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Yorodumi- PDB-4j8x: X-ray structure of NCP145 with bound chlorido(eta-6-p-cymene)(N-f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4j8x | ||||||
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Title | X-ray structure of NCP145 with bound chlorido(eta-6-p-cymene)(N-fluorophenyl-2-pyridinecarbothioamide)ruthenium(II) | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN/DNA / nucleosome / histone / 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: 2.87 Å | ||||||
Authors | Adhireksan, Z. / Davey, C.A. | ||||||
Citation | Journal: CHEM SCI / Year: 2013 Title: Novel metal(II) arene 2-pyridinecarbothioamides: a rationale to orally active organometallic anticancer agents Authors: Meier, S.M. / Hanif, M. / Adhireksan, Z. / Pichler, V. / Novak, M. / Jirkovsky, E. / Jakupec, M.A. / Arion, V.B. / Davey, C.A. / Keppler, B.K. / Hartinger, C.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4j8x.cif.gz | 322.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4j8x.ent.gz | 244.2 KB | Display | PDB format |
PDBx/mmJSON format | 4j8x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4j8x_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 4j8x_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4j8x_validation.xml.gz | 36 KB | Display | |
Data in CIF | 4j8x_validation.cif.gz | 51.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j8/4j8x ftp://data.pdbj.org/pub/pdb/validation_reports/j8/4j8x | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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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) / 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) / Gene: hist1h2aj, LOC494591 / 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 | #9: Chemical | ChemComp-MG / | |
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-Details
Nonpolymer details | CHLORIDO(ETA-6-P-CYMENE)(N-FLUOROPHENYL-2-PYRIDINECARBOTHIOAMIDE)RUTHENIUM(II) WAS USED IN ...CHLORIDO(ETA-6-P-CYMENE)(N-FLUOROPHEN |
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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: 2.68 Å3/Da / Density % sol: 54.04 % |
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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: 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 | Monochromator: Bartels Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5 Å / Relative weight: 1 |
Reflection | Resolution: 2.87→93.94 Å / Num. obs: 49232 |
Reflection shell | Resolution: 2.87→3.03 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.87→93.94 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.87 / SU B: 17.483 / SU ML: 0.338 / Cross valid method: THROUGHOUT / ESU R Free: 0.406 / 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: 71.532 Å2
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Refinement step | Cycle: LAST / Resolution: 2.87→93.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.87→2.945 Å / Total num. of bins used: 20
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