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- PDB-4wmk: Crystal structure of mouse Xyloside xylosyltransferase 1 complexe... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4wmk | |||||||||
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Title | Crystal structure of mouse Xyloside xylosyltransferase 1 complexed with manganese, product ligand and UDP (Product complex II) | |||||||||
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![]() | transferase/protein binding / glycosyltransferase / transferase-protein binding complex | |||||||||
Function / homology | ![]() xylosyl alpha-1,3-xylosyltransferase / xylosyl alpha-1,3-xylosyltransferase activity / UDP-xylosyltransferase activity / Defective F9 secretion / Defective gamma-carboxylation of F9 / coagulation factor IXa / O-glycan processing / Defective F9 activation / Defective factor IX causes thrombophilia / Defective cofactor function of FVIIIa variant ...xylosyl alpha-1,3-xylosyltransferase / xylosyl alpha-1,3-xylosyltransferase activity / UDP-xylosyltransferase activity / Defective F9 secretion / Defective gamma-carboxylation of F9 / coagulation factor IXa / O-glycan processing / 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 / manganese ion binding / collagen-containing extracellular matrix / endopeptidase activity / endoplasmic reticulum lumen / serine-type endopeptidase activity / calcium ion binding / endoplasmic reticulum membrane / magnesium ion binding / proteolysis / extracellular space / extracellular exosome / extracellular region / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Yu, H. / Li, H. | |||||||||
![]() | ![]() Title: Notch-modifying xylosyltransferase structures support an SNi-like retaining mechanism. Authors: Yu, H. / Takeuchi, M. / LeBarron, J. / Kantharia, J. / London, E. / Bakker, H. / Haltiwanger, R.S. / Li, H. / Takeuchi, H. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 87.7 KB | Display | ![]() |
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PDB format | ![]() | 63.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4wlgC ![]() 4wlmC ![]() 4wlzC ![]() 4wm0C ![]() 4wmaC ![]() 4wmbC ![]() 4wmiC ![]() 4wn2C 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, 3 molecules AD
#1: Protein | Mass: 35295.500 Da / Num. of mol.: 1 / Fragment: unp residues 87-392 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q3U4G3, Transferases; Glycosyltransferases; Pentosyltransferases |
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#2: Protein/peptide | Mass: 5710.229 Da / Num. of mol.: 1 / Fragment: unp residues 92-130 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Polysaccharide | alpha-D-xylopyranose-(1-3)-alpha-D-xylopyranose-(1-3)-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 4 types, 89 molecules ![](data/chem/img/MN.gif)
![](data/chem/img/UDP.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/UDP.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-MN / |
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#5: Chemical | ChemComp-UDP / |
#6: Chemical | ChemComp-SO4 / |
#7: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.22 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Li2SO4, 0.1 M Bis-Tris, and 21% PEG3350 / PH range: 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 11, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.08→40 Å / Num. obs: 22674 / % possible obs: 97.8 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 14 |
Reflection shell | Resolution: 2.08→2.15 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 2.3 / % possible all: 84.1 |
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Processing
Software | Name: REFMAC / Version: 5.6.0117 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.08→40 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.928 / Cross valid method: THROUGHOUT / ESU R: 0.222 / ESU R Free: 0.193 / 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: 32.348 Å2
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Refinement step | Cycle: LAST / Resolution: 2.08→40 Å
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