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Yorodumi- PDB-1p3o: Crystallographic Studies of Nucleosome Core Particles containing ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1p3o | ||||||
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Title | Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN/DNA / Sin mutants / Nucleosome Core Particle / chromatin / protein/DNA interaction / 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 | Homo sapiens (human) Xenopus laevis (African clawed frog) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.75 Å | ||||||
Authors | Muthurajan, U.M. / Bao, Y. / Forsberg, L.J. / Edayathumangalam, R.S. / Dyer, P.N. / White, C.L. / Luger, K. | ||||||
Citation | Journal: EMBO J. / Year: 2004 Title: Crystal structures of histone Sin mutant nucleosomes reveal altered protein-DNA interactions Authors: Muthurajan, U.M. / Bao, Y. / Forsberg, L.J. / Edayathumangalam, R.S. / Dyer, P.N. / White, C.L. / Luger, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1p3o.cif.gz | 327 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1p3o.ent.gz | 248.5 KB | Display | PDB format |
PDBx/mmJSON format | 1p3o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1p3o_validation.pdf.gz | 444.4 KB | Display | wwPDB validaton report |
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Full document | 1p3o_full_validation.pdf.gz | 481 KB | Display | |
Data in XML | 1p3o_validation.xml.gz | 23 KB | Display | |
Data in CIF | 1p3o_validation.cif.gz | 38.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p3/1p3o ftp://data.pdbj.org/pub/pdb/validation_reports/p3/1p3o | HTTPS FTP |
-Related structure data
Related structure data | 1p34C 1p3aC 1p3bC 1p3fC 1p3gC 1p3iC 1p3kC 1p3lC 1p3mC 1p3pC 1aoiS 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
#2: Protein | Mass: 15363.939 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: pET / Production host: Escherichia coli (E. coli) / Variant (production host): BL21 DE3 plysS / References: UniProt: Q7ZT64, UniProt: P84233*PLUS #3: Protein | Mass: 11235.178 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: pET / Production host: Escherichia coli (E. coli) / Variant (production host): BL21 DE3 plysS / References: UniProt: P62799 #4: Protein | Mass: 13962.241 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: pET / Production host: Escherichia coli (E. coli) / Variant (production host): BL21 DE3 plysS / References: UniProt: Q7ZT66, UniProt: P06897*PLUS #5: Protein | Mass: 13834.070 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: pET / Production host: Escherichia coli (E. coli) / Variant (production host): BL21 DE3 plysS / References: UniProt: P02281 |
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-DNA chain / Non-polymers , 2 types, 240 molecules IJ
#1: DNA chain | Mass: 45054.844 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pUC / Production host: Escherichia coli (E. coli) / Variant (production host): HB 101 #6: 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: 2.61 Å3/Da / Density % sol: 52.94 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6 Details: MnCl2, KCl, Potassium cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion / Details: Luger, K., (1997) Nature, 389, 251. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 21, 2002 / Details: Mirrors |
Radiation | Monochromator: Cu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→50 Å / Num. obs: 55146 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 2.75→2.81 Å / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.95 / % possible all: 97 |
Reflection | *PLUS Num. obs: 55911 |
Reflection shell | *PLUS % possible obs: 97 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1AOI Resolution: 2.75→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.75→50 Å
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Refine LS restraints |
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Refinement | *PLUS Rfactor Rfree: 0.28 / Rfactor Rwork: 0.22 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_d | |||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.41 / Rfactor Rwork: 0.37 |