+Open data
-Basic information
Entry | Database: PDB / ID: 1gx0 | ||||||
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Title | ALPHA-,1,3 GALACTOSYLTRANSFERASE - BETA-D-GALACTOSE COMPLEX | ||||||
Components | N-ACETYLLACTOSAMINIDE ALPHA-1,3-GALACTOSYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / GALACTOSYLTRANSFERASE / BLOOD GROUP SUGARS / LACTOSE / N-ACETYL LACTOSAMINE / GLYCOSYLTRANSFERASE | ||||||
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: 1.8 Å | ||||||
Authors | Boix, E. / Zhang, Y. / Swaminathan, G.J. / Brew, K. / Acharya, K.R. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: Structural Basis of Ordered Binding of Donor and Acceptor Substrates to the Retaining Glycosyltransferase, Alpha -1,3 Galactosyltransferase Authors: Boix, E. / Zhang, Y. / Swaminathan, G.J. / Brew, K. / Acharya, K.R. #1: Journal: J.Biol.Chem. / Year: 2001 Title: Structure of Udp Complex of Udp-Galactose:Beta-Galactoside-Alpha -1,3-Galactosyltransferase at 1.53-A Resolution Reveals a Conformational Change in the Catalytically Important C Terminus Authors: Boix, E. / Swaminathan, G.J. / Zhang, Y. / Natesh, R. / Brew, K. / Acharya, K.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gx0.cif.gz | 145.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gx0.ent.gz | 112 KB | Display | PDB format |
PDBx/mmJSON format | 1gx0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1gx0_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 1gx0_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1gx0_validation.xml.gz | 29.5 KB | Display | |
Data in CIF | 1gx0_validation.cif.gz | 42.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gx/1gx0 ftp://data.pdbj.org/pub/pdb/validation_reports/gx/1gx0 | HTTPS FTP |
-Related structure data
Related structure data | 1gwvC 1gwwC 1gx4C 1k4vS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein / Sugars , 2 types, 3 molecules AB
#1: Protein | Mass: 34090.164 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 80-368 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BOS TAURUS (cattle) / Plasmid: PSV-SPORT / Production host: ESCHERICHIA COLI (E. coli) / Variant (production host): DH5[ALPHA] / References: UniProt: P14769, EC: 2.4.1.151 #5: Sugar | ChemComp-GAL / | |
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-Non-polymers , 4 types, 503 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Compound details | CATALYSES THE TRANSFER OF GALACTOSE FROM UDP-GALACTOSE TO AN ACCEPTOR MOLECULE. UDP-GALACTOSE + ...CATALYSES THE TRANSFER OF GALACTOSE FROM UDP-GALACTOSE TO AN ACCEPTOR MOLECULE. UDP-GALACTOSE + BETA-D-GALACTOSYL |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 57.63 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.5 / Details: PEG6000, TRIS/HCL, pH 8.50 | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 16 ℃ / pH: 6 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Apr 15, 2001 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→40 Å / Num. obs: 69116 / % possible obs: 95.9 % / Redundancy: 9 % / Biso Wilson estimate: 20.2 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 12 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.388 / Mean I/σ(I) obs: 2.3 / % possible all: 88.8 |
Reflection | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 24 Å / Num. obs: 72098 / Num. measured all: 280613 |
Reflection shell | *PLUS Highest resolution: 1.8 Å / % possible obs: 88.8 % / Mean I/σ(I) obs: 2.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1K4V Resolution: 1.8→24.19 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1170138.46 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 50.847 Å2 / ksol: 0.373419 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→24.19 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 24 Å / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Lowest resolution: 1.86 Å |