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Open data
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Basic information
Entry | Database: PDB / ID: 3b6f | ||||||
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Title | Nucleosome core particle treated with cisplatin | ||||||
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![]() | STRUCTURAL PROTEIN/DNA / nucleosome / chromatin / platinum adduct / cisplatin / anti-cancer / drug / Acetylation / Chromosomal protein / DNA-binding / Methylation / Nucleosome core / Nucleus / Phosphorylation / Ubl conjugation / 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 | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Wu, B. / Davey, C.A. | ||||||
![]() | ![]() Title: Site selectivity of platinum anticancer therapeutics Authors: Wu, B. / Droge, P. / Davey, C.A. #1: ![]() Title: Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 a resolution Authors: Davey, C.A. / Sargent, D.F. / Luger, K. / Maeder, A.W. / Richmond, T.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 321.9 KB | Display | ![]() |
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PDB format | ![]() | 246.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 516 KB | Display | ![]() |
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Full document | ![]() | 570.6 KB | Display | |
Data in XML | ![]() | 40.7 KB | Display | |
Data in CIF | ![]() | 57.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3b6gC ![]() 1kx5S 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
-DNA chain , 2 types, 2 molecules IJ
#1: DNA chain | Mass: 45368.051 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: DNA chain | Mass: 45359.035 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Protein , 4 types, 8 molecules AEBFCGDH
#3: Protein | Mass: 15303.930 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #4: Protein | Mass: 11263.231 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #5: Protein | Mass: 13907.163 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #6: Protein | Mass: 13848.097 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 1 types, 1 molecules ![](data/chem/img/MN.gif)
#7: Chemical | ChemComp-MN / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.29 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 6 Details: MnCl2, KCl, K-Cacodylate, pH 6.0, vapor diffusion, temperature 291K | ||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 98 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 10, 2007 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.072 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.45→93.66 Å / Num. obs: 28162 / % possible obs: 99.1 % / Observed criterion σ(I): 1 / Redundancy: 7.3 % / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 5.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Starting model: PDB entry 1KX5 Resolution: 3.45→93.66 Å / Cor.coef. Fo:Fc: 0.891 / Cor.coef. Fo:Fc free: 0.833 / SU B: 49.488 / SU ML: 0.866 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.937 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 185.185 Å2
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Refinement step | Cycle: LAST / Resolution: 3.45→93.66 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.45→3.54 Å / Total num. of bins used: 20
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