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- PDB-4j8u: X-ray structure of NCP145 with chlorido(eta-6-p-cymene)(N-phenyl-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4j8u | ||||||
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Title | X-ray structure of NCP145 with chlorido(eta-6-p-cymene)(N-phenyl-2-pyridinecarbothioamide)osmium(II) | ||||||
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![]() | STRUCTURAL PROTEIN/DNA / nucleosome / histone / STRUCTURAL PROTEIN-DNA complex | ||||||
Function / homology | ![]() structural constituent of chromatin / nucleosome / nucleosome assembly / protein heterodimerization activity / DNA binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Adhireksan, Z. / Davey, C.A. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 324.5 KB | Display | ![]() |
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PDB format | ![]() | 245.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4j8vC ![]() 4j8wC ![]() 4j8xC ![]() 3rehS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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.) ![]() ![]() ![]() #2: Protein | Mass: 11263.231 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Protein | Mass: 13907.163 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #4: Protein | Mass: 13848.097 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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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, 7 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/ELJ.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ELJ.gif)
![](data/chem/img/MG.gif)
#7: Chemical | #8: Chemical | #9: Chemical | ChemComp-MG / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.3 % |
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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: ![]() ![]() ![]() |
Detector | Type: MAR225 / Detector: CCD / Date: Jul 1, 2011 |
Radiation | Monochromator: Bartels Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.14 Å / Relative weight: 1 |
Reflection | Resolution: 2.38→94.07 Å / Num. obs: 71204 |
Reflection shell | Resolution: 2.38→2.51 Å |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3REH Resolution: 2.38→94.07 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.904 / SU B: 8.968 / SU ML: 0.213 / Cross valid method: THROUGHOUT / ESU R: 0.486 / ESU R Free: 0.298 / 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: 75.744 Å2
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Refinement step | Cycle: LAST / Resolution: 2.38→94.07 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.38→2.442 Å / Total num. of bins used: 20
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