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- PDB-2ygv: Conserved N-terminal domain of the yeast Histone Chaperone Asf1 i... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2ygv | ||||||
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Title | Conserved N-terminal domain of the yeast Histone Chaperone Asf1 in complex with the C-terminal fragment of Rad53 | ||||||
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![]() | CHAPERONE/TRANSFERASE / CHAPERONE-TRANSFERASE COMPLEX / CHECKPOINT / DNA DAMAGE / CHROMATIN | ||||||
Function / homology | ![]() deoxyribonucleoside triphosphate biosynthetic process / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / H3 histone acetyltransferase complex / meiotic recombination checkpoint signaling / acetyltransferase activator activity / DNA replication-dependent chromatin assembly / negative regulation of phosphorylation / dual-specificity kinase / nucleosome disassembly / silent mating-type cassette heterochromatin formation ...deoxyribonucleoside triphosphate biosynthetic process / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / H3 histone acetyltransferase complex / meiotic recombination checkpoint signaling / acetyltransferase activator activity / DNA replication-dependent chromatin assembly / negative regulation of phosphorylation / dual-specificity kinase / nucleosome disassembly / silent mating-type cassette heterochromatin formation / DNA replication origin binding / telomere maintenance in response to DNA damage / negative regulation of DNA damage checkpoint / DNA replication initiation / subtelomeric heterochromatin formation / regulation of DNA repair / protein serine/threonine/tyrosine kinase activity / DNA damage checkpoint signaling / positive regulation of transcription elongation by RNA polymerase II / regulation of protein phosphorylation / protein modification process / protein localization / nucleosome assembly / chromatin organization / histone binding / regulation of gene expression / protein tyrosine kinase activity / chromosome, telomeric region / protein kinase activity / DNA repair / protein serine kinase activity / protein serine/threonine kinase activity / chromatin / regulation of transcription by RNA polymerase II / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jiao, Y. / Seeger, K. / Murciano, B. / Ledu, M.H. / Charbonnier, J.B. / Legrand, P. / Lautrette, A. / Gaubert, A. / Mousson, F. / Guerois, R. ...Jiao, Y. / Seeger, K. / Murciano, B. / Ledu, M.H. / Charbonnier, J.B. / Legrand, P. / Lautrette, A. / Gaubert, A. / Mousson, F. / Guerois, R. / Mann, C. / Ochsenbein, F. | ||||||
![]() | ![]() Title: Surprising Complexity of the Asf1 Histone Chaperone-Rad53 Kinase Interaction Authors: Jiao, Y. / Seeger, K. / Lautrette, A. / Gaubert, A. / Mousson, F. / Guerois, R. / Mann, C. / Ochsenbein, F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 145.8 KB | Display | ![]() |
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PDB format | ![]() | 116 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1rocS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 17874.141 Da / Num. of mol.: 4 / Fragment: CONSERVED N-TERMINAL DOMAIN, RESIDUES 1-156 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: W303 / Production host: ![]() ![]() #2: Protein/peptide | Mass: 2495.872 Da / Num. of mol.: 4 / Fragment: C-TERMINAL, RESIDUES 800-821 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() References: UniProt: P22216, non-specific serine/threonine protein kinase #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.88 % / Description: NONE |
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Crystal grow | pH: 6 / Details: 5% PEG 8000, 0.1M NACACO PH 6, 0.2M MG ACETATE |
-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 8, 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: 2.94→38.9 Å / Num. obs: 16378 / % possible obs: 98.7 % / Observed criterion σ(I): 2.36 / Redundancy: 3.96 % / Biso Wilson estimate: 61.41 Å2 / Rmerge(I) obs: 0.02 / Net I/σ(I): 10.59 |
Reflection shell | Resolution: 2.94→3.12 Å / Redundancy: 3.82 % / Rmerge(I) obs: 0.09 / Mean I/σ(I) obs: 2.36 / % possible all: 97.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1ROC Resolution: 2.94→38.9 Å / Cor.coef. Fo:Fc: 0.867 / Cor.coef. Fo:Fc free: 0.8082 / Cross valid method: THROUGHOUT / σ(F): 0 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY.
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Displacement parameters | Biso mean: 54.12 Å2
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Refine analyze | Luzzati coordinate error obs: 0.367 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.94→38.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.94→3.14 Å / Total num. of bins used: 8
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