[English] 日本語
![](img/lk-miru.gif)
- PDB-2ae7: Crystal Structure of Human M340H-Beta1,4-Galactosyltransferase-I ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2ae7 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal Structure of Human M340H-Beta1,4-Galactosyltransferase-I (M340H-B4GAL-T1) in Complex with Pentasaccharide | |||||||||
![]() | Beta-1,4-galactosyltransferase 1 | |||||||||
![]() | TRANSFERASE / beta1 / 4-Galactosyltransferase-I / Pentasaccharide / Closed conformation / Mutant | |||||||||
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 | ![]() ![]() ![]() | |||||||||
![]() | Ramasamy, V. / Ramakrishnan, B. / Boeggeman, E. / Ratner, D.M. / Seeberger, P.H. / Qasba, P.K. | |||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 196.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 154.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.2 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 2.3 MB | Display | |
Data in XML | ![]() | 39.9 KB | Display | |
Data in CIF | ![]() | 55.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2aecC ![]() 2aesC ![]() 2agdC ![]() 2ah9C ![]() 1o0rS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||
2 | ![]()
| ||||||||||
3 | ![]()
| ||||||||||
4 | ![]()
| ||||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 3 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.) ![]() Description: N-terminal carries t7 tag of 11 amino acids followed by GLY, SER & ALA Gene: B4GALT1, GGTB2 / Plasmid: PET23A / Production host: ![]() ![]() |
---|
-Sugars , 2 types, 3 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose | Source method: isolated from a genetically manipulated source |
---|
-Non-polymers , 6 types, 499 molecules ![](data/chem/img/MN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/UDH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/DIO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/UDH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/DIO.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | ChemComp-SO4 / #6: Chemical | #7: Chemical | ChemComp-GOL / #8: Chemical | ChemComp-DIO / | #9: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.8 Å3/Da / Density % sol: 67.3 % |
---|---|
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 |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 2, 2003 / 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: 1.98→50 Å / Num. obs: 101444 / % possible obs: 96.5 % / Observed criterion σ(I): 1 / Redundancy: 4.9 % / Biso Wilson estimate: 17.2 Å2 / Rsym value: 0.094 / Net I/σ(I): 15 |
Reflection shell | Resolution: 1.98→2.05 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 9651 / Rsym value: 0.59 / % possible all: 93.1 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB CODE: 1O0R Resolution: 2→40 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 3336750.69 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 50.3949 Å2 / ksol: 0.385291 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.2 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→40 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|