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- PDB-5dnn: Nucleosome core particle containing adducts of gold(I)-triethylph... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5dnn | ||||||
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Title | Nucleosome core particle containing adducts of gold(I)-triethylphosphane and ruthenium(II)-toluene PTA complexes | ||||||
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![]() | STRUCTURAL PROTEIN/DNA / nucleosome / gold antitumour compound / ruthenium antitumour compound / histone binding / STRUCTURAL PROTEIN-DNA complex | ||||||
Function / homology | ![]() structural constituent of chromatin / nucleosome / nucleosome assembly / protein heterodimerization activity / DNA binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Adhireksan, Z. / Ma, Z. / Davey, C.A. | ||||||
![]() | ![]() Title: Allosteric cross-talk in chromatin can mediate drug-drug synergy Authors: Adhireksan, Z. / Palermo, G. / Riedel, T. / Ma, Z. / Muhammad, R. / Rothlisberger, U. / Dyson, P.J. / Davey, C.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 326.6 KB | Display | ![]() |
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PDB format | ![]() | 248 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 35 KB | Display | |
Data in CIF | ![]() | 50.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5dnmSC S: Starting model for refinement C: citing same article ( |
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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
-Protein , 4 types, 8 molecules AEBFCGDH
#1: Protein | Mass: 15303.930 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 11263.231 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Protein | Mass: 13907.163 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #4: Protein | Mass: 13848.097 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-DNA chain , 2 types, 2 molecules IJ
#5: DNA chain | Mass: 44749.664 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#6: DNA chain | Mass: 44740.648 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 4 types, 8 molecules ![](data/chem/img/AUF.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/RAX.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/RAX.gif)
#7: Chemical | #8: Chemical | #9: Chemical | ChemComp-MG / | #10: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.36 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 9, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→48.87 Å / Num. obs: 51082 / % possible obs: 95.8 % / Redundancy: 5 % / Rmerge(I) obs: 0.037 / Net I/σ(I): 23.2 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 2 % / Rmerge(I) obs: 0.433 / Mean I/σ(I) obs: 1.6 / % possible all: 76.6 |
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Processing
Software | Name: REFMAC / Version: 5.6.0117 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]() Starting model: 5DNM Resolution: 2.8→48.87 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.948 / SU B: 14.221 / SU ML: 0.277 / Cross valid method: THROUGHOUT / ESU R: 6.83 / ESU R Free: 0.342 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 98.672 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→48.87 Å
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Refine LS restraints |
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