[English] 日本語
Yorodumi- PDB-1aio: CRYSTAL STRUCTURE OF A DOUBLE-STRANDED DNA CONTAINING THE MAJOR A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1aio | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF A DOUBLE-STRANDED DNA CONTAINING THE MAJOR ADDUCT OF THE ANTICANCER DRUG CISPLATIN | |||||||||
Components |
| |||||||||
Keywords | DNA / RIGHT HANDED DNA / DOUBLE HELIX / COMPLEXED WITH DRUG / MODIFIED | |||||||||
Function / homology | Cisplatin / DNA / DNA (> 10) Function and homology information | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 2.6 Å | |||||||||
Authors | Takahara, P.M. / Rosenzweig, A.C. / Frederick, C.A. / Lippard, S.J. | |||||||||
Citation | Journal: Nature / Year: 1995 Title: Crystal structure of double-stranded DNA containing the major adduct of the anticancer drug cisplatin. Authors: Takahara, P.M. / Rosenzweig, A.C. / Frederick, C.A. / Lippard, S.J. #1: Journal: J.Am.Chem.Soc. / Year: 1996 Title: Crystal Structure of the Anticancer Drug Cisplatin Bound to Duplex DNA Authors: Takahara, P.M. / Frederick, C.A. / Lippard, S.J. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1aio.cif.gz | 39.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1aio.ent.gz | 26.1 KB | Display | PDB format |
PDBx/mmJSON format | 1aio.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ai/1aio ftp://data.pdbj.org/pub/pdb/validation_reports/ai/1aio | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: DNA chain | Mass: 3630.186 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source #2: DNA chain | Mass: 3761.468 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 4 |
---|
-Sample preparation
Crystal | Density Matthews: 3.32 Å3/Da / Density % sol: 62.94 % | ||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 277.00K | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
| ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 6 | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 277 K |
---|---|
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 1995 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.6→8 Å / Num. obs: 5797 / Observed criterion σ(I): 1 |
Reflection | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 8 Å / % possible obs: 97 % / Rmerge(I) obs: 0.062 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.6→8 Å / Cross valid method: THROUGHOUT / σ(F): 1
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 8 Å / σ(F): 1 / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |