+Open data
-Basic information
Entry | Database: PDB / ID: 2idc | ||||||
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Title | Structure of the Histone H3-Asf1 Chaperone Interaction | ||||||
Components | ANTI-SILENCING PROTEIN 1 AND HISTONE H3 CHIMERA | ||||||
Keywords | Replication/Chaperone / Ig-like fold / Asf1 / H3 / histone / chaperone / chromatin / Replication-Chaperone COMPLEX | ||||||
Function / homology | Function and homology information : / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / sexual sporulation resulting in formation of a cellular spore / H3 histone acetyltransferase complex / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / acetyltransferase activator activity / DNA replication-dependent chromatin assembly / nucleosome disassembly / : ...: / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / sexual sporulation resulting in formation of a cellular spore / H3 histone acetyltransferase complex / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / acetyltransferase activator activity / DNA replication-dependent chromatin assembly / nucleosome disassembly / : / replication fork protection complex / silent mating-type cassette heterochromatin formation / positive regulation of transcription by RNA polymerase I / nucleolar large rRNA transcription by RNA polymerase I / rRNA transcription / negative regulation of DNA damage checkpoint / subtelomeric heterochromatin formation / regulation of DNA repair / CENP-A containing nucleosome / positive regulation of transcription elongation by RNA polymerase II / regulation of protein phosphorylation / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / histone binding / regulation of gene expression / chromosome, telomeric region / protein heterodimerization activity / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / DNA binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Antczak, A.J. / Tsubota, T. / Kaufman, P.D. / Berger, J.M. | ||||||
Citation | Journal: Bmc Struct.Biol. / Year: 2006 Title: Structure of the yeast histone H3-ASF1 interaction: implications for chaperone mechanism, species-specific interactions, and epigenetics. Authors: Antczak, A.J. / Tsubota, T. / Kaufman, P.D. / Berger, J.M. | ||||||
History |
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Remark 999 | SEQUENCE The yeast ASF1 gene was genetically modified in a pET28b (novagen) derivative plasmid that ...SEQUENCE The yeast ASF1 gene was genetically modified in a pET28b (novagen) derivative plasmid that contains a hepta-his tag, Maltose Binding Protein tag, and is tethered to Asf1 via a TEV protease cleavable linker. Ala A 1 is therefore a reminant of the TEV cleavage reaction. Ala A 156 and Ala A 157 are part of an Ala/Gly/Thr linker which connects Asf1 and H3, however, no density was seen for the other six residues in this linker region. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2idc.cif.gz | 50.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2idc.ent.gz | 34.7 KB | Display | PDB format |
PDBx/mmJSON format | 2idc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/id/2idc ftp://data.pdbj.org/pub/pdb/validation_reports/id/2idc | 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 |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 20084.734 Da / Num. of mol.: 1 / Fragment: Asf1, residues 2-155 and H3, residues 121-134 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c Gene: ASF1, CIA1, YJL115W, J0755, HHT1, YBR010W, YBR0201, HHT2, SIN2, YNL031C, N2749 Plasmid: pET28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P32447, UniProt: P61830 |
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#2: 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: 2.5 Å3/Da / Density % sol: 50.72 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: Tris-HCl, Li2SO4, PEG 4000, glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 30, 2005 |
Radiation | Monochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11587 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→44.687 Å / Num. all: 12061 / Num. obs: 12061 / % possible obs: 98.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.9 % / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 2 / Rsym value: 0.362 / % possible all: 98.8 |
-Phasing
Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ID 1ROC Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.92 / SU B: 10.866 / SU ML: 0.141 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.252 / ESU R Free: 0.204 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.29 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A
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