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Yorodumi- PDB-2r10: Structure of an acetylated Rsc4 tandem bromodomain Histone Chimera -
+Open data
-Basic information
Entry | Database: PDB / ID: 2r10 | ||||||
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Title | Structure of an acetylated Rsc4 tandem bromodomain Histone Chimera | ||||||
Components | Chromatin structure-remodeling complex protein RSC4, LINKER, Histone H3 | ||||||
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 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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Remark 999 | The sequence, TARKSTGG(ALY)APRK is Histone H3, and GG is the Linker fused with Rsc4 TBD. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2r10.cif.gz | 140.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2r10.ent.gz | 114.6 KB | Display | PDB format |
PDBx/mmJSON format | 2r10.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r1/2r10 ftp://data.pdbj.org/pub/pdb/validation_reports/r1/2r10 | HTTPS FTP |
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-Related 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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Details | biological unit is a monomer. There are 2 biological units in the assymetric unit (chain A and chain B) |
-Components
#1: Protein | Mass: 41614.430 Da / Num. of mol.: 2 Fragment: fusion protein comprises Histone H3 (6-18) and Rsc4 TBD (22-361) Mutation: k9(ALY), K25(ALY) 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 #2: Chemical | #3: Water | ChemComp-HOH / | |
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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: 3.09 Å3/Da / Density % sol: 60.26 % |
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Crystal grow | Temperature: 298 K / pH: 8.5 Details: 0.1M Tris, 0.2M lithium sulfate, 28% PEG 3000, pH 8.5, VAPOR DIFFUSION, temperature 298K, pH 8.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1 |
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: 2.2→50 Å / Num. obs: 49197 / % possible obs: 95.3 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 17.2 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.494 / % possible all: 83.9 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.929 / SU B: 10.542 / SU ML: 0.142 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.209 / ESU R Free: 0.192 / 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: 32.9 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.26 Å / Total num. of bins used: 20
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