+Open data
-Basic information
Entry | Database: PDB / ID: 2fvu | ||||||
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Title | Structure of the yeast Sir3 BAH domain | ||||||
Components | Regulatory protein SIR3 | ||||||
Keywords | TRANSCRIPTION / mainly beta | ||||||
Function / homology | Function and homology information establishment of protein-containing complex localization to telomere / nuclear-transcribed mRNA catabolic process, non-stop decay / telomere tethering at nuclear periphery / chromatin silencing complex / silent mating-type cassette heterochromatin formation / subtelomeric heterochromatin formation / nucleosome binding / heterochromatin / heterochromatin formation / double-strand break repair via nonhomologous end joining ...establishment of protein-containing complex localization to telomere / nuclear-transcribed mRNA catabolic process, non-stop decay / telomere tethering at nuclear periphery / chromatin silencing complex / silent mating-type cassette heterochromatin formation / subtelomeric heterochromatin formation / nucleosome binding / heterochromatin / heterochromatin formation / double-strand break repair via nonhomologous end joining / single-stranded DNA binding / double-stranded DNA binding / chromosome, telomeric region / nucleic acid binding / chromatin binding / nucleolus / mitochondrion / identical protein binding Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Xu, R.M. | ||||||
Citation | Journal: Mol.Cell.Biol. / Year: 2006 Title: Structure and function of the Saccharomyces cerevisiae Sir3 BAH domain. Authors: Connelly, J.J. / Yuan, P. / Hsu, H.C. / Li, Z. / Xu, R.M. / Sternglanz, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2fvu.cif.gz | 92.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fvu.ent.gz | 72 KB | Display | PDB format |
PDBx/mmJSON format | 2fvu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fv/2fvu ftp://data.pdbj.org/pub/pdb/validation_reports/fv/2fvu | 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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Details | There are two molecules per asymmetric unit, which may or may not have physiological meanings. The purified protein exits as a monomer in solution. |
-Components
#1: Protein | Mass: 26405.016 Da / Num. of mol.: 2 / Fragment: BAH domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: SIR3 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P06701 #2: 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: 3.05 Å3/Da / Density % sol: 59.63 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 3.75 Details: 4M sodium formate, pH 3.75, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 0.9 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 4, 2003 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 50308 / Num. obs: 47561 / % possible obs: 94.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.077 |
Reflection shell | Resolution: 1.9→1.97 Å / % possible all: 89.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→500 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 55.636 Å2 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.349 Å2
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Refinement step | Cycle: LAST / Resolution: 2→500 Å
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Xplor file |
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