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- PDB-7oxv: Crystal structure of depupylase Dop in the Dop-loop-inserted state -
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Open data
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Basic information
Entry | Database: PDB / ID: 7oxv | ||||||
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Title | Crystal structure of depupylase Dop in the Dop-loop-inserted state | ||||||
![]() | Depupylase | ||||||
![]() | HYDROLASE / depupylase / Dop-loop / deamidase / Pup | ||||||
Function / homology | ![]() protein pupylation / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / Hydrolases; Acting on peptide bonds (peptidases) / proteasomal protein catabolic process / modification-dependent protein catabolic process / 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 | ![]() | 240.6 KB | Display | ![]() |
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PDB format | ![]() | 194.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 463.3 KB | Display | ![]() |
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Full document | ![]() | 469.6 KB | Display | |
Data in XML | ![]() | 24.5 KB | Display | |
Data in CIF | ![]() | 37.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7oxyC ![]() 7oy3C ![]() 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 on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#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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-Non-polymers , 5 types, 462 molecules ![](data/chem/img/PGE.gif)
![](data/chem/img/SCN.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SCN.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-PGE / #3: Chemical | ChemComp-SCN / | #4: Chemical | #5: Chemical | ChemComp-EDO / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.81 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 14-20 % (w/v) PEG 3350, 100 mM Bis-Tris propane pH 6.0-6.5 and 100-200 mM potassium thiocyanate (KSCN) PH range: 6.0-6.5 |
-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: May 28, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.39→46.04 Å / Num. obs: 98553 / % possible obs: 99.85 % / Redundancy: 25.2 % / CC1/2: 1 / Net I/σ(I): 26.76 |
Reflection shell | Resolution: 1.39→1.444 Å / Redundancy: 22.6 % / Num. unique obs: 9612 / CC1/2: 0.587 / % possible all: 98.99 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5LRT Resolution: 1.394→46.037 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 15.17 / 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: 166.82 Å2 / Biso mean: 28.2503 Å2 / Biso min: 6.41 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.394→46.037 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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