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- PDB-2jcl: Crystal structure of alpha-1,3 Galactosyltransferase (R365K) in t... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2jcl | ||||||
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Title | Crystal structure of alpha-1,3 Galactosyltransferase (R365K) in the absence of ligands | ||||||
![]() | N-ACETYLLACTOSAMINIDE ALPHA-1,3-GALACTOSYLTRANSFERASE | ||||||
![]() | TRANSFERASE / TRANSMEMBRANE / GOLGI APPARATUS / ENZYME MECHANISM / GLYCOPROTEIN / METAL-BINDING / SIGNAL-ANCHOR / ALPHA-1 / MEMBRANE / MANGANESE / GLYCOSYLTRANSFERASE / SUBSTRATE SPECIFICITY | ||||||
Function / homology | ![]() N-acetyllactosaminide 3-alpha-galactosyltransferase / N-acetyllactosaminide 3-alpha-galactosyltransferase activity / Golgi cisterna / lipid glycosylation / Golgi cisterna membrane / glycosyltransferase activity / protein glycosylation / vesicle / carbohydrate metabolic process / Golgi apparatus / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jamaluddin, H. / Tumbale, P. / Withers, S.G. / Acharya, K.R. / Brew, K. | ||||||
![]() | ![]() Title: Conformational Changes Induced by Binding Udp-2F-Galactose to Alpha-1,3 Galactosyltransferase-Implications for Catalysis. Authors: Jamaluddin, H. / Tumbale, P. / Withers, S.G. / Acharya, K.R. / Brew, 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 | ![]() | 128.9 KB | Display | ![]() |
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PDB format | ![]() | 99.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 456.4 KB | Display | ![]() |
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Full document | ![]() | 300.7 KB | Display | |
Data in XML | ![]() | 24.5 KB | Display | |
Data in CIF | ![]() | 33.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2jcjC ![]() 2jckC ![]() 2jcoC ![]() 2vfzC ![]() 1k4vS S: Starting model for refinement C: citing same article ( |
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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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.9666, 0.00308, 0.25627), Vector: |
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Components
#1: Protein | Mass: 34062.148 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 80-368 / Mutation: YES Source method: isolated from a genetically manipulated source Details: SULPHATE ION / Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P14769, EC: 2.4.1.151, N-acetyllactosaminide 3-alpha-galactosyltransferase #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | Compound details | ENGINEERED | Sequence details | THE RESIDUE RANGE FOR THIS PROTEIN CONSTRUCT IS FROM 80 TO 368. THE RESIDUE RANGE MODELLED IN THE ...THE RESIDUE RANGE FOR THIS PROTEIN CONSTRUCT IS FROM 80 TO 368. THE RESIDUE RANGE MODELLED IN THE STRUCTURE IS 82-358 FOR MOL A AND MOL B. MUTATION IS R365K. | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.42 Å3/Da / Density % sol: 72 % |
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Crystal grow | pH: 8 Details: 0.3M SODIUM CACODYLATE BUFFER, PH 6.5, 1.4M SODIUM ACETATE, 2% DIOXANE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jun 9, 2005 / Details: MIRRORS |
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→50 Å / Num. obs: 18881 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 11.7 % / Rmerge(I) obs: 0.2 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 3.3→3.42 Å / Redundancy: 96 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.45 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1K4V Resolution: 3.29→25.81 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.835 / SU B: 20.29 / SU ML: 0.342 / Cross valid method: THROUGHOUT / ESU R Free: 0.487 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE ELECTRON DENSITY FOR REGION BETWEEN RESIDUES A1191 TO A 1199 IS DISORDERED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.12 Å2
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Refinement step | Cycle: LAST / Resolution: 3.29→25.81 Å
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Refine LS restraints |
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