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Yorodumi- PDB-4ocn: Crystal Structure of the Rpn8-Rpn11 MPN domain heterodimer, cryst... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ocn | ||||||
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Title | Crystal Structure of the Rpn8-Rpn11 MPN domain heterodimer, crystal form II | ||||||
Components |
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Keywords | HYDROLASE / PROTEIN BINDING / 26S proteasome / isopeptidase activity / regulatory particle / lid / ubiquitin | ||||||
Function / homology | Function and homology information peroxisome fission / proteasome storage granule assembly / proteasome regulatory particle, lid subcomplex / mitochondrial fission / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / Ub-specific processing proteases / proteasome binding / protein deubiquitination / proteasome storage granule ...peroxisome fission / proteasome storage granule assembly / proteasome regulatory particle, lid subcomplex / mitochondrial fission / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / Ub-specific processing proteases / proteasome binding / protein deubiquitination / proteasome storage granule / proteasome assembly / Neutrophil degranulation / proteasome complex / metallopeptidase activity / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / mitochondrion / metal ion binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) Lama glama (llama) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.25 Å | ||||||
Authors | Pathare, G.R. / Bracher, A. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2014 Title: Crystal structure of the proteasomal deubiquitylation module Rpn8-Rpn11. Authors: Pathare, G.R. / Nagy, I. / Sledz, P. / Anderson, D.J. / Zhou, H.J. / Pardon, E. / Steyaert, J. / Forster, F. / Bracher, A. / Baumeister, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ocn.cif.gz | 376 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ocn.ent.gz | 310.7 KB | Display | PDB format |
PDBx/mmJSON format | 4ocn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oc/4ocn ftp://data.pdbj.org/pub/pdb/validation_reports/oc/4ocn | HTTPS FTP |
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-Related structure data
Related structure data | 4oclSC 4ocmC S: Starting model for refinement C: citing same article (ref.) |
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Similar 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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-Components
#1: Protein | Mass: 20838.512 Da / Num. of mol.: 2 / Fragment: UNP residues 1-176 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: O5360, RPN8, YOR261C / Plasmid: pRSFDuet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q08723 #2: Protein | Mass: 24566.283 Da / Num. of mol.: 2 / Fragment: UNP residues 1-220 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: MPR1, RPN11, YFR004W / Plasmid: pRSFDuet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P43588 #3: Antibody | Mass: 14854.423 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Plasmid: pMESy4 / Production host: Escherichia coli (E. coli) / Strain (production host): WK6 Su #4: Water | ChemComp-HOH / | Sequence details | RPN8 AND RPN11 WERE EXPRESSED AS A FUSION PROTEIN CONNECTED BY A GSGGSGGSG LINKER. THEY HAVE BEEN ...RPN8 AND RPN11 WERE EXPRESSED AS A FUSION PROTEIN CONNECTED BY A GSGGSGGSG LINKER. THEY HAVE BEEN REPRESENTE | |
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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: 2.57 Å3/Da / Density % sol: 52.23 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 50 mM MES, pH 6.0, 100 mM magnesium chloride, 21% PEG3350, VAPOR DIFFUSION, HANGING DROPS, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 27, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.249→48.276 Å / Num. all: 61223 / Num. obs: 61223 / % possible obs: 99.8 % / Observed criterion σ(F): -100 / Observed criterion σ(I): -100 / Redundancy: 7.8 % / Biso Wilson estimate: 56.699 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.058 / Net I/σ(I): 20.3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4OCL Resolution: 2.25→30 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.915 / WRfactor Rfree: 0.2613 / WRfactor Rwork: 0.2156 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8051 / SU B: 16.267 / SU ML: 0.18 / SU R Cruickshank DPI: 0.2698 / SU Rfree: 0.2293 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.27 / ESU R Free: 0.229 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 121.37 Å2 / Biso mean: 54.6609 Å2 / Biso min: 27.08 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.249→2.307 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 |
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