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Yorodumi- PDB-6zuf: Urea-based Foldamer Inhibitor chimera C2 in complex with ASF1 His... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6zuf | |||||||||||||||||||||||||||
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Title | Urea-based Foldamer Inhibitor chimera C2 in complex with ASF1 Histone chaperone | |||||||||||||||||||||||||||
Components |
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Keywords | CHAPERONE / Histone chaperone Rational design Peptidomimetics Foldamers | |||||||||||||||||||||||||||
Function / homology | Function and homology information histone chaperone activity / muscle cell differentiation / DNA replication-dependent chromatin assembly / DNA repair-dependent chromatin remodeling / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / replication fork processing / osteoblast differentiation / nucleosome assembly / site of double-strand break / histone binding ...histone chaperone activity / muscle cell differentiation / DNA replication-dependent chromatin assembly / DNA repair-dependent chromatin remodeling / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / replication fork processing / osteoblast differentiation / nucleosome assembly / site of double-strand break / histone binding / DNA repair / chromatin binding / chromatin / protein-containing complex / nucleoplasm / nucleus Similarity search - Function | |||||||||||||||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.798 Å | |||||||||||||||||||||||||||
Authors | Bakail, M. / Mbianda, J. / Perrin, E.M. / Guerois, R. / Legrand, P. / Traore, S. / Douat, C. / Guichard, G. / Ochsenbein, F. | |||||||||||||||||||||||||||
Funding support | France, 8items
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Citation | Journal: Sci Adv / Year: 2021 Title: Optimal anchoring of a foldamer inhibitor of ASF1 histone chaperone through backbone plasticity. Authors: Mbianda, J. / Bakail, M. / Andre, C. / Moal, G. / Perrin, M.E. / Pinna, G. / Guerois, R. / Becher, F. / Legrand, P. / Traore, S. / Douat, C. / Guichard, G. / Ochsenbein, F. | |||||||||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6zuf.cif.gz | 151.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zuf.ent.gz | 119 KB | Display | PDB format |
PDBx/mmJSON format | 6zuf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zu/6zuf ftp://data.pdbj.org/pub/pdb/validation_reports/zu/6zuf | HTTPS FTP |
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-Related structure data
Related structure data | 2i32S 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: 17927.998 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ASF1A, CGI-98, HSPC146 / Plasmid: pETM30 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: Q9Y294 #2: Protein/peptide | Mass: 1297.617 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.47 Å3/Da / Density % sol: 50.16 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: 100 mM Sodium Citrate pH4.2, 300 mM LiSO4, 26% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 24, 2015 |
Radiation | Monochromator: 0.97857 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 1.798→48.291 Å / Num. obs: 31049 / % possible obs: 96.1 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 1.8→1.91 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.14 / Num. unique obs: 3697 / % possible all: 70.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2i32 Resolution: 1.798→48 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.932 / SU R Cruickshank DPI: 0.131 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.13 / SU Rfree Blow DPI: 0.116 / SU Rfree Cruickshank DPI: 0.117
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Displacement parameters | Biso mean: 35.61 Å2
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Refine analyze | Luzzati coordinate error obs: 0.23 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.798→48 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→2 Å
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Refinement TLS params. | Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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