[English] 日本語
Yorodumi- PDB-5ky2: mouse POFUT1 in complex with O-glucosylated mouse Factor VII EGF1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ky2 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | mouse POFUT1 in complex with O-glucosylated mouse Factor VII EGF1 and GDP | |||||||||
Components |
| |||||||||
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 / fucose metabolic process / regulation of Notch signaling pathway ...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 / fucose metabolic process / regulation of Notch signaling pathway / 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 / positive regulation of leukocyte chemotaxis / protein O-linked glycosylation / response to cholesterol / response to growth hormone / positive regulation of positive 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: 1.47 Å | |||||||||
Authors | Li, Z. / Rini, J.M. | |||||||||
Funding support | Canada, 1items
| |||||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5ky2.cif.gz | 254.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5ky2.ent.gz | 211.5 KB | Display | PDB format |
PDBx/mmJSON format | 5ky2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ky/5ky2 ftp://data.pdbj.org/pub/pdb/validation_reports/ky/5ky2 | HTTPS FTP |
---|
-Related structure data
Related structure data | 5kxhC 5kxqC 5ky0C 5ky3C 5ky4C 5ky5C 5ky7C 5ky8C 5ky9C 5kx3 C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein / Protein/peptide , 2 types, 2 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 |
---|---|
#2: Protein/peptide | Mass: 4419.888 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 |
-Sugars , 2 types, 3 molecules
#3: Sugar | #6: Sugar | ChemComp-BGC / | |
---|
-Non-polymers , 3 types, 378 molecules
#4: Chemical | ChemComp-GDP / | ||
---|---|---|---|
#5: Chemical | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.13 % |
---|---|
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 |
---|---|
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: 1.47→50 Å / Num. obs: 66097 / % possible obs: 100 % / Redundancy: 7.2 % / Biso Wilson estimate: 18 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.123 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 1.47→1.52 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.524 / Mean I/σ(I) obs: 1 / CC1/2: 0.466 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement |
---|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.47→46.935 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.98
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 120.85 Å2 / Biso mean: 30.2703 Å2 / Biso min: 10.89 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.47→46.935 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|