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Open data
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Basic information
Entry | Database: PDB / ID: 8add | |||||||||
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Title | Viral tegument-like DUBs | |||||||||
![]() | ATP-dependent DNA helicase | |||||||||
![]() | HYDROLASE / deubiquitinating enzyme / ubiquitin / tegument | |||||||||
Function / homology | ![]() DNA helicase activity / telomere maintenance / DNA recombination / DNA helicase / DNA repair / ATP hydrolysis activity / ATP binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Erven, I. / Abraham, E.T. / Hermanns, T. / Hofmann, K. / Baumann, U. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: A widely distributed family of eukaryotic and bacterial deubiquitinases related to herpesviral large tegument proteins. Authors: Erven, I. / Abraham, E. / Hermanns, T. / Baumann, U. / Hofmann, K. #1: ![]() Title: A structural basis for the diverse linkage specificities within the ZUFSP deubiquitinase family. Authors: Hermanns, T. / Pichlo, C. / Baumann, U. / Hofmann, K. #2: ![]() Title: A family of unconventional deubiquitinases with modular chain specificity determinants. Authors: Hermanns, T. / Pichlo, C. / Woiwode, I. / Klopffleisch, K. / Witting, K.F. / Ovaa, H. / Baumann, U. / Hofmann, K. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 159.5 KB | Display | ![]() |
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PDB format | ![]() | 107.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 423.6 KB | Display | ![]() |
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Full document | ![]() | 424.4 KB | Display | |
Data in XML | ![]() | 11.5 KB | Display | |
Data in CIF | ![]() | 16 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8adbC ![]() 8adcC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 24002.609 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 51.87 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M Tris pH 8.5, 20% w/v PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 4, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9747 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→100 Å / Num. obs: 37456 / % possible obs: 100 % / Redundancy: 10.6 % / Biso Wilson estimate: 23.32 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.162 / Rrim(I) all: 0.172 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 1.9→1.95 Å / Redundancy: 5.3 % / Rmerge(I) obs: 1.02 / Mean I/σ(I) obs: 1.72 / Num. unique obs: 2724 / CC1/2: 0.621 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.06 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→42.37 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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