document | 298d_full_validation.pdf.gz | 557.6 KB | Display | |
Data in XML | 298d_validation.xml.gz | 4.5 KB | Display | |
Data in CIF | 298d_validation.cif.gz | 5.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/98/298d ftp://data.pdbj.org/pub/pdb/validation_reports/98/298d | HTTPS FTP |
-Related 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: isolated from a natural source #2: Chemical | ChemComp-D18 / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.13 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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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 Temperature: 286 K / 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: Sep 12, 1995 |
Radiation | Monochromator: GRAPHITE / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 2.2 Å / Num. obs: 3146 / % possible obs: 87.6 % / Rmerge(I) obs: 0.073 |
Reflection | *PLUS Highest resolution: 2.2 Å / Num. all: 3592 / % possible obs: 87.6 % |
-Processing
Software |
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Refinement | Starting model: BDL001 Resolution: 2.2→8 Å / σ(F): 2 /
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Refine Biso |
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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: 3.5 Å / Lowest resolution: 8 Å / σ(F): 2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |