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Yorodumi- PDB-5cp6: Nucleosome Core Particle with Adducts from the Anticancer Compoun... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5cp6 | ||||||
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Title | Nucleosome Core Particle with Adducts from the Anticancer Compound, [(eta6-5,8,9,10-tetrahydroanthracene)Ru(ethylenediamine)Cl][PF6] | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN/DNA / nucleosome core particle / antitumour compound / STRUCTURAL PROTEIN-DNA complex | ||||||
Function / homology | Function and homology information structural constituent of chromatin / nucleosome / 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: 2.6 Å | ||||||
Authors | Ma, Z. / Adhireksan, Z. / Murray, B.S. / Dyson, P.J. / Davey, C.A. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2016 Title: An Organometallic Compound which Exhibits a DNA Topology-Dependent One-Stranded Intercalation Mode. Authors: Ma, Z. / Palermo, G. / Adhireksan, Z. / Murray, B.S. / von Erlach, T. / Dyson, P.J. / Rothlisberger, U. / 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 | 5cp6.cif.gz | 328 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5cp6.ent.gz | 248.1 KB | Display | PDB format |
PDBx/mmJSON format | 5cp6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cp/5cp6 ftp://data.pdbj.org/pub/pdb/validation_reports/cp/5cp6 | HTTPS FTP |
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-Related structure data
Related structure data | 4wu8S 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
-DNA chain , 2 types, 2 molecules IJ
#1: DNA chain | Mass: 44749.664 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#2: DNA chain | Mass: 44740.648 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-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) / Production host: Escherichia coli (E. coli) / 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) / Production host: Escherichia coli (E. coli) / 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: hist1h2aj, LOC494591 / Production host: Escherichia coli (E. coli) / 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) / Production host: Escherichia coli (E. coli) / References: UniProt: P02281 |
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-Non-polymers , 4 types, 42 molecules
#7: Chemical | #8: Chemical | #9: Chemical | ChemComp-MG / | #10: Water | ChemComp-HOH / | |
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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: 2.72 Å3/Da / Density % sol: 54.74 % |
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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 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 98 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.5 Å |
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: 2.6→76.39 Å / Num. obs: 57728 / % possible obs: 86.3 % / Redundancy: 4.8 % / Net I/σ(I): 15.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4WU8 Resolution: 2.6→76.39 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.943 / SU B: 12.742 / SU ML: 0.269 / Cross valid method: THROUGHOUT / ESU R: 0.719 / ESU R Free: 0.32 / 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: 84.143 Å2
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Refinement step | Cycle: 1 / Resolution: 2.6→76.39 Å
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Refine LS restraints |
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