+Open data
-Basic information
Entry | Database: PDB / ID: 3b6g | ||||||
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Title | Nucleosome core particle treated with oxaliplatin | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN/DNA / nucleosome / chromatin / platinum adduct / oxaliplatin / anti-cancer / drug / Acetylation / Chromosomal protein / DNA-binding / Methylation / Nucleosome core / Nucleus / Phosphorylation / Ubl conjugation / STRUCTURAL PROTEIN-DNA COMPLEX | ||||||
Function / homology | Function and homology information structural constituent of chromatin / nucleosome / nucleosome assembly / protein heterodimerization activity / DNA binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Xenopus laevis (African clawed frog) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.45 Å | ||||||
Authors | Wu, B. / Davey, C.A. | ||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2008 Title: Site selectivity of platinum anticancer therapeutics Authors: Wu, B. / Droge, P. / Davey, C.A. #1: Journal: J.Mol.Biol. / Year: 2002 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3b6g.cif.gz | 324.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3b6g.ent.gz | 247 KB | Display | PDB format |
PDBx/mmJSON format | 3b6g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3b6g_validation.pdf.gz | 520.1 KB | Display | wwPDB validaton report |
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Full document | 3b6g_full_validation.pdf.gz | 580.7 KB | Display | |
Data in XML | 3b6g_validation.xml.gz | 40.2 KB | Display | |
Data in CIF | 3b6g_validation.cif.gz | 56.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b6/3b6g ftp://data.pdbj.org/pub/pdb/validation_reports/b6/3b6g | HTTPS FTP |
-Related structure data
Related structure data | 3b6fC 1kx5S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Homo sapiens (human) / Plasmid: pUC19 / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 / References: PDB-3B6F |
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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.) Homo sapiens (human) / Plasmid: pUC19 / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 / References: PDB-3B6F |
-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.) Xenopus laevis (African clawed frog) / Plasmid: pET3d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P84233 #4: Protein | Mass: 11263.231 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P62799 #5: Protein | Mass: 13907.163 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: LOC494591 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q6AZJ8, UniProt: P06897*PLUS #6: Protein | Mass: 13848.097 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P02281 |
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-Non-polymers , 1 types, 1 molecules
#7: Chemical | ChemComp-MN / |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.71 % | ||||||||||||||||||||||||||||
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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: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.072 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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→94.072 Å / Num. obs: 28350 / % possible obs: 98.9 % / Observed criterion σ(I): 1 / Redundancy: 7.3 % / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 6.3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Starting model: PDB entry 1KX5 Resolution: 3.45→94.07 Å / Cor.coef. Fo:Fc: 0.873 / Cor.coef. Fo:Fc free: 0.775 / SU B: 44.335 / SU ML: 0.761 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 1.011 / 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: 190.681 Å2
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Refinement step | Cycle: LAST / Resolution: 3.45→94.07 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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