+Open data
-Basic information
Entry | Database: PDB / ID: 6fju | ||||||
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Title | Rpn11 homolog from Caldiarchaeum Subterraneum | ||||||
Components | 26S proteasome regulatory subunit N11-like protein | ||||||
Keywords | HYDROLASE / deubiquitination / deubiquitylation | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Candidatus Caldiarchaeum subterraneum (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Fuchs, A.C.D. / Albrecht, R. / Martin, J. / Hartmann, M.D. | ||||||
Citation | Journal: Nat Commun / Year: 2018 Title: Rpn11-mediated ubiquitin processing in an ancestral archaeal ubiquitination system. Authors: Fuchs, A.C.D. / Maldoner, L. / Wojtynek, M. / Hartmann, M.D. / Martin, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6fju.cif.gz | 160.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fju.ent.gz | 125.3 KB | Display | PDB format |
PDBx/mmJSON format | 6fju.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6fju_validation.pdf.gz | 453.5 KB | Display | wwPDB validaton report |
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Full document | 6fju_full_validation.pdf.gz | 455.6 KB | Display | |
Data in XML | 6fju_validation.xml.gz | 17.6 KB | Display | |
Data in CIF | 6fju_validation.cif.gz | 25.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fj/6fju ftp://data.pdbj.org/pub/pdb/validation_reports/fj/6fju | HTTPS FTP |
-Related structure data
Related structure data | 6fj7C 6fjvC 6fnnC 6fnoC 4oclS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _ / Auth seq-ID: 0 - 174 / Label seq-ID: 26 - 200
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-Components
#1: Protein | Mass: 25616.539 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candidatus Caldiarchaeum subterraneum (archaea) Gene: CSUB_C1473, HGMM_F04B03C04, HGMM_F21D07C20, HGMM_F30C12C32 Production host: Escherichia coli (E. coli) / References: UniProt: E6N8B9 #2: Chemical | #3: Chemical | ChemComp-SO4 / | #4: 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: 2.06 Å3/Da / Density % sol: 40.22 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / Details: 100 mM HEPES pH 7.0, 15% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 27, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→33.8 Å / Num. obs: 51685 / % possible obs: 99.7 % / Redundancy: 6.86 % / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Net I/σ(I): 18.8 |
Reflection shell | Resolution: 1.65→1.75 Å / Redundancy: 6.29 % / Rmerge(I) obs: 0.973 / Mean I/σ(I) obs: 1.77 / CC1/2: 0.791 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4OCL Resolution: 1.65→33.8 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.962 / SU B: 3.556 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.079 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.662 Å2
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Refinement step | Cycle: 1 / Resolution: 1.65→33.8 Å
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Refine LS restraints |
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