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Open data
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Basic information
Entry | Database: PDB / ID: 6fjv | ||||||
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Title | Rpn11 homolog from Caldiarchaeum Subterraneum, truncated | ||||||
![]() | 26S proteasome regulatory subunit N11-like protein | ||||||
![]() | HYDROLASE / deubiquitination / deubiquitylation | ||||||
Function / homology | JAB1/Mov34/MPN/PAD-1 ubiquitin protease / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / MPN domain profile. / proteasome complex / metallopeptidase activity / metal ion binding / 26S proteasome regulatory subunit N11-like protein![]() | ||||||
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 | ![]() | 80.2 KB | Display | ![]() |
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PDB format | ![]() | 59.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 431.3 KB | Display | ![]() |
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Full document | ![]() | 432.3 KB | Display | |
Data in XML | ![]() | 9.3 KB | Display | |
Data in CIF | ![]() | 12.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6fj7C ![]() 6fjuSC ![]() 6fnnC ![]() 6fnoC 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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Unit cell |
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Components
#1: Protein | Mass: 17061.760 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: CSUB_C1473, HGMM_F04B03C04, HGMM_F21D07C20, HGMM_F30C12C32 Production host: ![]() ![]() | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 42.97 % |
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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, 25% PEG 4000 |
-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: 1.35→38.2 Å / Num. obs: 34313 / % possible obs: 100 % / Redundancy: 12.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Net I/σ(I): 21.1 |
Reflection shell | Resolution: 1.35→1.43 Å / Redundancy: 11.5 % / Rmerge(I) obs: 1.11 / Mean I/σ(I) obs: 2.25 / CC1/2: 0.917 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6FJU Resolution: 1.35→38.2 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.01 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.059 / 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: 18.995 Å2
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Refinement step | Cycle: 1 / Resolution: 1.35→38.2 Å
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Refine LS restraints |
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