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- PDB-4ee4: Crystal structure of human M340H-beta-1,4-galactosyltransferase-1... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ee4 | |||||||||
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Title | Crystal structure of human M340H-beta-1,4-galactosyltransferase-1 (M340H-B4GAL-T1) in complex with tetrasaccharide from Lacto-N-neohexose | |||||||||
![]() | Beta-1,4-galactosyltransferase 1 | |||||||||
![]() | TRANSFERASE / protein-carbohydrate complex / GT-A fold / glycosyltransferase | |||||||||
Function / homology | ![]() 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 / galactose metabolic process / acute inflammatory response / 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 / azurophil granule membrane / Transferases; Glycosyltransferases; Hexosyltransferases / Golgi cisterna membrane / beta-tubulin binding / epithelial cell development / alpha-tubulin binding / cytoskeletal protein binding / extracellular matrix organization / secretory granule membrane / epithelial cell proliferation / filopodium / brush border membrane / lipid metabolic process / negative regulation of epithelial cell proliferation / manganese ion binding / basolateral plasma membrane / cell adhesion / positive regulation of apoptotic process / external side of plasma membrane / Golgi membrane / Neutrophil degranulation / Golgi apparatus / protein-containing complex / extracellular space / extracellular exosome / identical protein binding / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() | |||||||||
![]() | Ramakrishnan, B. / Qasba, P.K. | |||||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 205 KB | Display | ![]() |
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PDB format | ![]() | 162.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.6 MB | Display | ![]() |
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Full document | ![]() | 2.6 MB | Display | |
Data in XML | ![]() | 42.8 KB | Display | |
Data in CIF | ![]() | 61.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4ee3C ![]() 4ee5C ![]() 4eeaC ![]() 4eegC ![]() 4eemC ![]() 4eeoC ![]() 2aecS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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5 |
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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.) ![]() ![]() ![]() 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, 727 molecules ![](data/chem/img/UDP.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-SO4 / #6: Chemical | ChemComp-GOL / #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.85 Å3/Da / Density % sol: 68.02 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 100 mM mes buffer, 1.6 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: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 26, 2011 / 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: 1.95→50 Å / Num. obs: 97326 / % possible obs: 93.5 % / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Rsym value: 0.04 / Net I/σ(I): 24.6 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 3.8 / Num. unique all: 6991 / Rsym value: 0.267 / % possible all: 64.2 |
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Processing
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Refinement | Method to determine structure: Molecular placement Starting model: PDB entry 2AEC Resolution: 1.95→36.82 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.9 / SU ML: 0.084 / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R: 0.135 / ESU R Free: 0.133 / 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: 36.777 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→36.82 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.001 Å / Total num. of bins used: 20
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