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Yorodumi- PDB-1aoi: COMPLEX BETWEEN NUCLEOSOME CORE PARTICLE (H3,H4,H2A,H2B) AND 146 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1aoi | ||||||
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Title | COMPLEX BETWEEN NUCLEOSOME CORE PARTICLE (H3,H4,H2A,H2B) AND 146 BP LONG DNA FRAGMENT | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / NUCLEOSOME / CHROMATIN / HISTONE / PROTEIN DNA INTERACTION / NUCLEOPROTEIN / SUPERCOILED DNA / DNA BINDING PROTEIN-DNA COMPLEX | ||||||
Function / homology | Function and homology information structural constituent of chromatin / nucleosome / protein heterodimerization activity / DNA binding / nucleus Similarity search - Function | ||||||
Biological species | Xenopus laevis (African clawed frog) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.8 Å | ||||||
Authors | Luger, K. / Maeder, A.W. / Richmond, R.K. / Sargent, D.F. / Richmond, T.J. | ||||||
Citation | Journal: Nature / Year: 1997 Title: Crystal structure of the nucleosome core particle at 2.8 A resolution. Authors: Luger, K. / Mader, A.W. / Richmond, R.K. / Sargent, D.F. / Richmond, T.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1aoi.cif.gz | 294 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1aoi.ent.gz | 228.4 KB | Display | PDB format |
PDBx/mmJSON format | 1aoi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ao/1aoi ftp://data.pdbj.org/pub/pdb/validation_reports/ao/1aoi | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-DNA chain , 1 types, 2 molecules IJ
#1: DNA chain | Mass: 45053.855 Da / Num. of mol.: 2 / Source method: obtained synthetically |
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-Protein , 4 types, 8 molecules AEBFCGDH
#2: Protein | Mass: 13244.528 Da / Num. of mol.: 2 / Fragment: HISTONE H3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P02302 #3: Protein | Mass: 9990.770 Da / Num. of mol.: 2 / Fragment: HISTONE H4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) Description: SYNTHETIC GENE, OPTIMIZED CODON USAGE FOR ESCHERICHIA COLI; Production host: Escherichia coli (E. coli) / References: UniProt: P62799 #4: Protein | Mass: 12639.772 Da / Num. of mol.: 2 / Fragment: HISTONE H2A 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 #5: Protein | Mass: 11179.959 Da / Num. of mol.: 2 / Fragment: HISTONE H2B / Mutation: A7P 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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-Non-polymers , 2 types, 19 molecules
#6: Chemical | ChemComp-MN / #7: Water | ChemComp-HOH / | |
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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: 2.83 Å3/Da / Density % sol: 56.54 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 20 ℃ / pH: 6 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID13 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 15, 1995 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.8→25 Å / Num. obs: 52487 / % possible obs: 99 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.056 / Rsym value: 3.6 |
Reflection shell | Resolution: 2.8→2.85 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.132 / % possible all: 95 |
Reflection | *PLUS Num. measured all: 297397 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.8→25 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: BULK SOLVENT MODEL USED | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→25 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.843 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 3 / Rfactor obs: 0.224 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |