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- PDB-3uta: Crystal Structure of Nucleosome Core Particle Assembled with an A... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3uta | ||||||
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Title | Crystal Structure of Nucleosome Core Particle Assembled with an Alpha-Satellite Sequence Containing Two TTAAA elements (NCP-TA2) | ||||||
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![]() | STRUCTURAL PROTEIN/DNA / Nucleosome core particle / NCP / alpha satellite DNA / 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 | ![]() ![]() ![]() | ||||||
![]() | Chua, E.Y.D. / Vasudevan, D. / Davey, G.E. / Wu, B. / Davey, C.A. | ||||||
![]() | ![]() Title: The mechanics behind DNA sequence-dependent properties of the nucleosome Authors: Chua, E.Y.D. / Vasudevan, D. / Davey, G.E. / Wu, B. / Davey, C.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 325.6 KB | Display | ![]() |
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PDB format | ![]() | 246.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related 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: 15303.930 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: 13978.241 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #4: Protein | Mass: 13848.097 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: 44746.699 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic construct |
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#6: DNA chain | Mass: 44737.684 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic construct |
-Non-polymers , 3 types, 130 molecules ![](data/chem/img/CL.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/HOH.gif)
#7: Chemical | ChemComp-CL / #8: Chemical | ChemComp-MN / #9: Water | ChemComp-HOH / | |
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-Details
Sequence details | UNINTENTIO |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.3 % / Mosaicity: 0.25 ° |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 Details: K-cacodylate, KCl, MnCl2, pH 6.0, temperature 291K, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Detector | Type: PSI PILATUS 6M / Detector: PIXEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.067→94.13 Å / Num. all: 99095 / Num. obs: 99095 / % possible obs: 75.7 % / Redundancy: 4.2 % / Rpim(I) all: 0.035 / Rrim(I) all: 0.077 / Rsym value: 0.062 / Net I/av σ(I): 3.153 / Net I/σ(I): 12.1 / Num. measured all: 413096 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 156.92 Å2 / Biso mean: 67.4383 Å2 / Biso min: 17.24 Å2
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Refinement step | Cycle: LAST / Resolution: 2.07→94.13 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.067→2.121 Å / Total num. of bins used: 20
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