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Yorodumi- PDB-227d: A CRYSTALLOGRAPHIC AND SPECTROSCOPIC STUDY OF THE COMPLEX BETWEEN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 227d | ||||||||||||||||||
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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 | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / B-DNA / DOUBLE HELIX / COMPLEXED WITH DRUG | Function / homology | 2,5-BIS(4-GUANYLPHENYL)FURAN / DNA / DNA (> 10) | Function and homology information Method | X-RAY DIFFRACTION / Resolution: 2.2 Å | Authors | Laughton, C.A. / Tanious, F. / Nunn, C.M. / Boykin, D.W. / Wilson, W.D. / Neidle, S. | Citation | 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. #1: Journal: J.Med.Chem. / Year: 1995 Title: Dicationic Diarylfurans as Anti-Pneumocystis Carinii Agents Authors: Boykin, D.W. / Kumar, A. / Spychala, J. / Zhou, M. / Lombardy, R.J. / Wilson, W.D. / Dykstra, C.C. / Jones, S.K. / Hall, J.E. / Tidwell, R.R. / Laughton, C. / Nunn, C.M. / Neidle, S. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 227d.cif.gz | 25.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb227d.ent.gz | 15.9 KB | Display | PDB format |
PDBx/mmJSON format | 227d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/27/227d ftp://data.pdbj.org/pub/pdb/validation_reports/27/227d | HTTPS FTP |
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-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: 3663.392 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Chemical | ChemComp-BGF / | #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: 2.34 Å3/Da / Density % sol: 47.48 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 286 K / Method: vapor diffusion, sitting drop / pH: 7 Details: pH 7.00, VAPOR DIFFUSION, SITTING 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 |
Radiation | Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 2.2 Å / Num. all: 3693 / Num. obs: 3472 |
Reflection | *PLUS Highest resolution: 2.2 Å / Num. all: 3895 / Rmerge(I) obs: 0.088 |
Reflection shell | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 2.4 Å / % possible obs: 55 % / Mean I/σ(I) obs: 2 |
-Processing
Software | Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | 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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Refinement | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 8 Å / σ(F): 2 / Rfactor obs: 0.178 / Rfactor Rwork: 0.178 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |