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Yorodumi- PDB-3rek: 2.6 Angstrom Crystal Structure of the Nucleosome Core Particle As... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3rek | ||||||
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Title | 2.6 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with a 146 bp Alpha-Satellite DNA (NCP146b) Derivatized with Oxaliplatin | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN/DNA / nucleosome / 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) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Wu, B. / Davey, C.A. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2011 Title: Specific DNA structural attributes modulate platinum anticancer drug site selection and cross-link generation. Authors: Wu, B. / Davey, G.E. / Nazarov, A.A. / Dyson, P.J. / 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 | 3rek.cif.gz | 323.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3rek.ent.gz | 244.7 KB | Display | PDB format |
PDBx/mmJSON format | 3rek.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3rek_validation.pdf.gz | 531.7 KB | Display | wwPDB validaton report |
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Full document | 3rek_full_validation.pdf.gz | 559.8 KB | Display | |
Data in XML | 3rek_validation.xml.gz | 36.4 KB | Display | |
Data in CIF | 3rek_validation.cif.gz | 51.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/re/3rek ftp://data.pdbj.org/pub/pdb/validation_reports/re/3rek | HTTPS FTP |
-Related structure data
Related structure data | 3rehC 3reiC 3rejC 3relC 1kx4S S: Starting model for refinement C: citing same article (ref.) |
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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 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: 13978.241 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: P06897 #4: Protein | Mass: 13524.752 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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-DNA chain , 1 types, 2 molecules IJ
#5: DNA chain | Mass: 45054.840 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
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-Non-polymers , 3 types, 45 molecules
#6: Chemical | #7: Chemical | ChemComp-PT / #8: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 51.87 % |
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.07 Å |
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Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.07 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→57 Å / Num. obs: 57610 / % possible obs: 93.5 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 18.4 |
-Processing
Software | Name: REFMAC / Version: 5.2.0019 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1KX4 Resolution: 2.6→57 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.905 / SU B: 12.601 / SU ML: 0.274 / Cross valid method: THROUGHOUT / ESU R Free: 0.344 / 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: 90.86 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→57 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.668 Å / Total num. of bins used: 20
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