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Open data
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Basic information
Entry | Database: PDB / ID: 3pst | ||||||
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Title | Crystal structure of PUL and PFU(mutate) domain | ||||||
![]() | Protein DOA1 | ||||||
![]() | ![]() ![]() ![]() | ||||||
Function / homology | ![]() ribophagy / mitochondria-associated ubiquitin-dependent protein catabolic process / ubiquitin recycling / cytoplasmic side of mitochondrial outer membrane / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-modified protein reader activity / ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Liu, Y. / Sun, J. | ||||||
![]() | ![]() Title: Crystal structure of PUL and PFU(mutate) domain Authors: Liu, Y. / Sun, 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 | ![]() | 84.5 KB | Display | ![]() |
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PDB format | ![]() | 62.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
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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: 47245.961 Da / Num. of mol.: 1 / Fragment: PUL and PFU domains (UNP residues 325-715) / Mutation: F434L Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: DOA1, UFD3, ZZZ4, YKL213C / Production host: ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.8 % |
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Crystal grow![]() | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.15M Potassium bromide,30% w/v PEG 2000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.999→87.955 Å / Num. all: 28692 / Num. obs: 28692 / % possible obs: 100 % |
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Processing
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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 / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.33 Å2 / ksol: 0.34 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.999→37.533 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13
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