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Yorodumi- PDB-3zgg: Crystal structure of the Fucosylgalactoside alpha N- acetylgalact... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zgg | ||||||
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Title | Crystal structure of the Fucosylgalactoside alpha N- acetylgalactosaminyltransferase (GTA, cisAB mutant L266G, G268A) in complex with NPE caged UDP-Gal (C222(1) space group) | ||||||
Components | HISTO-BLOOD GROUP ABO SYSTEM TRANSFERASE | ||||||
Keywords | TRANSFERASE / GLYCOSYLTRANSFERASES / CATALYTIC DOMAIN | ||||||
Function / homology | Function and homology information fucosylgalactoside 3-alpha-galactosyltransferase / glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase / glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase activity / fucosylgalactoside 3-alpha-galactosyltransferase activity / ABO blood group biosynthesis / lipid glycosylation / Golgi cisterna membrane / protein glycosylation / antigen binding / manganese ion binding ...fucosylgalactoside 3-alpha-galactosyltransferase / glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase / glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase activity / fucosylgalactoside 3-alpha-galactosyltransferase activity / ABO blood group biosynthesis / lipid glycosylation / Golgi cisterna membrane / protein glycosylation / antigen binding / manganese ion binding / vesicle / carbohydrate metabolic process / Golgi membrane / nucleotide binding / Golgi apparatus / extracellular region Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Jorgensen, R. / Batot, G.O. / Hindsgaul, O. / Tanaka, H. / Perez, S. / Imberty, A. / Breton, C. / Royant, A. / Palcic, M.M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2014 Title: Structures of a Human Blood Group Glycosyltransferase in Complex with a Photo-Activatable Udp-Gal Derivative Reveal Two Different Binding Conformations Authors: Jorgensen, R. / Batot, G. / Mannerstedt, K. / Imberty, A. / Breton, C. / Hindsgaul, O. / Royant, A. / Palcic, M.M. #1: Journal: Carbohydr.Res. / Year: 2008 Title: Synthesis and Photolytic Activation of 6''-O-2-Nitrobenzyl Uridine-5'-Diphosphogalactose: A 'Caged' Udp-Gal Derivative. Authors: Mannerstedt, K. / Hindsgaul, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zgg.cif.gz | 77.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zgg.ent.gz | 54.8 KB | Display | PDB format |
PDBx/mmJSON format | 3zgg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zg/3zgg ftp://data.pdbj.org/pub/pdb/validation_reports/zg/3zgg | HTTPS FTP |
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-Related structure data
Related structure data | 3zgfC 3iohS C: citing same article (ref.) S: Starting model for refinement |
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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
#1: Protein | Mass: 34654.008 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR CATALYTIC DOMAIN, RESIDUES 64-354 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): GOLD References: UniProt: P16442, fucosylgalactoside 3-alpha-galactosyltransferase, glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase |
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#2: Chemical | ChemComp-IUG / |
#3: Chemical | ChemComp-GOL / |
#4: Chemical | ChemComp-MN / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46 % / Description: NONE |
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Crystal grow | pH: 7 Details: 7-12% POLYETHYLENE GLYCOL 3350, 0.1 - 0.3 M AMMONIUM SULPHATE, 0.05 M MNCL2, 0.05 M MOPS PH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9763 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 26, 2011 / Details: TOROIDAL MIROR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→49.74 Å / Num. obs: 24091 / % possible obs: 95.5 % / Observed criterion σ(I): 3 / Redundancy: 4 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 3 / % possible all: 80.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3IOH Resolution: 1.9→42.18 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.929 / SU B: 3.061 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES REFINED INDIVIDUALLY. ONLY ONE OF THE TWO POSSIBLE CONFORMATIONS OF THE CAGE HAS BEEN MODELED.
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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: 26.317 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→42.18 Å
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Refine LS restraints |
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