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Yorodumi- PDB-152d: DIVERSITY OF WATER RING SIZE AT DNA INTERFACES: HYDRATION AND DYN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 152d | ||||||||||||||||||
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Title | DIVERSITY OF WATER RING SIZE AT DNA INTERFACES: HYDRATION AND DYNAMICS OF DNA-ANTHRACYCLINE COMPLEXES | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / RIGHT HANDED DNA / DOUBLE HELIX / COMPLEXED WITH DRUG | Function / homology | DAUNOMYCIN / DNA | Function and homology information Method | X-RAY DIFFRACTION / Resolution: 1.4 Å | Authors | Lipscomb, L.A. / Peek, M.E. / Zhou, F.X. / Bertrand, J.A. / VanDerveer, D. / Williams, L.D. | Citation | Journal: Biochemistry / Year: 1994 | Title: Water ring structure at DNA interfaces: hydration and dynamics of DNA-anthracycline complexes. Authors: Lipscomb, L.A. / Peek, M.E. / Zhou, F.X. / Bertrand, J.A. / VanDerveer, D. / Williams, L.D. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 152d.cif.gz | 15.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb152d.ent.gz | 8.6 KB | Display | PDB format |
PDBx/mmJSON format | 152d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 152d_validation.pdf.gz | 416 KB | Display | wwPDB validaton report |
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Full document | 152d_full_validation.pdf.gz | 423.7 KB | Display | |
Data in XML | 152d_validation.xml.gz | 2.6 KB | Display | |
Data in CIF | 152d_validation.cif.gz | 3.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/52/152d ftp://data.pdbj.org/pub/pdb/validation_reports/52/152d | HTTPS FTP |
-Related structure data
-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.: 1 / Source method: obtained synthetically |
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#2: Chemical | ChemComp-DM1 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.14 % | ||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 6.5 / Details: pH 6.50, VAPOR DIFFUSION, SITTING DROP | ||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 |
Detector | Type: SDMS / Detector: AREA DETECTOR |
Radiation | Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Highest resolution: 1.4 Å / Num. all: 54233 / Num. obs: 3817 / Observed criterion σ(F): 1 |
Reflection | *PLUS Highest resolution: 1.4 Å / Observed criterion σ(F): 1 / Num. measured all: 54233 / Rmerge F obs: 0.0854 |
-Processing
Software | Name: NUCLSQ / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Highest resolution: 1.4 Å / σ(F): 1 /
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Refine Biso |
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Refinement step | Cycle: LAST / Highest resolution: 1.4 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 1.4 Å / σ(F): 1 / Rfactor obs: 0.226 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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