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- PDB-1p3m: Crystallographic Studies of Nucleosome Core Particles containing ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1p3m | ||||||
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Title | Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants | ||||||
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![]() | STRUCTURAL PROTEIN/DNA / Sin mutants / Nucleosome Core Particle / chromatin / protein/DNA interaction / STRUCTURAL PROTEIN-DNA COMPLEX | ||||||
Function / homology | ![]() structural constituent of chromatin / nucleosome / nucleosome assembly / protein heterodimerization activity / DNA binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Muthurajan, U.M. / Bao, Y. / Forsberg, L.J. / Edayathumangalam, R.S. / Dyer, P.N. / White, C.L. / Luger, K. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 324.5 KB | Display | ![]() |
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PDB format | ![]() | 246.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 439.3 KB | Display | ![]() |
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Full document | ![]() | 478.6 KB | Display | |
Data in XML | ![]() | 23.4 KB | Display | |
Data in CIF | ![]() | 38 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1p34C ![]() 1p3aC ![]() 1p3bC ![]() 1p3fC ![]() 1p3gC ![]() 1p3iC ![]() 1p3kC ![]() 1p3lC ![]() 1p3oC ![]() 1p3pC ![]() 1aoiS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 4 types, 8 molecules AEBFCGDH
#2: Protein | Mass: 15375.992 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Protein | Mass: 11263.231 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #4: Protein | Mass: 13962.241 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #5: Protein | Mass: 13834.070 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-DNA chain / Non-polymers , 2 types, 119 molecules IJ![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#1: DNA chain | Mass: 45054.844 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.71 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 15, 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: 2.9→35 Å / Num. obs: 37684 / % possible obs: 87.6 % / Observed criterion σ(I): -3 / Redundancy: 1.67 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 20.9 |
Reflection shell | Resolution: 2.9→2.97 Å / Rmerge(I) obs: 0.377 / Mean I/σ(I) obs: 2.3 / % possible all: 84.8 |
Reflection | *PLUS Highest resolution: 2.9 Å / Num. obs: 43053 / % possible obs: 87.4 % |
Reflection shell | *PLUS % possible obs: 84.8 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1AOI Resolution: 2.9→35 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: 2.9→35 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.9 Å / Rfactor Rwork: 0.21 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_d | |||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.42 / Rfactor Rwork: 0.38 |