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Open data
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Basic information
Entry | Database: PDB / ID: 5l95 | ||||||
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Title | Crystal structure of human UBA5 in complex with UFM1 and AMP | ||||||
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Function / homology | ![]() UFM1 activating enzyme activity / protein ufmylation / protein K69-linked ufmylation / megakaryocyte differentiation / regulation of intracellular estrogen receptor signaling pathway / reticulophagy / neuromuscular process / negative regulation of protein import into nucleus / localization / response to endoplasmic reticulum stress ...UFM1 activating enzyme activity / protein ufmylation / protein K69-linked ufmylation / megakaryocyte differentiation / regulation of intracellular estrogen receptor signaling pathway / reticulophagy / neuromuscular process / negative regulation of protein import into nucleus / localization / response to endoplasmic reticulum stress / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Oweis, W. / Padala, P. / Wiener, R. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Trans-Binding Mechanism of Ubiquitin-like Protein Activation Revealed by a UBA5-UFM1 Complex. Authors: Oweis, W. / Padala, P. / Hassouna, F. / Cohen-Kfir, E. / Gibbs, D.R. / Todd, E.A. / Berndsen, C.E. / Wiener, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 269.3 KB | Display | ![]() |
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PDB format | ![]() | 218 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5iaaSC 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
#1: Protein | Mass: 30994.381 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #2: Protein | Mass: 8590.877 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #3: Chemical | ChemComp-AMP / | ![]() #4: Chemical | #5: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.92 Å3/Da / Density % sol: 68.65 % |
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Crystal grow![]() | Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: 0.1M HEPES pH7.5, 10% PEG 6000 and 5% 2-Methyl-2,4-pentanediol (MPD) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 28, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.1→77 Å / Num. obs: 65695 / % possible obs: 99.8 % / Redundancy: 8.7 % / Rmerge(I) obs: 0.155 / Net I/σ(I): 8.5 |
Reflection shell | Highest resolution: 2.1 Å |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 5IAA Resolution: 2.1→76.999 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.77
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→76.999 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 |
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