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Yorodumi- PDB-2agd: Crystal Structure of Human M340H-Beta-1,4-Galactosyltransferase-I... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2agd | |||||||||
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Title | Crystal Structure of Human M340H-Beta-1,4-Galactosyltransferase-I(M340H-B4Gal-T1) in Complex with GlcNAc-beta1,4-Man-alpha1,3-Man-beta-OR | |||||||||
Components | Beta-1,4-galactosyltransferase 1 | |||||||||
Keywords | TRANSFERASE / beta1 / 4-Galactosyltransferase-I / Trisaccharide / closed conformation / Mutant | |||||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | |||||||||
Authors | Ramasamy, V. / Ramakrishnan, B. / Boeggeman, E. / Ratner, D.M. / Seeberger, P.H. / Qasba, P.K. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2005 Title: Oligosaccharide Preferences of beta1,4-Galactosyltransferase-I: Crystal Structures of Met340His Mutant of Human beta1,4-Galactosyltransferase-I with a Pentasaccharide and Trisaccharides of the N-Glycan Moiety Authors: Ramasamy, V. / Ramakrishnan, B. / Boeggeman, E. / Ratner, D.M. / Seeberger, P.H. / 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 | 2agd.cif.gz | 200 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2agd.ent.gz | 157.2 KB | Display | PDB format |
PDBx/mmJSON format | 2agd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2agd_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 2agd_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 2agd_validation.xml.gz | 40.1 KB | Display | |
Data in CIF | 2agd_validation.cif.gz | 56.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ag/2agd ftp://data.pdbj.org/pub/pdb/validation_reports/ag/2agd | HTTPS FTP |
-Related structure data
Related structure data | 2ae7C 2aecC 2aesC 2ah9C 1o0rS 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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3 |
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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, Residues 126-398 / Mutation: M340H, C338T, R337T Source method: isolated from a genetically manipulated source Details: N-acetyllactosamine synthase part / Source: (gene. exp.) Homo sapiens (human) Description: N-terminal carries t7 tag of 11 amino acids followed by GLY, SER & ALA Gene: B4GALT1, GGTB2 / Plasmid: PET23A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P15291, N-acetyllactosamine synthase #2: Polysaccharide | Source method: isolated from a genetically manipulated source |
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-Non-polymers , 7 types, 564 molecules
#3: Chemical | #4: Chemical | ChemComp-SO4 / #5: Chemical | #6: Chemical | ChemComp-GOL / #7: Chemical | ChemComp-DIO / | #8: Chemical | ChemComp-MES / | #9: Water | ChemComp-HOH / | |
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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: 3.8 Å3/Da / Density % sol: 67.3 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: mes, ammonium sulfate, dioxane, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.97946 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 23, 2004 / Details: Mirrors |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→40 Å / Num. obs: 118434 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 6.1 % / Biso Wilson estimate: 17 Å2 / Rsym value: 0.063 / Net I/σ(I): 28.4 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 3.4 / Num. unique all: 11733 / Rsym value: 0.468 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1O0R Resolution: 1.9→40 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 3307113.13 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 45.3818 Å2 / ksol: 0.39085 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.006 / Total num. of bins used: 6
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Xplor file |
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