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- PDB-6fno: Caldiarchaeum Subterraneum Ubiquitin:Rpn11-homolog complex, zinc soak -
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Open data
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Basic information
Entry | Database: PDB / ID: 6fno | ||||||
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Title | Caldiarchaeum Subterraneum Ubiquitin:Rpn11-homolog complex, zinc soak | ||||||
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![]() | HYDROLASE / deubiquitination / deubiquitylation / JAMM protease | ||||||
Function / homology | ![]() polyubiquitin modification-dependent protein binding / proteasome complex / metallopeptidase activity / ubiquitin-dependent protein catabolic process / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fuchs, A.C.D. / Albrecht, R. / Martin, J. / Hartmann, M.D. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 203.6 KB | Display | ![]() |
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PDB format | ![]() | 161.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 469.8 KB | Display | ![]() |
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Full document | ![]() | 474.7 KB | Display | |
Data in XML | ![]() | 22.1 KB | Display | |
Data in CIF | ![]() | 31.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6fj7C ![]() 6fjuC ![]() 6fjvC ![]() 6fnnSC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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: 17061.760 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: CSUB_C1473, HGMM_F04B03C04, HGMM_F21D07C20, HGMM_F30C12C32 Production host: ![]() ![]() #2: Protein | Mass: 11365.131 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: CSUB_C1474, HGMM_F04B03C03, HGMM_F21D07C21, HGMM_F30C12C33 Production host: ![]() ![]() #3: Chemical | #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 59.01 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop Details: 100 mM sodium acetate pH 4.6, 1.5 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 24, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→37.8 Å / Num. obs: 50327 / % possible obs: 99.7 % / Redundancy: 6.9 % / CC1/2: 1 / Rmerge(I) obs: 0.081 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 1.95→2.06 Å / Redundancy: 6.88 % / Rmerge(I) obs: 1.03 / Mean I/σ(I) obs: 1.7 / CC1/2: 0.759 / % possible all: 98.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6FNN Resolution: 1.95→37.8 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.957 / SU B: 6.607 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.114 / 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: 44.397 Å2
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Refinement step | Cycle: 1 / Resolution: 1.95→37.8 Å
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Refine LS restraints |
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