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Yorodumi- PDB-4wnh: Crystal structure of mouse Xyloside xylosyltransferase 1 complexe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4wnh | |||||||||
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Title | Crystal structure of mouse Xyloside xylosyltransferase 1 complexed with manganese,acceptor ligand and UDP-Xylose | |||||||||
Components |
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Keywords | transferase/protein binding / glycolsyltransferase / transferase-protein binding complex | |||||||||
Function / homology | Function and homology information 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 | Mus musculus (house mouse) Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | |||||||||
Authors | Yu, H. / Li, H. | |||||||||
Citation | Journal: To Be Published Title: Crystal structure of mouse Xyloside xylosyltransferase 1 complexed with manganese,acceptor ligand and UDP-Xylose Authors: Yu, H. / Li, H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4wnh.cif.gz | 88.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4wnh.ent.gz | 62.6 KB | Display | PDB format |
PDBx/mmJSON format | 4wnh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wn/4wnh ftp://data.pdbj.org/pub/pdb/validation_reports/wn/4wnh | HTTPS FTP |
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-Related structure data
Related structure data | |
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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, 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.) Mus musculus (house mouse) / Gene: Xxylt1 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) 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.) Homo sapiens (human) / Gene: F9 / Production host: Escherichia coli (E. coli) / References: UniProt: P00740, coagulation factor IXa |
#3: Polysaccharide | alpha-D-xylopyranose-(1-3)-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 3 types, 90 molecules
#4: Chemical | ChemComp-MN / |
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#5: Chemical | ChemComp-UDX / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.13 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2 M Li2SO4, 0.1 M Bis-Tris, pH 6.5, and 21% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 15, 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: 1.95→50 Å / Num. obs: 28026 / % possible obs: 100 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 19.5 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.651 / Mean I/σ(I) obs: 2.3 / % possible all: 100 |
-Processing
Software | Name: REFMAC / Version: 5.8.0049 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→50 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.107 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.165 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 33.55 Å2
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Refinement step | Cycle: 1 / Resolution: 1.95→50 Å
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