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Yorodumi- PDB-3lel: Structural Insight into the Sequence-Dependence of Nucleosome Pos... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3lel | ||||||
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Title | Structural Insight into the Sequence-Dependence of Nucleosome Positioning | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN/DNA / nucleosome / nucleosome positioning / DNA flexibility / chromatin / Acetylation / Chromosomal protein / DNA-binding / Methylation / Nucleosome core / Nucleus / 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: 2.95 Å | ||||||
Authors | Wu, B. / Vasudevan, D. / Davey, C.A. | ||||||
Citation | Journal: Structure / Year: 2010 Title: Structural insight into the sequence dependence of nucleosome positioning Authors: Wu, B. / Mohideen, K. / Vasudevan, D. / 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 | 3lel.cif.gz | 626.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3lel.ent.gz | 481.5 KB | Display | PDB format |
PDBx/mmJSON format | 3lel.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/le/3lel ftp://data.pdbj.org/pub/pdb/validation_reports/le/3lel | HTTPS FTP |
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-Related structure data
Related structure data | 1kx5S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
-Protein , 4 types, 16 molecules AEKOBFLPCGMQDHNR
#1: Protein | Mass: 15435.126 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / References: UniProt: P84233 #2: Protein | Mass: 11263.231 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / References: UniProt: P62799 #3: Protein | Mass: 13907.163 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / References: UniProt: Q6AZJ8 #4: Protein | Mass: 13848.097 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / References: UniProt: P02281 |
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-DNA chain , 2 types, 4 molecules ISJT
#5: DNA chain | Mass: 45363.109 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: Synthetic DNA with modified human alpha satellite DNA sequence #6: DNA chain | Mass: 45354.094 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: Synthetic DNA with modified human alpha satellite DNA sequence |
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-Non-polymers , 1 types, 34 molecules
#7: Chemical | ChemComp-MN / |
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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: 2.57 Å3/Da / Density % sol: 52.13 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 85mM MnCl2, 60mM KCl, 20mM K-Cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 20, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→60 Å / Num. obs: 76011 / % possible obs: 89.7 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 2.95→3.11 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.471 / Mean I/σ(I) obs: 1.5 / Num. unique all: 6849 / % possible all: 55.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1KX5 Resolution: 2.95→60 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.889 / SU B: 23.99 / SU ML: 0.449 / Cross valid method: THROUGHOUT / ESU R Free: 0.529 / 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: 97.265 Å2
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Refinement step | Cycle: LAST / Resolution: 2.95→60 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.95→3.026 Å / Total num. of bins used: 20
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