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- PDB-2fy7: Crystal structure of the catalytic domain of the human beta1,4-ga... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2fy7 | ||||||
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Title | Crystal structure of the catalytic domain of the human beta1,4-galactosyltransferase mutant M339H in apo form | ||||||
![]() | Beta-1,4-galactosyltransferase 1 | ||||||
![]() | TRANSFERASE / M339H mutant / apo enzyme | ||||||
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. / Ramasamy, V. / Qasba, P.K. | ||||||
![]() | ![]() Title: Structural Snapshots of beta-1,4-Galactosyltransferase-I Along the Kinetic Pathway. Authors: Ramakrishnan, B. / Ramasamy, V. / 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 | ![]() | 75.3 KB | Display | ![]() |
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PDB format | ![]() | 55.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 445.6 KB | Display | ![]() |
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Full document | ![]() | 449.1 KB | Display | |
Data in XML | ![]() | 15.6 KB | Display | |
Data in CIF | ![]() | 23.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2fyaC ![]() 2fybC ![]() 2fycC ![]() 2fydC ![]() 1oorS 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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Unit cell |
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Components
#1: Protein | Mass: 32773.230 Da / Num. of mol.: 1 / Fragment: catalytic domain, residues 125-397 / Mutation: R337T, C338T, M340H Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.72 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 5.6 Details: 50 mM sodium citrate buffer, 6% PEG 4000, pH 5.6, VAPOR DIFFUSION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 31, 2002 / 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: 1.6→20 Å / Num. obs: 38674 / % possible obs: 90.3 % / Observed criterion σ(I): 1 / Redundancy: 3.3 % / Biso Wilson estimate: 21.9 Å2 / Rsym value: 0.049 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 1.6→1.66 Å / Mean I/σ(I) obs: 1.3 / Num. unique all: 2527 / Rsym value: 0.407 / % possible all: 60 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1OOR Resolution: 1.7→19.75 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1637527.64 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: Residues 343 to 351 could not be traced due to low electron density
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 43.5119 Å2 / ksol: 0.347019 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→19.75 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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