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Yorodumi- PDB-5ejo: Crystal structure of the winged helix domain in Chromatin assembl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ejo | ||||||
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Title | Crystal structure of the winged helix domain in Chromatin assembly factor 1 subunit p90 | ||||||
Components | Chromatin assembly factor 1 subunit p90 | ||||||
Keywords | NUCLEAR PROTEIN / Chromatin assembly factor 1 / Winged helix domain / Nucleosome assembly | ||||||
Function / homology | Function and homology information CAF-1 complex / DNA replication-dependent chromatin assembly / chromosome, centromeric region / nucleosome assembly / nucleosome / chromatin organization / DNA replication / DNA repair / chromatin / nucleus Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae S288c (yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.75 Å | ||||||
Authors | Zhang, K. / Gao, Y. / Li, J. / Burgess, R. / Han, J. / Liang, H. / Zhang, Z. / Liu, Y. | ||||||
Funding support | China, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2016 Title: A DNA binding winged helix domain in CAF-1 functions with PCNA to stabilize CAF-1 at replication forks Authors: Zhang, K. / Gao, Y. / Li, J. / Burgess, R. / Han, J. / Liang, H. / Zhang, Z. / Liu, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ejo.cif.gz | 28.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ejo.ent.gz | 18.2 KB | Display | PDB format |
PDBx/mmJSON format | 5ejo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ej/5ejo ftp://data.pdbj.org/pub/pdb/validation_reports/ej/5ejo | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 10549.084 Da / Num. of mol.: 1 / Fragment: UNP residues 519-606 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / Gene: RLF2, CAC1, YPR018W, YP9531.12 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12495 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.11 Å3/Da / Density % sol: 74.47 % Description: the entry contains Friedel pairs in F_Plus/Minus columns |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M NaCl, 1.5 M (NH4)2SO4, 0.1 M BIS-Tris |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 1, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→50 Å / Num. obs: 8556 / % possible obs: 98 % / Redundancy: 19.4 % / Net I/σ(I): 67.7 |
Reflection shell | Resolution: 2.75→2.8 Å / Redundancy: 20.6 % / Rmerge(I) obs: 0.657 / Mean I/σ(I) obs: 8.37 / % possible all: 96.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.75→31.832 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.94 / Stereochemistry target values: ML Details: the entry contains Friedel pairs in F_Plus/Minus columns
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.75→31.832 Å
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Refine LS restraints |
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LS refinement shell |
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