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Yorodumi- PDB-5ky3: mouse POFUT1 in complex with mouse Factor VII EGF1 mutant (T101A)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ky3 | ||||||
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Title | mouse POFUT1 in complex with mouse Factor VII EGF1 mutant (T101A) and GDP-fucose | ||||||
Components |
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Keywords | TRANSFERASE / glycosyltransferase | ||||||
Function / homology | Function and homology information Extrinsic Pathway of Fibrin Clot Formation / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Removal of aminoterminal propeptides from gamma-carboxylated proteins / peptide-O-fucosyltransferase / protein O-linked fucosylation / peptide-O-fucosyltransferase activity / fucosyltransferase activity / regulation of Notch signaling pathway / fucose metabolic process ...Extrinsic Pathway of Fibrin Clot Formation / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Removal of aminoterminal propeptides from gamma-carboxylated proteins / peptide-O-fucosyltransferase / protein O-linked fucosylation / peptide-O-fucosyltransferase activity / fucosyltransferase activity / regulation of Notch signaling pathway / fucose metabolic process / coagulation factor VIIa / response to Thyroid stimulating hormone / response to 2,3,7,8-tetrachlorodibenzodioxine / response to astaxanthin / response to thyrotropin-releasing hormone / response to genistein / serine-type peptidase complex / positive regulation of platelet-derived growth factor receptor signaling pathway / response to vitamin K / response to carbon dioxide / response to thyroxine / protein O-linked glycosylation / response to cholesterol / response to growth hormone / positive regulation of positive chemotaxis / positive regulation of leukocyte chemotaxis / positive regulation of TOR signaling / positive regulation of blood coagulation / animal organ regeneration / somitogenesis / Notch signaling pathway / response to nutrient levels / protein processing / circadian rhythm / response to estrogen / blood coagulation / response to estradiol / nervous system development / heart development / angiogenesis / endopeptidase activity / vesicle / response to hypoxia / serine-type endopeptidase activity / signaling receptor binding / calcium ion binding / endoplasmic reticulum / extracellular space / extracellular region / membrane Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.53 Å | ||||||
Authors | Li, Z. / Rini, J.M. | ||||||
Citation | Journal: Nat. Chem. Biol. / Year: 2017 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ky3.cif.gz | 239 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ky3.ent.gz | 197.4 KB | Display | PDB format |
PDBx/mmJSON format | 5ky3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ky3_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 5ky3_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5ky3_validation.xml.gz | 21 KB | Display | |
Data in CIF | 5ky3_validation.cif.gz | 31.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ky/5ky3 ftp://data.pdbj.org/pub/pdb/validation_reports/ky/5ky3 | HTTPS FTP |
-Related structure data
Related structure data | 5kxhC 5kxqC 5ky0C 5ky2C 5ky4C 5ky5C 5ky7C 5ky8C 5ky9C C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein / Protein/peptide / Sugars , 3 types, 4 molecules AB
#1: Protein | Mass: 40457.266 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pofut1 / Plasmid: PB-T-PAF / Production host: Homo sapiens (human) / References: UniProt: Q91ZW2, peptide-O-fucosyltransferase |
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#2: Protein/peptide | Mass: 4389.862 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: F7, Cf7 / Production host: Escherichia coli (E. coli) / References: UniProt: P70375, coagulation factor VIIa |
#3: Sugar |
-Non-polymers , 3 types, 409 molecules
#4: Chemical | ChemComp-GOL / |
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#5: Chemical | ChemComp-GFB / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.51 % |
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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: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Apr 1, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 1.526→50 Å / Num. obs: 59408 / % possible obs: 100 % / Redundancy: 7.2 % / Biso Wilson estimate: 18.4 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.083 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 1.53→1.58 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 2.3 / CC1/2: 0.806 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.53→47.127 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.32 / 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: 126.85 Å2 / Biso mean: 31.4295 Å2 / Biso min: 12.61 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.53→47.127 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: 21
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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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