[English] 日本語
![](img/lk-miru.gif)
- PDB-2fyc: Crystal structure of the catalytic domain of bovine beta1,4-galac... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2fyc | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the catalytic domain of bovine beta1,4-galactosyltransferase-I in complex with alpha-lactalbumin, Ca and UDP-galactose | ||||||
![]() |
| ||||||
![]() | TRANSFERASE / lactose synthase / M344H mutation / Ca binding | ||||||
Function / homology | ![]() Lactose synthesis / protein galactosylation / Keratan sulfate biosynthesis / Interaction With Cumulus Cells And The Zona Pellucida / Lactose synthesis / N-Glycan antennae elongation / lactose synthase / neolactotriaosylceramide beta-1,4-galactosyltransferase / beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase / N-acetyllactosamine synthase ...Lactose synthesis / protein galactosylation / Keratan sulfate biosynthesis / Interaction With Cumulus Cells And The Zona Pellucida / Lactose synthesis / N-Glycan antennae elongation / 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 / UDP-galactosyltransferase activity / Golgi trans cisterna / lactose synthase activity / lactose biosynthetic process / oligosaccharide biosynthetic process / desmosome / protein N-linked glycosylation / Neutrophil degranulation / Transferases; Glycosyltransferases; Hexosyltransferases / Golgi cisterna membrane / beta-tubulin binding / alpha-tubulin binding / cytoskeletal protein binding / filopodium / brush border membrane / lipid metabolic process / lysozyme activity / manganese ion binding / basolateral plasma membrane / external side of plasma membrane / calcium ion binding / Golgi apparatus / protein-containing complex / extracellular space / extracellular region / identical protein binding 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 196 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 151.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 2fy7C ![]() 2fyaC ![]() 2fybC ![]() 2fydC ![]() 1oqmS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
| ||||||||
Details | 1:1 complex between the alpha-lactalbumin and the catalytic domain of beta 1, 4-galactosyltransferase |
-
Components
-Protein , 2 types, 4 molecules ACBD
#1: Protein | Mass: 14015.835 Da / Num. of mol.: 2 / Mutation: C342T, M344H Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 32856.531 Da / Num. of mol.: 2 / Fragment: residues 57-329 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P08037, Transferases; Glycosyltransferases; Hexosyltransferases |
---|
-Non-polymers , 5 types, 774 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/GDU.gif)
![](data/chem/img/UDP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/GDU.gif)
![](data/chem/img/UDP.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-MES / | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.41 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 6.5 Details: 500 Mes-NaOH, 6% PEG 4000%, pH 6.5, VAPOR DIFFUSION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 13, 2003 / Details: mirrors |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→32.56 Å / Num. obs: 69858 / % possible obs: 96 % / Observed criterion σ(I): 1 / Redundancy: 2.8 % / Biso Wilson estimate: 19.3 Å2 / Rsym value: 0.043 / Net I/σ(I): 17 |
Reflection shell | Resolution: 1.98→2.05 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 6450 / Rsym value: 0.465 / % possible all: 89 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1OQM Resolution: 2→32.56 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1664884.26 / 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: 61.4715 Å2 / ksol: 0.338919 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.9 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→32.56 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|