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- PDB-1yro: Crystal structure of beta14,-galactosyltransferase mutant ARG228L... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1yro | ||||||
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Title | Crystal structure of beta14,-galactosyltransferase mutant ARG228Lys in complex with alpha-lactalbumin in the presence of UDP-galactose and Mn | ||||||
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![]() | TRANSFERASE ACTIVATOR/TRANSFERASE / ARG228LYS mutation / UDP-gal complex / TRANSFERASE ACTIVATOR-TRANSFERASE COMPLEX | ||||||
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 / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / 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. / Boeggeman, E. / Qasba, P.K. | ||||||
![]() | ![]() Title: Mutation of Arginine 228 to Lysine Enhances the Glucosyltransferase Activity of Bovine beta-1,4-Galactosyltransferase I 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 | ![]() | 198.4 KB | Display | ![]() |
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PDB format | ![]() | 153.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 43.4 KB | Display | |
Data in CIF | ![]() | 62.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1nkhS 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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Unit cell |
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Details | The molecules A & B and C & D form a 1:1 protein complexes |
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Components
-Protein , 2 types, 4 molecules ACBD
#1: Protein | Mass: 14015.835 Da / Num. of mol.: 2 / Fragment: REGULATORY SUBUNIT OF LACTOSE SYNTHASE Source method: isolated from a genetically manipulated source Details: CHAINS A AND B FORM FIRST, C AND D SECOND LACTOSE SYNTHASE COMPLEX Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 32821.566 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 130-402 / Mutation: D129, R228K, C342T Source method: isolated from a genetically manipulated source Details: CHAINS A AND B FORM FIRST, C AND D SECOND LACTOSE SYNTHASE COMPLEX Source: (gene. exp.) ![]() ![]() Description: N-terminal carries a tag containing 13 amino acids Gene: beta1,4-galactosyltransferase / Plasmid: pET23c / Species (production host): Escherichia coli / Production host: ![]() ![]() References: UniProt: P08037, lactose synthase, N-acetyllactosamine synthase, beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase |
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-Non-polymers , 7 types, 841 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/GDU.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/UDP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/GDU.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/UDP.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-MES / | #5: Chemical | #6: Chemical | #7: Chemical | #8: Chemical | #9: Water | ChemComp-HOH / | |
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-Details
Sequence details | SEQUENCE THE N-TERMINAL OF CHAINS B AND D CARRIES A FUSION TAG CONTAINING |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.3 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 6 Details: PEG 4000, Mes-NaOH, sodium chloride, pH 6.0, VAPOR DIFFUSION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 14, 2003 / Details: mirrors |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.88→40 Å / Num. all: 85018 / Num. obs: 82383 / Observed criterion σ(I): 1 / Redundancy: 3.1 % / Biso Wilson estimate: 20.8 Å2 / Rsym value: 0.053 / Net I/σ(I): 18 |
Reflection shell | Resolution: 1.88→1.95 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2 / Num. unique all: 8460 / Rsym value: 0.47 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1NKH.pdb Resolution: 1.9→32.55 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1582053.99 / 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: 55.1063 Å2 / ksol: 0.347116 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→32.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
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Xplor file |
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