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Yorodumi- PDB-3l3f: Crystal structure of a PFU-PUL domain pair of Saccharomyces cerev... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3l3f | ||||||
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Title | Crystal structure of a PFU-PUL domain pair of Saccharomyces cerevisiae Doa1/Ufd3 | ||||||
Components | Protein DOA1 | ||||||
Keywords | PROTEIN BINDING / Armadillo-like repeat structure / Nucleus / Ubl conjugation pathway | ||||||
Function / homology | Function and homology information ribophagy / mitochondria-associated ubiquitin-dependent protein catabolic process / ubiquitin recycling / cytoplasmic side of mitochondrial outer membrane / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-modified protein reader activity / ubiquitin binding / double-strand break repair via nonhomologous end joining / proteasome-mediated ubiquitin-dependent protein catabolic process / endosome membrane ...ribophagy / mitochondria-associated ubiquitin-dependent protein catabolic process / ubiquitin recycling / cytoplasmic side of mitochondrial outer membrane / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-modified protein reader activity / ubiquitin binding / double-strand break repair via nonhomologous end joining / proteasome-mediated ubiquitin-dependent protein catabolic process / endosome membrane / protein-containing complex binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å | ||||||
Authors | Komori, H. / Nishimasu, R. / Kuno, T. / Higuchi, Y. | ||||||
Citation | Journal: KOBE J.MED.SCI. / Year: 2010 Title: Crystal Structure of a PFU-PUL Domain Pair of Saccharomyces Cerevisiae Doa1/Ufd3 Authors: Nishimasu, R. / Komori, H. / Higuchi, Y. / Nishimasu, H. / Hiroaki, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3l3f.cif.gz | 76.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3l3f.ent.gz | 60.9 KB | Display | PDB format |
PDBx/mmJSON format | 3l3f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l3/3l3f ftp://data.pdbj.org/pub/pdb/validation_reports/l3/3l3f | 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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-Components
#1: Protein | Mass: 40814.117 Da / Num. of mol.: 1 / Fragment: PFU-PUL domain, residues 354-715 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Plasmid: pET-28 / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3) / References: UniProt: P36037 |
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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: 2.71 Å3/Da / Density % sol: 54.64 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M Tris-HCl (pH 7.5), 28% PEG 3350, 0.1M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9789, 0.9792, 0.9640 | ||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 10, 2007 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.9→33.75 Å / Num. obs: 34591 / % possible obs: 100 % / Redundancy: 11.2 % / Rmerge(I) obs: 0.062 | ||||||||||||
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 11.2 % / Rmerge(I) obs: 0.256 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.9→33.426 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.934 / SU B: 2.784 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.123 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.49 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→33.426 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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