[English] 日本語
Yorodumi- PDB-4j8v: X-ray structure of NCP145 with bound chlorido(eta-6-p-cymene)(N-p... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4j8v | ||||||
---|---|---|---|---|---|---|---|
Title | X-ray structure of NCP145 with bound chlorido(eta-6-p-cymene)(N-phenyl-2-pyridinecarbothioamide)ruthenium(II) | ||||||
Components |
| ||||||
Keywords | STRUCTURAL PROTEIN/DNA / nucleosome / histone / 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: 2.58 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4j8v.cif.gz | 320.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4j8v.ent.gz | 243.7 KB | Display | PDB format |
PDBx/mmJSON format | 4j8v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j8/4j8v ftp://data.pdbj.org/pub/pdb/validation_reports/j8/4j8v | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
Unit cell |
|
-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 |
---|
-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) |
---|---|
#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 / | |
---|
-Details
Compound details | CHLORIDO(ETA-6-P-CYMENE)(N-PHENYL-2-PYRIDINECARBOTHIOAMIDE)RUTHENIUM(II) WAS USED IN ...CHLORIDO(ETA-6-P-CYMENE)(N-PHENYL-2-PYRIDINECA |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.42 % |
---|---|
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 |
---|---|
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: 2.58→94.07 Å / Num. obs: 57178 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.58→94.07 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.898 / SU B: 11.367 / SU ML: 0.256 / Cross valid method: THROUGHOUT / ESU R: 0.869 / ESU R Free: 0.35 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 77.273 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.58→94.07 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.58→2.647 Å / Total num. of bins used: 20
|