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- PDB-2vxl: Screening a Limited Structure-based Library Identifies UDP-GalNAc... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2vxl | ||||||
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Title | Screening a Limited Structure-based Library Identifies UDP-GalNAc- Specific Mutants of alpha-1,3 Galactosyltransferase | ||||||
![]() | N-ACETYLLACTOSAMINIDE ALPHA-1,3-GALACTOSYLTRANSFERASE | ||||||
![]() | TRANSFERASE / GLYCOSYLTRANSFERASE / GALACTOSYLTRANSFERASE / TRANSMEMBRANE / GOLGI APPARATUS / ENZYME MECHANISM / GLYCOPROTEIN / METAL-BINDING / SIGNAL-ANCHOR / ALPHA-1 / MEMBRANE / MANGANESE / TRANSFERASE 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 | ![]() ![]() ![]() | ||||||
![]() | Tumbale, P. / Jamaluddin, H. / Thiyagarajan, N. / Acharya, K.R. / Brew, K. | ||||||
![]() | ![]() Title: Screening a Limited Structure-Based Library Identifies Udp-Galnac-Specific Mutants of {Alpha}-1,3-Galactosyltransferase. Authors: Tumbale, P. / Jamaluddin, H. / Thiyagarajan, N. / 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 | ![]() | 73 KB | Display | ![]() |
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PDB format | ![]() | 53.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 722.6 KB | Display | ![]() |
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Full document | ![]() | 723.3 KB | Display | |
Data in XML | ![]() | 12.2 KB | Display | |
Data in CIF | ![]() | 16 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2vxmC ![]() 2jcjS 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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Unit cell |
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Components
#1: Protein | Mass: 32560.500 Da / Num. of mol.: 1 / Fragment: RESIDUES 82-358 / Mutation: YES Source method: isolated from a genetically manipulated source Details: UDP-GALACTOSE / Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P14769, N-acetyllactosaminide 3-alpha-galactosyltransferase |
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#2: Chemical | ChemComp-MN / |
#3: Chemical | ChemComp-UDP / |
#4: Water | ChemComp-HOH / |
Compound details | ENGINEERED RESIDUE IN CHAIN A, HIS 280 TO ALA ENGINEERED RESIDUE IN CHAIN A, ALA 281 TO GLY ...ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.4 % / Description: NONE |
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Crystal grow | pH: 8 Details: PROTEIN: 5 MG/ML IN 20 MM MES-NAOH BUFFER, PH 6.0, 10% GLYCEROL, CONTAINING 10 MM MNCL2 AND 10 MM UDP-GALNAC MOTHER LIQUOR: 10-15% PEG 6000, 0.1 M TRIS-HCL, PH 8.0 AND 15-25% MPD |
-Data collection
Diffraction | Mean temperature: 300 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 6, 2006 / Details: MIRROR |
Radiation | Monochromator: SI(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. obs: 11624 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 46.6 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 2.7→2.85 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2.04 / % possible all: 98.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2JCJ Resolution: 2.7→43.91 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL | ||||||||||||||||||||
Displacement parameters | Biso mean: 26.9 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→43.91 Å
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LS refinement shell | Resolution: 2.7→2.77 Å / Total num. of bins used: 20 /
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