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Yorodumi- PDB-102d: SEQUENCE-DEPENDENT DRUG BINDING TO THE MINOR GROOVE OF DNA: THE C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 102d | ||||||||||||||||||
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Title | SEQUENCE-DEPENDENT DRUG BINDING TO THE MINOR GROOVE OF DNA: THE CRYSTAL STRUCTURE OF THE DNA DODECAMER D(CGCAAATTTGCG)2 COMPLEXED WITH PROPAMIDINE | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / B-DNA / DOUBLE HELIX / COMPLEXED WITH DRUG | Function / homology | 1,3-BIS(AMIDINOPHENOXY)PROPANE / DNA / DNA (> 10) | Function and homology information Method | X-RAY DIFFRACTION / Resolution: 2.2 Å | Authors | Nunn, C.M. / Neidle, S. | Citation | Journal: J.Med.Chem. / Year: 1995 | Title: Sequence-dependent drug binding to the minor groove of DNA: crystal structure of the DNA dodecamer d(CGCAAATTTGCG)2 complexed with propamidine. Authors: 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 | 102d.cif.gz | 25.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb102d.ent.gz | 16.1 KB | Display | PDB format |
PDBx/mmJSON format | 102d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/02/102d ftp://data.pdbj.org/pub/pdb/validation_reports/02/102d | 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: 3662.404 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Chemical | ChemComp-TNT / | #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: 2.28 Å3/Da / Density % sol: 46.06 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: pH 7.00, VAPOR DIFFUSION, SITTING DROP, temperature 277.00K | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 289 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: 12110 / Num. obs: 3410 / Rmerge(I) obs: 0.053 |
Reflection | *PLUS Highest resolution: 2.2 Å / Num. obs: 2341 / Observed criterion σ(F): 2 / Rmerge(I) obs: 0.053 |
-Processing
Software |
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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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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 8 Å / σ(F): 2 / Rfactor obs: 0.155 / Rfactor Rwork: 0.155 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 4 |