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Yorodumi- PDB-5vyg: Crystal structure of hFA9 EGF repeat with O-glucose trisaccharide -
+Open data
-Basic information
Entry | Database: PDB / ID: 5vyg | |||||||||
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Title | Crystal structure of hFA9 EGF repeat with O-glucose trisaccharide | |||||||||
Components | Coagulation factor IX | |||||||||
Keywords | transferase / hydrolase / Notch regulation / EGF repeat / glycosylation / Transferase-Hydrolase complex | |||||||||
Function / homology | Function and homology information Defective F9 secretion / Defective gamma-carboxylation of F9 / coagulation factor IXa / Defective F9 activation / Defective factor IX causes thrombophilia / Defective cofactor function of FVIIIa variant / Defective F9 variant does not activate FX / zymogen activation / Extrinsic Pathway of Fibrin Clot Formation / Protein hydroxylation ...Defective F9 secretion / Defective gamma-carboxylation of F9 / coagulation factor IXa / Defective F9 activation / Defective factor IX causes thrombophilia / Defective cofactor function of FVIIIa variant / Defective F9 variant does not activate FX / zymogen activation / Extrinsic Pathway of Fibrin Clot Formation / Protein hydroxylation / 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 / Intrinsic Pathway of Fibrin Clot Formation / Golgi lumen / blood coagulation / collagen-containing extracellular matrix / endopeptidase activity / endoplasmic reticulum lumen / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space / extracellular exosome / extracellular region / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||
Authors | Yu, H.J. / Li, H.L. | |||||||||
Citation | Journal: J. Biol. Chem. / Year: 2017 Title: O-Glycosylation modulates the stability of epidermal growth factor-like repeats and thereby regulates Notch trafficking Authors: Takeuchi, H. / Yu, H. / Hao, H. / Takeuchi, M. / Ito, A. / Li, H. / Haltiwanger, R.S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5vyg.cif.gz | 43.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vyg.ent.gz | 28.7 KB | Display | PDB format |
PDBx/mmJSON format | 5vyg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vy/5vyg ftp://data.pdbj.org/pub/pdb/validation_reports/vy/5vyg | HTTPS FTP |
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-Related structure data
Related structure data | 1edmS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 5710.229 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: F9 / Production host: Escherichia coli (E. coli) / References: UniProt: P00740, coagulation factor IXa #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.69 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M Tris pH 8.5, 15% Glycerol, 1.6 M (NH4)2SO4, 5% 2,2,2-Trifluoroethanol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Sep 6, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 7814 / % possible obs: 99.8 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 2.2→2.32 Å / Rmerge(I) obs: 0.515 / Mean I/σ(I) obs: 4.5 / Num. unique obs: 1200 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1edm Resolution: 2.2→46.16 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.913 / SU B: 6.412 / SU ML: 0.16 / Cross valid method: THROUGHOUT / ESU R: 0.265 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.999 Å2
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Refinement step | Cycle: 1 / Resolution: 2.2→46.16 Å
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