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Yorodumi- PDB-2r0y: Structure of the Rsc4 tandem bromodomain in complex with an acety... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2r0y | ||||||
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Title | Structure of the Rsc4 tandem bromodomain in complex with an acetylated H3 peptide | ||||||
Components |
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Keywords | TRANSCRIPTION / bromodomain / chromatin / remodeler / RSC / histone / acetylation / Chromatin regulator / Nucleus / Phosphorylation / Transcription regulation | ||||||
Function / homology | Function and homology information nucleosome disassembly / RSC-type complex / transcription elongation by RNA polymerase II / lysine-acetylated histone binding / chromatin remodeling / chromatin binding / chromatin Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.75 Å | ||||||
Authors | VanDemark, A.P. / Kasten, M.M. / Ferris, E. / Heroux, A. / Hill, C.P. / Cairns, B.R. | ||||||
Citation | Journal: Mol.Cell / Year: 2007 Title: Autoregulation of the rsc4 tandem bromodomain by gcn5 acetylation. Authors: VanDemark, A.P. / Kasten, M.M. / Ferris, E. / Heroux, A. / Hill, C.P. / Cairns, B.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2r0y.cif.gz | 76.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2r0y.ent.gz | 60.4 KB | Display | PDB format |
PDBx/mmJSON format | 2r0y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2r0y_validation.pdf.gz | 435 KB | Display | wwPDB validaton report |
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Full document | 2r0y_full_validation.pdf.gz | 437.7 KB | Display | |
Data in XML | 2r0y_validation.xml.gz | 15.4 KB | Display | |
Data in CIF | 2r0y_validation.cif.gz | 22.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r0/2r0y ftp://data.pdbj.org/pub/pdb/validation_reports/r0/2r0y | HTTPS FTP |
-Related structure data
-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: 36405.484 Da / Num. of mol.: 1 / Fragment: Rsc4 tandem bromodomain (36-340) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: RSC4 / Plasmid: pET151-D/TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Codon+ / References: UniProt: Q02206 |
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#2: Protein/peptide | Mass: 1403.631 Da / Num. of mol.: 1 / Fragment: Residues 6-18 / Mutation: Acetylated at K14 / Source method: obtained synthetically / Details: Synthesized peptide Histone H3 (6-18) K14ac |
#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: 2.68 Å3/Da / Density % sol: 54.08 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 4.2 Details: 0.1M phosphate-citrate, 0.2M NaCl, 0.2M ammonium sulfate, 20% PEG 3000, 5% Glycerol, pH 4.2, vapor diffusion, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 2005 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.75→50 Å / Num. all: 41226 / Num. obs: 39000 / % possible obs: 94.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.068 / Χ2: 2.253 / Net I/σ(I): 17.3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Resolution: 1.75→25 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.74 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.107 / 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: 19.212 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.795 Å / Total num. of bins used: 20
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