+Open data
-Basic information
Entry | Database: PDB / ID: 5oy7 | |||||||||||||||
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Title | Structure of the 4_601_157 tetranucleosome (P1 form) | |||||||||||||||
Components |
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Keywords | GENE REGULATION / nucleosome / histone / DNA / tetranucleosome / chromatin fiber | |||||||||||||||
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 / molecular replacement / Resolution: 5.774 Å | |||||||||||||||
Authors | Ekundayo, B. / Richmond, T.J. / Schalch, T. | |||||||||||||||
Funding support | Switzerland, 4items
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Citation | Journal: J. Mol. Biol. / Year: 2017 Title: Capturing Structural Heterogeneity in Chromatin Fibers. Authors: Ekundayo, B. / Richmond, T.J. / Schalch, T. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5oy7.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5oy7.ent.gz | 873.4 KB | Display | PDB format |
PDBx/mmJSON format | 5oy7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oy/5oy7 ftp://data.pdbj.org/pub/pdb/validation_reports/oy/5oy7 | HTTPS FTP |
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-Related structure data
Related structure data | 5oxvC 3lz0S C: citing same article (ref.) 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, 32 molecules LPDHTXbfMQIAEUYcNRJBFVZdOCGKSWae
#1: Protein | Mass: 13979.291 Da / Num. of mol.: 8 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 #2: Protein | Mass: 15303.930 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: hist1h3g, H3l / Production host: Escherichia coli (E. coli) / References: UniProt: Q92133, UniProt: P84233*PLUS #3: Protein | Mass: 11263.231 Da / Num. of mol.: 8 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 #4: Protein | Mass: 14109.436 Da / Num. of mol.: 8 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 |
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-DNA chain , 2 types, 2 molecules gh
#5: DNA chain | Mass: 194770.531 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) |
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#6: DNA chain | Mass: 195070.594 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) |
-Non-polymers , 1 types, 8 molecules
#7: Chemical | ChemComp-CL / |
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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: 3.28 Å3/Da / Density % sol: 62.53 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 30-60 mM KCl, 90-110 mM MgCl2 and 5 mM Na-cacodyalte, pH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Nov 25, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 5.77→141.5 Å / Num. obs: 24331 / % possible obs: 93.8 % / Redundancy: 1.9 % / Biso Wilson estimate: 229.72 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.11 / Rrim(I) all: 0.076 / Net I/σ(I): 4.9 |
Reflection shell | Highest resolution: 5.77 Å / Mean I/σ(I) obs: 1.63 / Num. unique all: 3457 / Num. unique obs: 4652 / CC1/2: 0.571 / Rrim(I) all: 0.506 / % possible all: 82 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3LZ0 Resolution: 5.774→111.407 Å / SU ML: 0.91 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 28.53
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 5.774→111.407 Å
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Refine LS restraints |
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