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Yorodumi- PDB-4xuj: Nucleosome core particle containing adducts from treatment with a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xuj | ||||||
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Title | Nucleosome core particle containing adducts from treatment with a thiomorpholine-substituted [(eta-6-p-cymene)Ru(3-hydroxy-2-pyridone)Cl] compound | ||||||
Components |
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Keywords | DNA-BINDING PROTEIN/DNA / nucleosome / ruthenium agent / DNA-BINDIG PROTEIN-DNA complex / DNA-BINDING 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: 3.18 Å | ||||||
Authors | Adhireksan, Z. / Davey, C.A. | ||||||
Citation | Journal: To Be Published Title: Contrasting Cytotoxicity and Reactivity of RuII-Arene Complexes of Morpholine vs Thiomorpholine Substituted 3-Hydroxy-2-pyridone Ligands Authors: Hanif, M. / Meier, S.M. / Adhireksan, Z. / Henke, H. / Martic, S. / Labib, M. / Kandioller, W. / Jakupec, M.A. / Kraatz, H.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 | 4xuj.cif.gz | 321.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xuj.ent.gz | 243.6 KB | Display | PDB format |
PDBx/mmJSON format | 4xuj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4xuj_validation.pdf.gz | 535.8 KB | Display | wwPDB validaton report |
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Full document | 4xuj_full_validation.pdf.gz | 557.1 KB | Display | |
Data in XML | 4xuj_validation.xml.gz | 35 KB | Display | |
Data in CIF | 4xuj_validation.cif.gz | 50 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xu/4xuj ftp://data.pdbj.org/pub/pdb/validation_reports/xu/4xuj | HTTPS FTP |
-Related structure data
Related structure data | 3rehS 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 / Fragment: UNP residues 2-136 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 / Fragment: UNP residues 2-103 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 / Fragment: UNP residues 2-126 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 / Fragment: UNP residues 2-126 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 , 4 types, 8 molecules
#7: Chemical | #8: Chemical | #9: Chemical | ChemComp-MG / | #10: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | AUTHORS STATE THAT NUCLEOSOME CRYSTALS WERE SOAKED WITH A RUII-ARENE COMPLEX OF THIOMORPHOLINE ...AUTHORS STATE THAT NUCLEOSOME |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.21 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS. |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 40mM MnCl2, 30mM KCl, 20mM 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: Aug 5, 2010 |
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: 3.18→93.89 Å / Num. obs: 35645 / % possible obs: 98.2 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 3.18→3.36 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.498 / Mean I/σ(I) obs: 3.4 / % possible all: 89.2 |
-Processing
Software | Name: REFMAC / Version: 5.5.0102 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3REH Resolution: 3.18→93.89 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.898 / SU B: 29.555 / SU ML: 0.514 / Cross valid method: THROUGHOUT Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
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Solvent computation | Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 105.18 Å2
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Refinement step | Cycle: LAST / Resolution: 3.18→93.89 Å
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Refine LS restraints |
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