+Open data
-Basic information
Entry | Database: PDB / ID: 3mgr | ||||||
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Title | Binding of Rubidium ions to the Nucleosome Core Particle | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN/DNA / PROTEIN-DNA COMPLEX / STRUCTURAL PROTEIN-DNA complex | ||||||
Function / homology | Function and homology information structural constituent of chromatin / nucleosome / nucleosome assembly / protein heterodimerization activity / DNA binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Xenopus laevis (African clawed frog) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Mohideen, K. / Muhammad, R. / Davey, C.A. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2010 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3mgr.cif.gz | 325.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mgr.ent.gz | 246.6 KB | Display | PDB format |
PDBx/mmJSON format | 3mgr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3mgr_validation.pdf.gz | 512.7 KB | Display | wwPDB validaton report |
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Full document | 3mgr_full_validation.pdf.gz | 532.2 KB | Display | |
Data in XML | 3mgr_validation.xml.gz | 34.7 KB | Display | |
Data in CIF | 3mgr_validation.cif.gz | 50.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mg/3mgr ftp://data.pdbj.org/pub/pdb/validation_reports/mg/3mgr | HTTPS FTP |
-Related structure data
Related structure data | 3mgpC 3mgqC 3mgsC 1kx5S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Xenopus laevis (African clawed frog) / Gene: Histone 3 or H3 / Plasmid: pET3D / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: P84233 #2: Protein | Mass: 11263.231 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: Histone 4 or H4 / Plasmid: pET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: P62799 #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.) Xenopus laevis (African clawed frog) / Gene: Histone 2A or H2A, LOC494591 / Plasmid: pET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: Q6AZJ8 #4: Protein | Mass: 13848.097 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: Histone 2B or H2B / Plasmid: pET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: P02281 |
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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 , 3 types, 23 molecules
#7: Chemical | ChemComp-CL / #8: Chemical | ChemComp-RB / #9: Chemical | ChemComp-MN / |
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-Details
Sequence details | THE CONFLICTS REPRESENT UNINTENTIO |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.34 % |
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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: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.81 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 22, 2009 / Details: vertically collimating mirror |
Radiation | Monochromator: Bartels Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.81 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→94.07 Å / Num. all: 85891 / Num. obs: 84087 / % possible obs: 90.3 % / Redundancy: 6.7 % / Biso Wilson estimate: 44.1 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 21.1 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.478 / Mean I/σ(I) obs: 3.2 / Num. unique all: 7966 / % possible all: 58.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1KX5 Resolution: 2.3→60 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.911 / SU B: 7.339 / SU ML: 0.183 / Cross valid method: THROUGHOUT / ESU R: 0.341 / ESU R Free: 0.244 / 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: 60.23 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→60 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
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