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- PDB-7oy3: Crystal structure of depupylase Dop in complex with phosphorylate... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7oy3 | |||||||||
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Title | Crystal structure of depupylase Dop in complex with phosphorylated Pup and ADP | |||||||||
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![]() | HYDROLASE / depupylase / ATP hydrolysis / deamidase / phosphorylated Pup binding | |||||||||
Function / homology | ![]() protein pupylation / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / Hydrolases; Acting on peptide bonds (peptidases) / proteasome binding / proteasomal protein catabolic process / modification-dependent protein catabolic process / protein tag activity / peptidase activity / ATP binding / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||
![]() | Cui, H. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structures of prokaryotic ubiquitin-like protein Pup in complex with depupylase Dop reveal the mechanism of catalytic phosphate formation. Authors: Cui, H. / Muller, A.U. / Leibundgut, M. / Tian, J. / Ban, N. / Weber-Ban, E. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 135 KB | Display | ![]() |
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PDB format | ![]() | 99.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.5 MB | Display | ![]() |
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Full document | ![]() | 2.5 MB | Display | |
Data in XML | ![]() | 26.1 KB | Display | |
Data in CIF | ![]() | 38.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7oxvC ![]() 7oxyC ![]() 7oyfC ![]() 7oyhC ![]() 5lrtS 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
-Protein / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | Mass: 57288.332 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The C-terminal ENLYFQ fragment is a leftover from TEV clevage site. Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: A0LU48, Hydrolases; Acting on peptide bonds (peptidases) |
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#2: Protein/peptide | Mass: 3279.369 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: The C-terminal glumate (E) of this peptide was phosphorylated in the presence of ATP during crystallization. The phosphorylated glumate was renamed as GLP. Source: (synth.) ![]() |
-Non-polymers , 8 types, 479 molecules ![](data/chem/img/K.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-K / | ||||||||||||
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#4: Chemical | #5: Chemical | ChemComp-EDO / #6: Chemical | ChemComp-ADP / | #7: Chemical | #8: Chemical | ChemComp-PEG / | #9: Chemical | ChemComp-PGE / | #10: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.95 Å3/Da / Density % sol: 58.28 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 100 mM Tris-acetate pH 7.0-8.5, 10 mM ADP, 40 mM MgCl2 and 0.75-1.0 M KH2PO4 PH range: 7.0-8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 10, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.815 Å / Relative weight: 1 |
Reflection | Resolution: 1.775577→47.9101 Å / Num. obs: 68753 / % possible obs: 99.83 % / Redundancy: 20.6 % / CC1/2: 0.999 / Net I/σ(I): 12.56 |
Reflection shell | Resolution: 1.78→1.844 Å / Num. unique obs: 6798 / CC1/2: 0.774 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5LRT Resolution: 1.78→46.78 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 20.82 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 98.32 Å2 / Biso mean: 30.5869 Å2 / Biso min: 14.86 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.78→46.78 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30
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