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Yorodumi- PDB-1g8o: CRYSTALLOGRAPHIC STRUCTURE OF THE NATIVE BOVINE ALPHA-1,3-GALACTO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1g8o | ||||||
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Title | CRYSTALLOGRAPHIC STRUCTURE OF THE NATIVE BOVINE ALPHA-1,3-GALACTOSYLTRANSFERASE CATALYTIC DOMAIN | ||||||
Components | N-ACETYLLACTOSAMINIDE ALPHA-1,3-GALACTOSYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / ALPHA-BETA-ALPHA / UDP BINDING PROTEIN | ||||||
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: 2.3 Å | ||||||
Authors | Gastinel, L.N. / Bigon, 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 | 1g8o.cif.gz | 77.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1g8o.ent.gz | 57.2 KB | Display | PDB format |
PDBx/mmJSON format | 1g8o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g8/1g8o ftp://data.pdbj.org/pub/pdb/validation_reports/g8/1g8o | HTTPS FTP |
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-Related structure data
Related structure data | 1fg5SC 1g93C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#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: Chemical | ChemComp-MN / |
#3: Chemical | ChemComp-U5P / |
#4: 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: 3.53 Å3/Da / Density % sol: 65.19 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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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 UMP, 2 mM MnCl2, 500 mM NaCl, 0.1 M cacodylate, pH 6.50, 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: ID14-2 / Wavelength: 0.9324 Å |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Sep 17, 1999 |
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: 2.3→29 Å / Num. all: 434477 / Num. obs: 23769 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.9 % / Biso Wilson estimate: 38.2 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 8 |
Reflection shell | Resolution: 2.3→2.39 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.075 / Mean I/σ(I) obs: 7.8 / % possible all: 100 |
Reflection | *PLUS Lowest resolution: 29 Å / Num. obs: 31286 / % possible obs: 96.5 % / Num. measured all: 434477 |
Reflection shell | *PLUS % possible obs: 96 % / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 1.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Model MAD solved at 2.8 Angstroms resolution 1fg5.pdb Resolution: 2.3→2.44 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: bulk solvent modeling, Flat model
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Displacement parameters | Biso mean: 51.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→2.44 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.017
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 15 Å / σ(F): 0 / Rfactor obs: 0.21 / Rfactor Rfree: 0.25 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 51.9 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.3 Å / Rfactor Rfree: 0.335 / Rfactor Rwork: 0.274 |