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Open data
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Basic information
Entry | Database: PDB / ID: 3i0c | ||||||
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Title | Crystal structure of GTB C80S/C196S unliganded | ||||||
![]() | ABO glycosyltransferase | ||||||
![]() | TRANSFERASE / GTB / glycosyltransferase / ABO Blood group / retaining | ||||||
Function / homology | ![]() fucosylgalactoside 3-alpha-galactosyltransferase / glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase / glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase activity / fucosylgalactoside 3-alpha-galactosyltransferase activity / ABO blood group biosynthesis / lipid glycosylation / Golgi cisterna membrane / protein glycosylation / antigen binding / manganese ion binding ...fucosylgalactoside 3-alpha-galactosyltransferase / glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase / glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase activity / fucosylgalactoside 3-alpha-galactosyltransferase activity / ABO blood group biosynthesis / lipid glycosylation / Golgi cisterna membrane / protein glycosylation / antigen binding / manganese ion binding / vesicle / carbohydrate metabolic process / Golgi membrane / nucleotide binding / Golgi apparatus / extracellular region / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Schuman, B. / Persson, M. / Landry, R.C. / Polakowski, R. / Weadge, J.T. / Seto, N.O.L. / Borisova, S. / Palcic, M.M. / Evans, S.V. | ||||||
![]() | ![]() Title: Cysteine-to-serine mutants dramatically reorder the active site of human ABO(H) blood group B glycosyltransferase without affecting activity: structural insights into cooperative substrate binding Authors: Schuman, B. / Persson, M. / Landry, R.C. / Polakowski, R. / Weadge, J.T. / Seto, N.O. / Borisova, S.N. / Palcic, M.M. / Evans, S.V. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 78.5 KB | Display | ![]() |
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PDB format | ![]() | 56.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3i0dC ![]() 3i0eC ![]() 3i0fC ![]() 3i0gC ![]() 3i0hC ![]() 3i0iC ![]() 3i0jC ![]() 3i0kC ![]() 3i0lC ![]() 1lz7S 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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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 33421.387 Da / Num. of mol.: 1 / Fragment: UNP residues 59 to 344 / Mutation: C80S/C196S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q70V26, UniProt: P16442*PLUS, fucosylgalactoside 3-alpha-galactosyltransferase |
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#2: Water | ChemComp-HOH / |
Sequence details | AUTHORS STATE THAT GLU 355 IS THE BIOLOGICAL |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 46.99 % |
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Crystal grow | Temperature: 279.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 35mM sodium acetate pH 4.6, 45 mM ADA, 30mM sodium chloride, 3-4 mM magnesium chloride, 3-3.5% PEG 4000, vapor diffusion, hanging drop, temperature 279.15K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 27, 2005 / Details: Osmic Blue | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Ni FILTER / Protocol: Molecular Replacement / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.55→19.91 Å / Num. obs: 43878 / % possible obs: 96.4 % / Redundancy: 4.41 % / Rmerge(I) obs: 0.042 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1LZ7 Resolution: 1.55→19.91 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.949 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 1.338 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.444 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→19.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.59 Å / Total num. of bins used: 20
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