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Yorodumi- PDB-159d: SIDE BY SIDE BINDING OF TWO DISTAMYCIN A DRUGS IN THE MINOR GROOV... -
+Open data
-Basic information
Entry | Database: PDB / ID: 159d | ||||||||||||||||||
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Title | SIDE BY SIDE BINDING OF TWO DISTAMYCIN A DRUGS IN THE MINOR GROOVE OF AN ALTERNATING B-DNA DUPLEX | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / B-DNA / DOUBLE HELIX / COMPLEXED WITH DRUG / MODIFIED | Function / homology | DISTAMYCIN A / DNA | Function and homology information Method | X-RAY DIFFRACTION / Resolution: 1.8 Å | Authors | Chen, X. / Ramakrishnan, B. / Rao, S.T. / Sundaralingam, M. | Citation | Journal: Nat.Struct.Biol. / Year: 1994 | Title: Binding of two distamycin A molecules in the minor groove of an alternating B-DNA duplex. Authors: Chen, X. / Ramakrishnan, B. / Rao, S.T. / Sundaralingam, M. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 159d.cif.gz | 14.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb159d.ent.gz | 9.8 KB | Display | PDB format |
PDBx/mmJSON format | 159d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 159d_validation.pdf.gz | 613.5 KB | Display | wwPDB validaton report |
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Full document | 159d_full_validation.pdf.gz | 613.6 KB | Display | |
Data in XML | 159d_validation.xml.gz | 3.6 KB | Display | |
Data in CIF | 159d_validation.cif.gz | 4.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/59/159d ftp://data.pdbj.org/pub/pdb/validation_reports/59/159d | 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: 2368.537 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: Chemical | ChemComp-DMY / |
#3: Chemical | ChemComp-MG / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.19 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7 / Details: pH 7.00, VAPOR DIFFUSION, HANGING DROP / Temp details: ROOM TEMPERATURE | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS pH: 7 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: ROTATING ANODE |
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Detector | Type: SIEMENS / Detector: AREA DETECTOR |
Radiation | Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.8→16 Å / Num. all: 10245 / Num. obs: 2423 |
Reflection | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 16 Å / % possible obs: 94 % / Num. measured all: 10245 / Rmerge(I) obs: 0.018 |
-Processing
Software | Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 1.8→10 Å / σ(F): 2 /
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Refine Biso |
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Refinement step | Cycle: LAST / Resolution: 1.8→10 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 10 Å / σ(F): 2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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