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Yorodumi- PDB-3lz1: Crystal Structure of Nucleosome Core Particle Composed of the Wid... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3lz1 | ||||||
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Title | Crystal Structure of Nucleosome Core Particle Composed of the Widom 601 DNA Sequence (orientation 2) | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN/DNA / nucleosome / 601-sequence DNA / NCP and Nucleosome core / STRUCTURAL PROTEIN-DNA complex | ||||||
Function / homology | Function and homology information structural constituent of chromatin / nucleosome / 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: 2.5 Å | ||||||
Authors | Vasudevan, D. / Chua, E.Y.D. / Davey, C.A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2010 Title: Crystal structures of nucleosome core particles containing the '601' strong positioning sequence Authors: Vasudevan, D. / Chua, E.Y. / 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 | 3lz1.cif.gz | 317.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3lz1.ent.gz | 239.7 KB | Display | PDB format |
PDBx/mmJSON format | 3lz1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lz/3lz1 ftp://data.pdbj.org/pub/pdb/validation_reports/lz/3lz1 | HTTPS FTP |
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-Related structure data
Related structure data | 3lz0C 1kx4S C: citing same article (ref.) S: Starting model for refinement |
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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) / Plasmid: pET3d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(pLysS) / 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) / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(pLysS) / References: UniProt: P62799 #3: Protein | Mass: 12941.095 Da / Num. of mol.: 2 / Fragment: residues 2-120 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(pLysS) / 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) / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(pLysS) / References: UniProt: P02281 |
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-DNA chain , 2 types, 2 molecules IJ
#5: DNA chain | Mass: 44991.660 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic construct |
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#6: DNA chain | Mass: 44520.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic construct |
-Non-polymers , 2 types, 8 molecules
#7: Chemical | ChemComp-MN / #8: Chemical | |
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-Details
Sequence details | 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: 2.64 Å3/Da / Density % sol: 53.35 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 Details: Kcacodylate, KCl, MnCl2, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 15, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→93.04 Å / Num. all: 65509 / Num. obs: 65509 / % possible obs: 90.6 % / Redundancy: 4.6 % / Rsym value: 0.08 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.384 / Mean I/σ(I) obs: 1.9 / Num. unique all: 6362 / Rsym value: 0.384 / % possible all: 61.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: NCP146b (pdb code 1KX4) Resolution: 2.5→93.04 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.915 / Occupancy max: 1 / Occupancy min: 1 / SU B: 23.954 / SU ML: 0.476 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.6 / ESU R Free: 0.359 / 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 max: 204.25 Å2 / Biso mean: 109.4 Å2 / Biso min: 39.82 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→93.04 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.565 Å / Total num. of bins used: 20
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