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Yorodumi- PDB-1g93: CRYSTAL STRUCTURE OF THE BOVINE CATALYTIC DOMAIN OF ALPHA-1,3-GAL... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1g93 | ||||||
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Title | CRYSTAL STRUCTURE OF THE BOVINE CATALYTIC DOMAIN OF ALPHA-1,3-GALACTOSYLTRANSFERASE IN THE PRESENCE OF UDP-GALACTOSE | ||||||
Components | N-ACETYLLACTOSAMINIDE ALPHA-1,3-GALACTOSYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / ALPHA-BETA-ALPHA / UDP binding protein / 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: 2.5 Å | ||||||
Authors | Gastinel, L.N. / Bignon, C. / Misra, A.K. / Hindsgaul, O. / Shaper, J.H. / Joziasse, D.H. | ||||||
Citation | Journal: EMBO J. / Year: 2001 Title: Bovine alpha1,3-galactosyltransferase catalytic domain structure and its relationship with ABO histo-blood group and glycosphingolipid glycosyltransferases. Authors: Gastinel, L.N. / Bignon, C. / Misra, A.K. / Hindsgaul, O. / Shaper, J.H. / Joziasse, D.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1g93.cif.gz | 76.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1g93.ent.gz | 55.4 KB | Display | PDB format |
PDBx/mmJSON format | 1g93.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1g93_validation.pdf.gz | 843.2 KB | Display | wwPDB validaton report |
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Full document | 1g93_full_validation.pdf.gz | 858.3 KB | Display | |
Data in XML | 1g93_validation.xml.gz | 15.8 KB | Display | |
Data in CIF | 1g93_validation.cif.gz | 21.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g9/1g93 ftp://data.pdbj.org/pub/pdb/validation_reports/g9/1g93 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 36392.727 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: GGTA1 / Plasmid: PET15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P14769, EC: 2.4.1.151 |
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#2: Sugar | ChemComp-GAL / |
-Non-polymers , 4 types, 100 molecules
#3: Chemical | ChemComp-MN / |
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#4: Chemical | ChemComp-HG / |
#5: Chemical | ChemComp-UPG / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.48 Å3/Da / Density % sol: 64.6 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.3 to 1.6 M Sodium Acetate, 10 mM MnCl2, 10 mM Hg-UDP-galactgose, 500 mM NaCl, 100 mM cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 8 | ||||||||||||||||||||||||||||||||||||||||||||||||
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: ESRF / Beamline: ID14-3 / Wavelength: 0.9324 Å |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Oct 10, 2000 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9324 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→15 Å / Num. all: 452447 / Num. obs: 18010 / % possible obs: 98.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.7 % / Biso Wilson estimate: 56.2 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 2.5→2.66 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.227 / Mean I/σ(I) obs: 2.4 / % possible all: 99.4 |
Reflection | *PLUS Lowest resolution: 30 Å / % possible obs: 99.5 % / Num. measured all: 452447 |
Reflection shell | *PLUS % possible obs: 99.5 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: native crystal structure Resolution: 2.5→15 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh and Huber
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Displacement parameters |
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.023
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 15 Å / σ(F): 0 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.5 Å / Rfactor Rfree: 0.41 / Rfactor Rwork: 0.341 |