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Yorodumi- PDB-3e9f: Crystal structure short-form (residue1-113) of Eaf3 chromo domain -
+Open data
-Basic information
Entry | Database: PDB / ID: 3e9f | ||||||
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Title | Crystal structure short-form (residue1-113) of Eaf3 chromo domain | ||||||
Components | Chromatin modification-related protein EAF3 | ||||||
Keywords | TRANSCRIPTION / chromatin remodeling / Eaf3 / chromo domain / transcription factor / transcription regulation / Chromatin regulator / DNA damage / DNA repair / Nucleus | ||||||
Function / homology | Function and homology information nucleosome disassembly/reassembly complex / negative regulation of antisense RNA transcription / Rpd3S complex / regulation of RNA stability / DNA replication-dependent chromatin assembly / nucleosome disassembly / regulation of DNA-templated DNA replication initiation / NuA4 histone acetyltransferase complex / histone acetyltransferase complex / transcription elongation by RNA polymerase II ...nucleosome disassembly/reassembly complex / negative regulation of antisense RNA transcription / Rpd3S complex / regulation of RNA stability / DNA replication-dependent chromatin assembly / nucleosome disassembly / regulation of DNA-templated DNA replication initiation / NuA4 histone acetyltransferase complex / histone acetyltransferase complex / transcription elongation by RNA polymerase II / positive regulation of transcription elongation by RNA polymerase II / nucleosome assembly / DNA repair / negative regulation of DNA-templated transcription / DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / nucleus Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Sun, B. / Hong, J. / Zhang, P. / Lin, D. / Ding, J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: Molecular Basis of the Interaction of Saccharomyces cerevisiae Eaf3 Chromo Domain with Methylated H3K36 Authors: Sun, B. / Hong, J. / Zhang, P. / Dong, X. / Shen, X. / Lin, D. / Ding, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3e9f.cif.gz | 59.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3e9f.ent.gz | 42.5 KB | Display | PDB format |
PDBx/mmJSON format | 3e9f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e9/3e9f ftp://data.pdbj.org/pub/pdb/validation_reports/e9/3e9f | HTTPS FTP |
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-Related structure data
Related structure data | 3e9gC 2f5kS C: citing same article (ref.) 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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Unit cell |
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-Components
#1: Protein | Mass: 14103.966 Da / Num. of mol.: 1 / Fragment: Eaf3, UNP residues 1-113 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q12432 |
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#2: Chemical | ChemComp-MES / |
#3: 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: 2.39 Å3/Da / Density % sol: 48.5 % / Mosaicity: 0.75 ° |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 30% polyethylene glycol 6000, 0.1M MES, pH 6.0, hanging drop, temperature 277K, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 23, 2006 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→50 Å / Num. obs: 12156 / % possible obs: 99.3 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.11 / Χ2: 1.064 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2F5K Resolution: 1.8→25.81 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.947 / Occupancy max: 1 / Occupancy min: 1 / SU B: 2.185 / SU ML: 0.069 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.196 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 61.46 Å2 / Biso mean: 26.1 Å2 / Biso min: 14.55 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→25.81 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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