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Yorodumi- PDB-1nab: The crystal structure of the complex between a disaccharide anthr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nab | ||||||||||||||||||
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Title | The crystal structure of the complex between a disaccharide anthracycline and the DNA hexamer d(CGATCG) reveals two different binding sites involving two DNA duplexes | ||||||||||||||||||
Components | 5'-D(*Keywords | DNA / right handed dna / double helix / complexed with drug | Function / homology | Chem-44D / DNA | Function and homology information Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | Authors | Temperini, C. / Messori, L. / Orioli, P. / Di Bugno, C. / Animati, F. / Ughetto, G. | Citation | Journal: Nucleic Acids Res. / Year: 2003 Title: The crystal structure of the complex between a disaccharide anthracycline and the DNA hexamer d(CGATCG) reveals two different binding sites involving two DNA duplexes Authors: Temperini, C. / Messori, L. / Orioli, P. / Di Bugno, C. / Animati, F. / Ughetto, G. #1: Journal: Biochemistry / Year: 1990 Title: Structural comparison of anticancer drug-dna complexes: adriamycin and daunomycin Authors: Frederick, C.A. / Williams, L.D. / Ughetto, G. / van der Marel, G.A. / van Boom, J.H. / Rich, A. / Wang, A.H. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nab.cif.gz | 22.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nab.ent.gz | 13.1 KB | Display | PDB format |
PDBx/mmJSON format | 1nab.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nab_validation.pdf.gz | 991.2 KB | Display | wwPDB validaton report |
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Full document | 1nab_full_validation.pdf.gz | 1017.9 KB | Display | |
Data in XML | 1nab_validation.xml.gz | 7.7 KB | Display | |
Data in CIF | 1nab_validation.cif.gz | 8.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/na/1nab ftp://data.pdbj.org/pub/pdb/validation_reports/na/1nab | HTTPS FTP |
-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: 1809.217 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: automatic synthesis #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.11 Å3/Da / Density % sol: 60.49 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: magnesium chloride, cacodylate, spermine hydrochloride, MPD, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 4 ℃ | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.03 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 27, 2001 / Details: mirrors |
Radiation | Monochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→18.9 Å / Num. all: 28812 / Num. obs: 28737 / % possible obs: 95.4 % / Observed criterion σ(I): 1 / Redundancy: 10.9 % / Biso Wilson estimate: 41.56 Å2 / Rmerge(I) obs: 0.118 / Net I/σ(I): 5.4 |
Reflection shell | Resolution: 2.1→2.17 Å / Rmerge(I) obs: 0.0874 / % possible all: 75.6 |
Reflection | *PLUS Lowest resolution: 8 Å / Num. obs: 2621 |
Reflection shell | *PLUS Highest resolution: 2.15 Å / % possible obs: 75.6 % / Rmerge(I) obs: 0.531 / Mean I/σ(I) obs: 1.37 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→8 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Hendrickson, W.A.
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Refinement step | Cycle: LAST / Resolution: 2.15→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.2 Å /
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Refinement | *PLUS Lowest resolution: 8 Å / % reflection Rfree: 10 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 2.15 Å / Lowest resolution: 2.17 Å |