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Open data
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Basic information
Entry | Database: PDB / ID: 3mgp | ||||||
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Title | Binding of Cobalt ions to the Nucleosome Core Particle | ||||||
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![]() | STRUCTURAL PROTEIN/DNA / PROTEIN-DNA COMPLEX / 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 | ![]() ![]() ![]() | ||||||
![]() | Mohideen, K. / Muhammad, R. / Davey, C.A. | ||||||
![]() | ![]() Title: Perturbations in nucleosome structure from heavy metal association. Authors: Mohideen, K. / Muhammad, R. / 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 | ![]() | 327.4 KB | Display | ![]() |
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PDB format | ![]() | 248.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 514.9 KB | Display | ![]() |
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Full document | ![]() | 537.5 KB | Display | |
Data in XML | ![]() | 35.9 KB | Display | |
Data in CIF | ![]() | 51.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3mgqC ![]() 3mgrC ![]() 3mgsC ![]() 1kx5S 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: 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: 12941.095 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 2-120 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: 45368.051 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Synthetic Palindromic DNA expressed in pUC18 plasmid using E.coli HB101 cells. |
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#6: DNA chain | Mass: 45359.035 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Synthetic Palindromic DNA expressed in pUC18 plasmid using E.coli HB101 cells. |
-Non-polymers , 2 types, 47 molecules ![](data/chem/img/CL.gif)
![](data/chem/img/CO.gif)
![](data/chem/img/CO.gif)
#7: Chemical | ChemComp-CL / #8: Chemical | ChemComp-CO / |
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-Details
Sequence details | THE CONFLICTS REPRESENT UNINTENTIO |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.75 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 6 Details: 85mM MnCl2, 60mM KCl, 40mM K-cacodylate, pH 6.0, VAPOR DIFFUSION, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 22, 2009 / Details: Dynamically bendable mirror |
Radiation | Monochromator: LN2 cooled fixed-exit Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.6 Å / Relative weight: 1 |
Reflection | Resolution: 2.44→94.49 Å / Num. all: 73764 / Num. obs: 72231 / % possible obs: 91.6 % / Redundancy: 4.7 % / Biso Wilson estimate: 64 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 17 |
Reflection shell | Resolution: 2.44→2.57 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.442 / Mean I/σ(I) obs: 1 / Num. unique all: 6843 / % possible all: 59.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1KX5 Resolution: 2.44→52.6 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.895 / SU B: 10.238 / SU ML: 0.238 / Cross valid method: THROUGHOUT / ESU R: 0.439 / ESU R Free: 0.294 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 83.713 Å2
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Refinement step | Cycle: LAST / Resolution: 2.44→52.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.44→2.57 Å / Total num. of bins used: 20
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