+Open data
-Basic information
Entry | Database: PDB / ID: 5omx | ||||||
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Title | X-ray Structure of the H2A-N38C Nucleosome Core Particle | ||||||
Components |
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Keywords | DNA BINDING PROTEIN / nucleosome core particle / histone / DNA | ||||||
Function / homology | Function and homology information structural constituent of chromatin / nucleosome / protein heterodimerization activity / DNA binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Xenopus laevis (African clawed frog) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å | ||||||
Authors | Frouws, T.D. / Richmond, T.J. | ||||||
Citation | Journal: J. Mol. Biol. / Year: 2018 Title: Site-Specific Disulfide Crosslinked Nucleosomes with Enhanced Stability. Authors: Frouws, T.D. / Barth, P.D. / Richmond, T.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5omx.cif.gz | 331.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5omx.ent.gz | 251.4 KB | Display | PDB format |
PDBx/mmJSON format | 5omx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/om/5omx ftp://data.pdbj.org/pub/pdb/validation_reports/om/5omx | HTTPS FTP |
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-Related structure data
Related structure data | 5ongC 5onwC 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
-DNA chain , 2 types, 2 molecules IJ
#1: DNA chain | Mass: 45368.051 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: alpha satellite / Plasmid: pUC57 / Production host: Escherichia coli (E. coli) |
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#2: DNA chain | Mass: 45359.035 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pUC57 / Production host: Escherichia coli (E. coli) / Variant (production host): DH10B |
-Protein , 4 types, 8 molecules AEBFCGDH
#3: Protein | Mass: 15271.863 Da / Num. of mol.: 2 / Mutation: C110A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): PLysS / References: UniProt: P84233 #4: Protein | Mass: 11394.426 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: P62799 #5: Protein | Mass: 13967.281 Da / Num. of mol.: 2 / Mutation: N38C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: hist1h2aj, LOC494591 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: Q6AZJ8, UniProt: P06897*PLUS #6: Protein | Mass: 13524.752 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: P02281 |
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-Non-polymers , 3 types, 209 molecules
#7: Chemical | ChemComp-MN / #8: Chemical | ChemComp-CL / #9: Water | ChemComp-HOH / | |
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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: 2.68 Å3/Da / Density % sol: 54.18 % / Description: Hollow hexagonal rods |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 8 mg/ml sample was mixed 1:1 with 10 mM K-Cacodylate (pH 6.0), 140-150 mM MnCl2, 100 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: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 22, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.32→47.14 Å / Num. obs: 80720 / % possible obs: 86.7 % / Redundancy: 3.2 % / Biso Wilson estimate: 49.2 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 2.32→2.45 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.212 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 3876 / % possible all: 28.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1KX5 Resolution: 2.32→47.14 Å / Cross valid method: FREE R-VALUE Details: Simulated annealing and rounds of model rebuilding. Final energy minimization and water picking.
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Displacement parameters | Biso mean: 75 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.32→47.14 Å
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