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Yorodumi- PDB-6yjs: Crystal structure of MGAT5 (alpha-1,6-mannosylglycoprotein 6-beta... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6yjs | ||||||
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Title | Crystal structure of MGAT5 (alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase V) luminal domain with a Lys329-Ile345 loop truncation, in complex with biantennary pentasaccharide M592 | ||||||
Components | Alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A | ||||||
Keywords | TRANSFERASE / Carbohydrate / Enzyme / N-glycosylation / GlcNAc | ||||||
Function / homology | Function and homology information alpha-1,6-mannosyl-glycoprotein 6-beta-N-acetylglucosaminyltransferase / alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase activity / N-Glycan antennae elongation / positive regulation of receptor signaling pathway via STAT / negative regulation of protein tyrosine phosphatase activity / protein N-linked glycosylation via asparagine / protein N-linked glycosylation / protein phosphatase inhibitor activity / manganese ion binding / Maturation of spike protein ...alpha-1,6-mannosyl-glycoprotein 6-beta-N-acetylglucosaminyltransferase / alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase activity / N-Glycan antennae elongation / positive regulation of receptor signaling pathway via STAT / negative regulation of protein tyrosine phosphatase activity / protein N-linked glycosylation via asparagine / protein N-linked glycosylation / protein phosphatase inhibitor activity / manganese ion binding / Maturation of spike protein / viral protein processing / positive regulation of cell migration / Golgi membrane / Golgi apparatus / extracellular exosome / membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Wu, L. / Darby, J.F. / Gilio, A.K. / Davies, G.J. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Acs Catalysis / Year: 2020 Title: Substrate Engagement and Catalytic Mechanisms of N-Acetylglucosaminyltransferase V Authors: Darby, J.F. / Gilio, A.K. / Piniello, B. / Roth, C. / Blagova, E. / Rovira, C. / Hubbard, R.E. / Davies, G.J. / Wu, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6yjs.cif.gz | 409.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6yjs.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6yjs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6yjs_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 6yjs_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 6yjs_validation.xml.gz | 41.4 KB | Display | |
Data in CIF | 6yjs_validation.cif.gz | 59.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yj/6yjs ftp://data.pdbj.org/pub/pdb/validation_reports/yj/6yjs | HTTPS FTP |
-Related structure data
Related structure data | 6yjqC 6yjrC 6yjtC 6yjuC 6yjvC 5zicS S: Starting model for refinement 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain: (Details: Chains AAA BBB) |
-Components
-Protein , 1 types, 2 molecules AAABBB
#1: Protein | Mass: 58996.906 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MGAT5, GGNT5 / Production host: Trichoplusia ni (cabbage looper) References: UniProt: Q09328, alpha-1,6-mannosyl-glycoprotein 6-beta-N-acetylglucosaminyltransferase |
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-Sugars , 2 types, 4 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Sugar | |
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-Non-polymers , 3 types, 487 molecules
#3: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-SO4 / #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.16 Å3/Da / Density % sol: 43.01 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M HEPES pH 8.0, 0.3 M Li2SO4, 30 % (w/v) PEG 3350, 10 % (v/v) ethylene glycol wXHPcQHrME |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 15, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→42.52 Å / Num. obs: 125194 / % possible obs: 96.2 % / Redundancy: 3.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.034 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 1.6→1.64 Å / Rmerge(I) obs: 1.162 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 9094 / CC1/2: 0.524 / Rpim(I) all: 0.722 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5zic Resolution: 1.6→42.52 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.494 / SU ML: 0.104 / Cross valid method: FREE R-VALUE / ESU R: 0.094 / ESU R Free: 0.093 Details: Hydrogens have been added in their 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.716 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→42.52 Å
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Refine LS restraints |
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LS refinement shell |
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