[English] 日本語
Yorodumi- PDB-2vxl: Screening a Limited Structure-based Library Identifies UDP-GalNAc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vxl | ||||||
---|---|---|---|---|---|---|---|
Title | Screening a Limited Structure-based Library Identifies UDP-GalNAc- Specific Mutants of alpha-1,3 Galactosyltransferase | ||||||
Components | N-ACETYLLACTOSAMINIDE ALPHA-1,3-GALACTOSYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / GLYCOSYLTRANSFERASE / GALACTOSYLTRANSFERASE / TRANSMEMBRANE / GOLGI APPARATUS / ENZYME MECHANISM / GLYCOPROTEIN / METAL-BINDING / SIGNAL-ANCHOR / ALPHA-1 / MEMBRANE / MANGANESE / TRANSFERASE SUBSTRATE SPECIFICITY | ||||||
Function / homology | Function and homology information 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 | BOS TAURUS (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Tumbale, P. / Jamaluddin, H. / Thiyagarajan, N. / Acharya, K.R. / Brew, K. | ||||||
Citation | Journal: Glycobiology / Year: 2008 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2vxl.cif.gz | 73 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2vxl.ent.gz | 53.1 KB | Display | PDB format |
PDBx/mmJSON format | 2vxl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vx/2vxl ftp://data.pdbj.org/pub/pdb/validation_reports/vx/2vxl | HTTPS FTP |
---|
-Related structure data
Related structure data | 2vxmC 2jcjS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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.) BOS TAURUS (cattle) / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P14769, N-acetyllactosaminide 3-alpha-galactosyltransferase |
---|---|
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.4 % / Description: NONE |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 0.98 |
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 |
-Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| ||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL | ||||||||||||||||||||
Displacement parameters | Biso mean: 26.9 Å2
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→43.91 Å
| ||||||||||||||||||||
LS refinement shell | Resolution: 2.7→2.77 Å / Total num. of bins used: 20 /
|