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- PDB-3azg: Crystal Structure of Human Nucleosome Core Particle Containing H3... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3azg | ||||||
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Title | Crystal Structure of Human Nucleosome Core Particle Containing H3K115Q mutation | ||||||
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Function / homology | ![]() negative regulation of megakaryocyte differentiation / CENP-A containing nucleosome / Packaging Of Telomere Ends / Chromatin modifying enzymes / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Iwasaki, W. / Tachiwana, H. / Kawaguchi, K. / Shibata, T. / Kagawa, W. / Kurumizaka, H. | ||||||
![]() | ![]() Title: Comprehensive Structural Analysis of Mutant Nucleosomes Containing Lysine to Glutamine (KQ) Substitutions in the H3 and H4 Histone-Fold Domains Authors: Iwasaki, W. / Tachiwana, H. / Kawaguchi, K. / Shibata, T. / Kagawa, W. / Kurumizaka, H. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 317.2 KB | Display | ![]() |
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PDB format | ![]() | 250 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 384.7 KB | Display | ![]() |
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Full document | ![]() | 429.7 KB | Display | |
Data in XML | ![]() | 42.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3aywC ![]() 3azeC ![]() 3azfC ![]() 3azhC ![]() 3aziC ![]() 3azjC ![]() 3azkC ![]() 3azlC ![]() 3azmC ![]() 3aznC ![]() 2cv5S C: citing same article ( S: Starting model for refinement |
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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: 15718.393 Da / Num. of mol.: 2 / Mutation: K115Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #2: Protein | ![]() Mass: 11676.703 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #3: Protein | Mass: 14447.825 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #4: Protein | Mass: 14217.516 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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-DNA chain , 1 types, 2 molecules IJ
#5: DNA chain | Mass: 45053.855 Da / Num. of mol.: 2 / Source method: obtained synthetically |
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-Non-polymers , 3 types, 116 molecules 




#6: Chemical | ChemComp-CL / ![]() #7: Chemical | ChemComp-MN / #8: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.34 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 23, 2009 |
Radiation | Monochromator: Double-crystal monochromator, Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.4→50 Å / Num. obs: 84116 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 56.1 Å2 / Rsym value: 0.085 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 8254 / Rsym value: 0.768 / % possible all: 99.5 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 2CV5 Resolution: 2.4→39.16 Å / σ(F): 0
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→39.16 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.48 Å / Total num. of bins used: 10
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Xplor file |
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