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- PDB-4mnb: Crystal Structure of a complex between the marine anticancer drug... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4mnb | ||||||||||||||||||
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Title | Crystal Structure of a complex between the marine anticancer drug Variolin B and DNA | ||||||||||||||||||
![]() | 5'-D(*![]() DNA / DNA duplex / Intercalation / Drug binding / Nucleus | Function / homology | : / COBALT HEXAMMINE(III) / Chem-VAR / DNA | ![]() Method | ![]() ![]() ![]() ![]() Canals, A. / Arribas-Bosacoma, R. / Alvarez, M. / Albericio, F. / Aymami, J. / Coll, M. | ![]() ![]() Title: Intercalative DNA binding of the marine anticancer drug variolin B. Authors: Canals, A. / Arribas-Bosacoma, R. / Albericio, F. / Alvarez, M. / Aymami, J. / Coll, M. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 18.8 KB | Display | ![]() |
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PDB format | ![]() | 11.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 3.8 KB | Display | |
Data in CIF | ![]() | 4.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-DNA chain , 1 types, 2 molecules AB
#1: DNA chain | Mass: 1809.217 Da / Num. of mol.: 2 / Source method: obtained synthetically |
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-Non-polymers , 5 types, 32 molecules ![](data/chem/img/VAR.gif)
![](data/chem/img/NCO.gif)
![](data/chem/img/CO.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NCO.gif)
![](data/chem/img/CO.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-CO / | #5: Chemical | ChemComp-NA / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.06 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.8 Details: 8% v/v MPD, 40 mM Na Cacodylate pH 5.8, 4 mM Hexamine Cobalt, 12 mM NaCl, 80 mM KCl, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 28, 2007 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→40.8 Å / Num. all: 6471 / Num. obs: 6465 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.544 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→40.79 Å
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Refine LS restraints |
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