+Open data
-Basic information
Entry | Database: PDB / ID: 1d17 | ||||||||||||||||||
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Title | DNA-NOGALAMYCIN INTERACTIONS | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / RIGHT HANDED DNA / DOUBLE HELIX / COMPLEXED WITH DRUG / MODIFIED | Function / homology | NOGALAMYCIN / DNA | Function and homology information Method | X-RAY DIFFRACTION / Resolution: 2 Å | Authors | Egli, M. / Williams, L.D. / Frederick, C.A. / Rich, A. | Citation | Journal: Biochemistry / Year: 1991 Title: DNA-nogalamycin interactions. Authors: Egli, M. / Williams, L.D. / Frederick, C.A. / Rich, A. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1990 Title: Structure of Nogalamycin Bound to a DNA Hexamer Authors: Williams, L.D. / Egli, M. / Gao, Q. / Bash, P. / Van Der Marel, G.A. / Van Boom, J.H. / Rich, A. / Frederick, C.A. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1d17.cif.gz | 15.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1d17.ent.gz | 9.4 KB | Display | PDB format |
PDBx/mmJSON format | 1d17.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1d17_validation.pdf.gz | 414.8 KB | Display | wwPDB validaton report |
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Full document | 1d17_full_validation.pdf.gz | 418.5 KB | Display | |
Data in XML | 1d17_validation.xml.gz | 2.6 KB | Display | |
Data in CIF | 1d17_validation.cif.gz | 3.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d1/1d17 ftp://data.pdbj.org/pub/pdb/validation_reports/d1/1d17 | 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: 1837.271 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: Chemical | ChemComp-NGM / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.73 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 6 / Details: pH 6.00, VAPOR DIFFUSION, SITTING DROP / Temp details: ROOM TEMPERATURE | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS pH: 6 / Method: vapor diffusion, sitting dropDetails: Williams, L.D., (1990) Proc.Natl.Acad.Sci.USA, 87, 2225. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 300 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: RIGAKU AFC-5 / Detector: DIFFRACTOMETER |
Radiation | Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
-Processing
Software | Name: X-PLOR / Classification: refinement | |||||||||||||||||||||||||||||||||
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Refinement | Highest resolution: 2 Å / σ(F): 2 /
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Refine Biso |
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Refinement step | Cycle: LAST / Highest resolution: 2 Å
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Software | *PLUS Name: NUCLSQ / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 2 / Highest resolution: 2 Å / Lowest resolution: 2.5 Å / Num. reflection obs: 809 / Rfactor obs: 0.206 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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