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Open data
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Basic information
Entry | Database: PDB / ID: 5ky5 | ||||||
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Title | mouse POFUT1 in complex with EGF(+) and GDP | ||||||
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![]() | TRANSFERASE / glycosyltransferase | ||||||
Function / homology | ![]() peptide-O-fucosyltransferase / protein O-linked fucosylation / peptide-O-fucosyltransferase activity / fucosyltransferase activity / fucose metabolic process / regulation of Notch signaling pathway / protein O-linked glycosylation / somitogenesis / Notch signaling pathway / nervous system development ...peptide-O-fucosyltransferase / protein O-linked fucosylation / peptide-O-fucosyltransferase activity / fucosyltransferase activity / fucose metabolic process / regulation of Notch signaling pathway / protein O-linked glycosylation / somitogenesis / Notch signaling pathway / nervous system development / heart development / angiogenesis / endoplasmic reticulum / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() | ||||||
![]() | Li, Z. / Rini, J.M. | ||||||
![]() | ![]() Title: Recognition of EGF-like domains by the Notch-modifying O-fucosyltransferase POFUT1. Authors: Li, Z. / Han, K. / Pak, J.E. / Satkunarajah, M. / Zhou, D. / Rini, J.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 246.4 KB | Display | ![]() |
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PDB format | ![]() | 203 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5kxhC ![]() 5kxqC ![]() 5ky0C ![]() 5ky2C ![]() 5ky3C ![]() 5ky4C ![]() 5ky7C ![]() 5ky8C ![]() 5ky9C 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 / Sugars , 3 types, 4 molecules AB![](data/chem/img/NAG.gif)
![](data/chem/img/NAG.gif)
#1: Protein | Mass: 40457.266 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 4111.439 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Gene: F7, Cf7 / Production host: ![]() ![]() |
#3: Sugar |
-Non-polymers , 3 types, 450 molecules ![](data/chem/img/GDP.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-GDP / |
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#5: Chemical | ChemComp-GOL / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.46 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 20% PEG2000 MME, 50 mM Tris pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Dec 11, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 63046 / % possible obs: 100 % / Redundancy: 7.3 % / Biso Wilson estimate: 18.8 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.109 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 7.3 % / Rmerge(I) obs: 1.092 / Mean I/σ(I) obs: 1.7 / CC1/2: 0.696 / % possible all: 100 |
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Processing
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Refinement | Resolution: 1.5→47.156 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.9
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 115.44 Å2 / Biso mean: 30.7758 Å2 / Biso min: 11.12 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.5→47.156 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: 23 / % reflection obs: 100 %
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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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