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Yorodumi- PDB-6ae8: Structure insight into histone chaperone Chz1-mediated H2A.Z reco... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ae8 | |||||||||
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Title | Structure insight into histone chaperone Chz1-mediated H2A.Z recognition and replacement | |||||||||
Components |
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Keywords | CHAPERONE / histone variants | |||||||||
Function / homology | Function and homology information Condensation of Prophase Chromosomes / nuclear-transcribed mRNA catabolic process, non-stop decay / replication fork protection complex / postreplication repair / silent mating-type cassette heterochromatin formation / euchromatin / chromatin DNA binding / structural constituent of chromatin / nucleosome / chromatin organization ...Condensation of Prophase Chromosomes / nuclear-transcribed mRNA catabolic process, non-stop decay / replication fork protection complex / postreplication repair / silent mating-type cassette heterochromatin formation / euchromatin / chromatin DNA binding / structural constituent of chromatin / nucleosome / chromatin organization / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / chromatin binding / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / DNA binding / identical protein binding / nucleus Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae S288c (yeast) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | |||||||||
Authors | Wang, Y.Y. / Shan, S. / Zhou, Z. | |||||||||
Funding support | China, 2items
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Citation | Journal: Plos Biol. / Year: 2019 Title: Structural insights into histone chaperone Chz1-mediated H2A.Z recognition and histone replacement. Authors: Wang, Y. / Liu, S. / Sun, L. / Xu, N. / Shan, S. / Wu, F. / Liang, X. / Huang, Y. / Luk, E. / Wu, C. / Zhou, Z. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ae8.cif.gz | 95.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ae8.ent.gz | 69.7 KB | Display | PDB format |
PDBx/mmJSON format | 6ae8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ae/6ae8 ftp://data.pdbj.org/pub/pdb/validation_reports/ae/6ae8 | HTTPS FTP |
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-Related structure data
Related structure data | 5chlS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 21205.436 Da / Num. of mol.: 2 / Fragment: UNP residues 37-131, UNP residues 23-119 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / Production host: Escherichia coli (E. coli) / References: UniProt: P02293, UniProt: Q12692 #2: Protein | Mass: 13511.188 Da / Num. of mol.: 2 / Fragment: UNP residues 64-153 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / Gene: CHZ1 / Production host: Escherichia coli (E. coli) / References: UniProt: P40019 #3: Chemical | #4: 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: 1.38 Å3/Da / Density % sol: 10.91 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / Details: Bicine,1,4-Dioxane,PEG 20000 |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 6, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→50 Å / Num. obs: 42986 / % possible obs: 96.5 % / Redundancy: 3.9 % / Rpim(I) all: 0.048 / Net I/σ(I): 20 |
Reflection shell | Resolution: 1.65→1.71 Å / Num. unique obs: 4146 / Rpim(I) all: 0.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5CHL Resolution: 1.65→50 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.375 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.102 / 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: 24.642 Å2
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Refinement step | Cycle: 1 / Resolution: 1.65→50 Å
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