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Yorodumi- PDB-3f5r: The crystal structure of a subunit of the heterodimeric FACT comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3f5r | ||||||
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Title | The crystal structure of a subunit of the heterodimeric FACT complex (Spt16p-Pob3p). | ||||||
Components | FACT complex subunit POB3FACT (biology) | ||||||
Keywords | transcription regulator / APC7736 / FACT complex (Spt16p-Pob3p) / Saccharomyces cerevisiae / structural genomics / PSI-2 / protein structure initiative / midwest center for structural genomics / MCSG / Chromosomal protein / DNA damage / DNA repair / DNA replication / Nucleus / Phosphoprotein / Transcription / Transcription regulation | ||||||
Function / homology | Function and homology information Regulation of TP53 Activity through Phosphorylation / FACT complex / regulation of chromatin organization / nucleosome organization / replication fork protection complex / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Pre-transcription Events / positive regulation of RNA polymerase II transcription preinitiation complex assembly / DNA-templated DNA replication / chromatin organization ...Regulation of TP53 Activity through Phosphorylation / FACT complex / regulation of chromatin organization / nucleosome organization / replication fork protection complex / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Pre-transcription Events / positive regulation of RNA polymerase II transcription preinitiation complex assembly / DNA-templated DNA replication / chromatin organization / DNA repair / chromatin / DNA binding Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å | ||||||
Authors | Tan, K. / Xu, X. / Cui, H. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: The crystal structure of a subunit of the heterodimeric FACT complex (Spt16p-Pob3p). Authors: Tan, K. / Xu, X. / Cui, H. / Savchenko, A. / Edwards, A. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3f5r.cif.gz | 42.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3f5r.ent.gz | 28.3 KB | Display | PDB format |
PDBx/mmJSON format | 3f5r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f5/3f5r ftp://data.pdbj.org/pub/pdb/validation_reports/f5/3f5r | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | Experimentally unknown. It is predicted to be monomer. |
-Components
#1: Protein | Mass: 21984.727 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: POB3, Saccharomyces cerevisiae, YML069W / Plasmid: p15Tv lic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q04636 |
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#2: Chemical | ChemComp-CL / |
#3: Chemical | ChemComp-FMT / |
#4: Chemical | ChemComp-GOL / |
#5: 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: 2.07 Å3/Da / Density % sol: 40.68 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1M Bis-tris, 1.5M (NH4)2SO4., pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97926 Å |
Detector | Type: SBC-3 / Detector: CCD / Date: Jun 26, 2008 / Details: Mirror |
Radiation | Monochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97926 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→22.3 Å / Num. all: 20548 / Num. obs: 20548 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.4 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 36.8 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 2.1 / Num. unique all: 1001 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.7→22.3 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.964 / SU B: 3.43 / SU ML: 0.052 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.084 / ESU R Free: 0.079 / 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: 23.465 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→22.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.698→1.742 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -0.744 Å / Origin y: 51.428 Å / Origin z: 2.306 Å
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