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Open data
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Basic information
Entry | Database: PDB / ID: 5f99 | ||||||
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Title | X-ray Structure of the MMTV-A Nucleosome Core Particle | ||||||
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![]() | DNA BINDING PROTEIN / nucleosome core particle histone DNA | ||||||
Function / homology | ![]() structural constituent of chromatin / nucleosome / nucleosome assembly / protein heterodimerization activity / DNA binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Frouws, T.D. / Richmond, T.J. | ||||||
![]() | ![]() Title: X-ray structure of the MMTV-A nucleosome core. Authors: Frouws, T.D. / Duda, S.C. / Richmond, T.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 361 KB | Display | ![]() |
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PDB format | ![]() | 274 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 521.2 KB | Display | ![]() |
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Full document | ![]() | 594.4 KB | Display | |
Data in XML | ![]() | 60.1 KB | Display | |
Data in CIF | ![]() | 86.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1kx5S 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: 15271.863 Da / Num. of mol.: 2 / Mutation: C110A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 11413.473 Da / Num. of mol.: 2 / Mutation: H18R Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Protein | Mass: 13978.241 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #4: Protein | Mass: 13524.752 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-DNA chain , 2 types, 2 molecules IJ
#5: DNA chain | Mass: 44849.496 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#6: DNA chain | Mass: 45901.312 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Non-polymers , 3 types, 941 molecules 




#7: Chemical | ChemComp-CL / #8: Chemical | ChemComp-MG / | #9: 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: 53.46 % / Description: Hollow hexagonal rods |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6 Details: sample was mixed 1:1 with 10 mM K-cacodylate, pH 6.0, 180 mM MgCl2, 50 mM KCl and equilibrated against a 1:4 dilution of the same solution Temp details: Rumed incubator |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 28, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.63→29.68 Å / Num. obs: 59659 / % possible obs: 94.2 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 2.63→2.78 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.333 / Mean I/σ(I) obs: 1.8 / % possible all: 73.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1KX5 Resolution: 2.63→29.68 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 2.63→29.68 Å
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