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Open data
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Basic information
Entry | Database: PDB / ID: 6fj7 | ||||||
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Title | Caldiarchaeum Subterraneum Ubiquitin | ||||||
![]() | Ubiquitin-like protein | ||||||
![]() | PROTEIN BINDING / ubiquitination / ubiquitylation | ||||||
Function / homology | ![]() polyubiquitin modification-dependent protein binding / ubiquitin-dependent protein catabolic process / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wojtynek, M. / 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 | ![]() | 50.2 KB | Display | ![]() |
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PDB format | ![]() | 35.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 435.2 KB | Display | ![]() |
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Full document | ![]() | 436 KB | Display | |
Data in XML | ![]() | 6.8 KB | Display | |
Data in CIF | ![]() | 8.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6fjuC ![]() 6fjvC ![]() 6fnnC ![]() 6fnoC ![]() 1ubqS 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: 8359.806 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: CSUB_C1474, HGMM_F04B03C03, HGMM_F21D07C21, HGMM_F30C12C33 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: 1.94 Å3/Da / Density % sol: 36.53 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop Details: 100 mM sodium acetate pH 4.5, 200 mM lithium sulfate, 50% PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 22, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.05→32.9 Å / Num. obs: 30589 / % possible obs: 98.2 % / Redundancy: 11 % / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Net I/σ(I): 22.39 |
Reflection shell | Resolution: 1.05→1.11 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.627 / Mean I/σ(I) obs: 2.18 / Num. unique obs: 4406 / CC1/2: 0.862 / % possible all: 89 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1UBQ Resolution: 1.05→32.89 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.946 / SU B: 0.938 / SU ML: 0.021 / Cross valid method: THROUGHOUT / ESU R: 0.03 / ESU R Free: 0.034 / 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: 15.22 Å2
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Refinement step | Cycle: 1 / Resolution: 1.05→32.89 Å
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Refine LS restraints |
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