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Yorodumi- PDB-4ee3: Crystal structure of human M340H-beta-1,4-galactosyltransferase-1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ee3 | |||||||||
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Title | Crystal structure of human M340H-beta-1,4-galactosyltransferase-1 (M340H-B4GAL-T1) in complex with pentasaccharide | |||||||||
Components | Beta-1,4-galactosyltransferase 1 | |||||||||
Keywords | TRANSFERASE / Protein-carbohydrate complex / GT-A fold / glycosyltransferase | |||||||||
Function / homology | Function and homology information Defective B4GALT1 causes CDG-2d / galactosyltransferase activity / Interaction With Cumulus Cells And The Zona Pellucida / Defective B4GALT1 causes B4GALT1-CDG (CDG-2d) / penetration of zona pellucida / Lactose synthesis / regulation of acrosome reaction / Keratan sulfate biosynthesis / lactose synthase / neolactotriaosylceramide beta-1,4-galactosyltransferase ...Defective B4GALT1 causes CDG-2d / galactosyltransferase activity / Interaction With Cumulus Cells And The Zona Pellucida / Defective B4GALT1 causes B4GALT1-CDG (CDG-2d) / penetration of zona pellucida / Lactose synthesis / regulation of acrosome reaction / Keratan sulfate biosynthesis / lactose synthase / neolactotriaosylceramide beta-1,4-galactosyltransferase / beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase / N-acetyllactosamine synthase / N-acetyllactosamine synthase activity / positive regulation of circulating fibrinogen levels / beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity / N-Glycan antennae elongation / UDP-galactosyltransferase activity / Golgi trans cisterna / macrophage migration / lactose synthase activity / development of secondary sexual characteristics / lactose biosynthetic process / oligosaccharide biosynthetic process / desmosome / acute inflammatory response / galactose metabolic process / positive regulation of epithelial cell proliferation involved in wound healing / Pre-NOTCH Processing in Golgi / binding of sperm to zona pellucida / angiogenesis involved in wound healing / protein N-linked glycosylation / Transferases; Glycosyltransferases; Hexosyltransferases / azurophil granule membrane / Golgi cisterna membrane / epithelial cell development / beta-tubulin binding / alpha-tubulin binding / epithelial cell proliferation / cytoskeletal protein binding / extracellular matrix organization / secretory granule membrane / filopodium / lipid metabolic process / brush border membrane / negative regulation of epithelial cell proliferation / manganese ion binding / basolateral plasma membrane / cell adhesion / positive regulation of apoptotic process / Golgi membrane / external side of plasma membrane / Neutrophil degranulation / Golgi apparatus / protein-containing complex / extracellular space / extracellular exosome / identical protein binding / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / Molecular placement / Resolution: 2.3 Å | |||||||||
Authors | Ramakrishnan, B. / Qasba, P.K. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Binding of N-acetylglucosamine (GlcNAc) beta 1-6-branched oligosaccharide acceptors to beta 4-galactosyltransferase I reveals a new ligand binding mode. Authors: Ramakrishnan, B. / Boeggeman, E. / Qasba, P.K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ee3.cif.gz | 201.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ee3.ent.gz | 160.1 KB | Display | PDB format |
PDBx/mmJSON format | 4ee3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ee3_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 4ee3_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 4ee3_validation.xml.gz | 40.2 KB | Display | |
Data in CIF | 4ee3_validation.cif.gz | 56.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ee/4ee3 ftp://data.pdbj.org/pub/pdb/validation_reports/ee/4ee3 | HTTPS FTP |
-Related structure data
Related structure data | 4ee4C 4ee5C 4eeaC 4eegC 4eemC 4eeoC 2aecS 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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Unit cell |
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-Components
-Protein / Sugars , 2 types, 6 molecules ABC
#1: Protein | Mass: 32773.230 Da / Num. of mol.: 3 / Fragment: Catalytic domain / Mutation: R337T, C338T, M340H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: B4GALT1, beta4Gal-T1, GGTB2 / Plasmid: pET23a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 References: UniProt: P15291, Transferases; Glycosyltransferases; Hexosyltransferases, lactose synthase, N-acetyllactosamine synthase, beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase #2: Polysaccharide | Source method: isolated from a genetically manipulated source |
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-Non-polymers , 5 types, 554 molecules
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-SO4 / #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | IN THE ELECTRON DENSITY MAPS OF ALL THREE MOLECULES THE ELECTRON DENSITY FOR THE GLYCOSIDIC BOND ...IN THE ELECTRON DENSITY MAPS OF ALL THREE MOLECULES THE ELECTRON DENSITY FOR THE GLYCOSIDIC |
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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: 3.84 Å3/Da / Density % sol: 67.94 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 100 mM Mes buffer, 1.6 M ammonium sulfate, 2% Dioxane, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 9, 2005 / Details: mirrors |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 57756 / % possible obs: 91 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.4 % / Rsym value: 0.092 / Net I/σ(I): 17.9 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 3.3 / Num. unique all: 4424 / Rsym value: 0.366 / % possible all: 66.7 |
-Processing
Software |
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Refinement | Method to determine structure: Molecular placement Starting model: PDB entry 2AEC Resolution: 2.3→36.31 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.919 / SU B: 5.449 / SU ML: 0.132 / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R: 0.237 / ESU R Free: 0.21 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.054 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→36.31 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.364 Å / Total num. of bins used: 20
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