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Yorodumi- PDB-166d: DRUG-DNA MINOR GROOVE RECOGNITION: CRYSTAL STRUCTURE OF GAMMA-OXA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 166d | ||||||||||||||||||
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Title | DRUG-DNA MINOR GROOVE RECOGNITION: CRYSTAL STRUCTURE OF GAMMA-OXAPENTAMIDINE COMPLEXED WITH D(CGCGAATTCGCG)2 | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / B-DNA / DOUBLE HELIX / COMPLEXED WITH DRUG | Function / homology | 1,5-DI(4-AMIDINOPHENOXY)-3-OXA-PENTANE / DNA / DNA (> 10) | Function and homology information Method | X-RAY DIFFRACTION / Resolution: 2.2 Å | Authors | Nunn, C.M. / Jenkins, T.C. / Neidle, S. | Citation | Journal: Eur.J.Biochem. / Year: 1994 | Title: Crystal structure of gamma-oxapentamidine complexed with d(CGCGAATTCGCG)2. The effects of drug structural change on DNA minor-groove recognition. Authors: Nunn, C.M. / Jenkins, T.C. / Neidle, S. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 166d.cif.gz | 26 KB | Display | PDBx/mmCIF format |
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PDB format | pdb166d.ent.gz | 16.3 KB | Display | PDB format |
PDBx/mmJSON format | 166d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/66/166d ftp://data.pdbj.org/pub/pdb/validation_reports/66/166d | 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-PET / | #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: 2.26 Å3/Da / Density % sol: 45.54 % | ||||||||||||||||||||||||||||||||||||||||||
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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: 2.1 Å / Num. all: 9633 / Num. obs: 3846 |
Reflection | *PLUS Highest resolution: 2.1 Å / Num. all: 4315 / % possible obs: 89.1 % / Num. measured all: 11165 / Rmerge(I) obs: 0.078 |
-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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Refinement | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 8 Å / σ(F): 2 | ||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||
Refine LS restraints | *PLUS
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