+Open data
-Basic information
Entry | Database: PDB / ID: 6xaw | ||||||
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Title | Crystal Structure Analysis of SIN3-UME6 | ||||||
Components |
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Keywords | TRANSCRIPTION / RPD3 histone deacetylase complexes / pigenetic repression | ||||||
Function / homology | Function and homology information : / : / nitrogen catabolite repression of transcription from RNA polymerase II promoter / DNA-binding transcription factor binding => GO:0140297 / spore germination / pseudohyphal growth / negative regulation of silent mating-type cassette heterochromatin formation / Rpd3L complex / Rpd3S complex / Rpd3L-Expanded complex ...: / : / nitrogen catabolite repression of transcription from RNA polymerase II promoter / DNA-binding transcription factor binding => GO:0140297 / spore germination / pseudohyphal growth / negative regulation of silent mating-type cassette heterochromatin formation / Rpd3L complex / Rpd3S complex / Rpd3L-Expanded complex / negative regulation of rDNA heterochromatin formation / rDNA chromatin condensation / nucleophagy / lipid droplet organization / negative regulation of transcription by RNA polymerase I / regulation of DNA-templated DNA replication initiation / Sin3-type complex / transcription factor binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / nucleosome assembly / double-strand break repair via nonhomologous end joining / transcription corepressor activity / sequence-specific DNA binding / transcription coactivator activity / chromatin remodeling / cell cycle / RNA polymerase II cis-regulatory region sequence-specific DNA binding / cell division / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.84 Å | ||||||
Authors | Seo, H.-S. / Dhe-Paganon, S. | ||||||
Funding support | United States, 1items
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Citation | Journal: To be published Title: Crystal Structure Analysis of SIN3-UME6 Authors: Seo, H.-S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6xaw.cif.gz | 52.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xaw.ent.gz | 36.8 KB | Display | PDB format |
PDBx/mmJSON format | 6xaw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xa/6xaw ftp://data.pdbj.org/pub/pdb/validation_reports/xa/6xaw | 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 9052.236 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: SIN3, CPE1, GAM2, RPD1, SDI1, SDS16, UME4, YOL004W / Production host: Escherichia coli (E. coli) / References: UniProt: P22579 | ||||
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#2: Protein/peptide | Mass: 4848.395 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: UME6, CAR80, CARGR1, NIM2, RIM16, YDR207C, YD8142.04C / Production host: Escherichia coli (E. coli) / References: UniProt: P39001 | ||||
#3: Chemical | ChemComp-BR / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.85 Å3/Da / Density % sol: 33.58 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.8 / Details: 100mM Tris, pH 8.8, 1.36M sodium citrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9197 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 15, 2018 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9197 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.84→33.99 Å / Num. obs: 17236 / % possible obs: 99.8 % / Redundancy: 12.3 % / Biso Wilson estimate: 29.05 Å2 / Rpim(I) all: 0.049 / Rrim(I) all: 0.174 / Net I/σ(I): 16.4 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: SAD |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.84→33.99 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.47 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 96.77 Å2 / Biso mean: 31.1753 Å2 / Biso min: 15.99 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.84→33.99 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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