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- PDB-3c1c: The effect of H3 K79 dimethylation and H4 K20 trimethylation on n... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3c1c | ||||||
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Title | The effect of H3 K79 dimethylation and H4 K20 trimethylation on nucleosome and chromatin structure | ||||||
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![]() | Structural PROTEIN/DNA / Nucleosome / chromatin / Histone H3 / trimethylation / histone modification / nucleosomal surface / nucleosomal array / Acetylation / Chromosomal protein / DNA-binding / Methylation / Nucleosome core / Nucleus / Phosphoprotein / Ubl conjugation / 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 | ![]() Xenopus tropicalis | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lu, X. / Simon, M. / Chodaparambil, J. / Hansen, J. / Shokat, K. / Luger, K. | ||||||
![]() | ![]() Title: The effect of H3K79 dimethylation and H4K20 trimethylation on nucleosome and chromatin structure. Authors: Lu, X. / Simon, M.D. / Chodaparambil, J.V. / Hansen, J.C. / Shokat, K.M. / Luger, K. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 296.7 KB | Display | ![]() |
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PDB format | ![]() | 225.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 510.7 KB | Display | ![]() |
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Full document | ![]() | 559.9 KB | Display | |
Data in XML | ![]() | 44.5 KB | Display | |
Data in CIF | ![]() | 63.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3c1bC ![]() 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
#1: Protein | Mass: 15316.947 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 11263.231 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Protein | Mass: 14008.268 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #4: Protein | Mass: 13808.033 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: hist2h2bf, TGas058p09.1-001 / Production host: ![]() ![]() |
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-DNA chain / Non-polymers , 2 types, 286 molecules IJ![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#5: DNA chain | Mass: 45054.844 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic DNA #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.51 % | ||||||||||||||||||||
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6 Details: Manganese chloride, Potassium chloride, Potassium cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K | ||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 292 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Detector: CCD / Date: Sep 7, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 3.15→53 Å / Num. obs: 34295 / % possible obs: 90 % / Observed criterion σ(F): 1452 / Observed criterion σ(I): 32813 / Rmerge(I) obs: 0.088 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 3.15→3.26 Å / Rmerge(I) obs: 0.285 / Mean I/σ(I) obs: 3.8 / Num. unique all: 193527 / % possible all: 90 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1AOI Resolution: 3.15→53 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 3.15→53 Å
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Refine LS restraints |
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