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Yorodumi- PDB-5dnm: Nucleosome core particle containing adducts of ruthenium(II)-tolu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5dnm | ||||||
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Title | Nucleosome core particle containing adducts of ruthenium(II)-toluene PTA complex | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN/DNA / nucleosome / ruthenium antitumour compound / histone binding / 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 | Xenopus laevis (African clawed frog) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å | ||||||
Authors | Adhireksan, Z. / Muhammad, R. / Davey, C.A. | ||||||
Citation | Journal: Nat Commun / Year: 2017 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5dnm.cif.gz | 325.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dnm.ent.gz | 247.7 KB | Display | PDB format |
PDBx/mmJSON format | 5dnm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5dnm_validation.pdf.gz | 870.3 KB | Display | wwPDB validaton report |
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Full document | 5dnm_full_validation.pdf.gz | 883.7 KB | Display | |
Data in XML | 5dnm_validation.xml.gz | 34 KB | Display | |
Data in CIF | 5dnm_validation.cif.gz | 49.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dn/5dnm ftp://data.pdbj.org/pub/pdb/validation_reports/dn/5dnm | HTTPS FTP |
-Related structure data
Related structure data | 5dnnC 3mnnS C: citing same article (ref.) S: Starting model for refinement |
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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
-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.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P84233 #2: 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) / Production host: Escherichia coli (E. coli) / References: UniProt: P62799 #3: 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: hist1h2aj, LOC494591 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6AZJ8, UniProt: P06897*PLUS #4: 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) / Production host: Escherichia coli (E. coli) / References: UniProt: P02281 |
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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 , 3 types, 6 molecules
#7: Chemical | #8: Chemical | ChemComp-MG / | #9: Chemical | |
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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: 2.7 Å3/Da / Density % sol: 54.37 % |
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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 / PH range: 6 |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.5 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 3, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5 Å / Relative weight: 1 |
Reflection | Resolution: 2.81→60.78 Å / Num. obs: 50790 / % possible obs: 96.2 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 2.81→2.96 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.501 / Mean I/σ(I) obs: 2.3 / % possible all: 78.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3MNN Resolution: 2.81→58.612 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.933 / SU B: 15.185 / SU ML: 0.292 / Cross valid method: THROUGHOUT / ESU R: 1.764 / ESU R Free: 0.34 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 94.519 Å2
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Refinement step | Cycle: LAST / Resolution: 2.81→58.612 Å
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Refine LS restraints |
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