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- PDB-8hte: Crystal structure of an effector mutant in complex with ubiquitin -
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Open data
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Basic information
Entry | Database: PDB / ID: 8hte | |||||||||||||||||||||
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Title | Crystal structure of an effector mutant in complex with ubiquitin | |||||||||||||||||||||
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![]() | TRANSFERASE / Ubiquitination | |||||||||||||||||||||
Function / homology | ![]() glycosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / ribosomal large subunit export from nucleus / ribosomal large subunit assembly / modification-dependent protein catabolic process / protein tag activity / host cell / ribosome biogenesis / cytosolic large ribosomal subunit / cytoplasmic translation ...glycosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / ribosomal large subunit export from nucleus / ribosomal large subunit assembly / modification-dependent protein catabolic process / protein tag activity / host cell / ribosome biogenesis / cytosolic large ribosomal subunit / cytoplasmic translation / protein ubiquitination / structural constituent of ribosome / ubiquitin protein ligase binding / extracellular region / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||||||||||||||
Biological species | ![]() ![]() ![]() | |||||||||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||||||||
![]() | Tan, J. / Wang, X. / Zhou, Y. / Zhu, Y. | |||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Molecular basis of threonine ADP-ribosylation of ubiquitin by bacterial ARTs. Authors: Tan, J. / Xu, Y. / Wang, X. / Yan, F. / Xian, W. / Liu, X. / Chen, Y. / Zhu, Y. / Zhou, Y. | |||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 141.1 KB | Display | ![]() |
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PDB format | ![]() | 106.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 971.5 KB | Display | ![]() |
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Full document | ![]() | 973 KB | Display | |
Data in XML | ![]() | 16.6 KB | Display | |
Data in CIF | ![]() | 24 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8htcC ![]() 8htdC ![]() 8htfC 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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Unit cell |
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Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 26020.902 Da / Num. of mol.: 1 / Mutation: E220A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 12472 / DSM 30191 / JCM 1249 / NBRC 12614 / NCIMB 9131 / NCTC 9757 Gene: cteC, CV_1467 / Production host: ![]() ![]() References: UniProt: Q7NY09, Transferases; Glycosyltransferases; Pentosyltransferases |
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#2: Protein | Mass: 8568.769 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Non-polymers , 5 types, 265 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/NCA.gif)
![](data/chem/img/AR6.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/NCA.gif)
![](data/chem/img/AR6.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-NCA / | #6: Chemical | ChemComp-AR6 / [( | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.86 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 100 mM BIS-TRIS propane, pH 7.0, and 1.5 M ammonium sulfate |
-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: Jun 30, 2018 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→50 Å / Num. obs: 17106 / % possible obs: 99.3 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.058 / Rrim(I) all: 0.123 / Χ2: 0.473 / Net I/σ(I): 3.9 / Num. measured all: 73589 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
Software |
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 115.25 Å2 / Biso mean: 27.7243 Å2 / Biso min: 5.66 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.307→32.84 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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