+Open data
-Basic information
Entry | Database: PDB / ID: 3i0i | ||||||
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Title | Crystal structure of GTB C80S/C196S/C209S + UDP | ||||||
Components | ABO glycosyltransferase | ||||||
Keywords | TRANSFERASE / GTB / glycosyltransferase / ABO Blood group / retaining | ||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Schuman, B. / Persson, M. / Landry, R.C. / Polakowski, R. / Weadge, J.T. / Seto, N.O.L. / Borisova, S. / Palcic, M.M. / Evans, S.V. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2010 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3i0i.cif.gz | 77.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3i0i.ent.gz | 55.7 KB | Display | PDB format |
PDBx/mmJSON format | 3i0i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3i0i_validation.pdf.gz | 765.5 KB | Display | wwPDB validaton report |
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Full document | 3i0i_full_validation.pdf.gz | 769.3 KB | Display | |
Data in XML | 3i0i_validation.xml.gz | 15.4 KB | Display | |
Data in CIF | 3i0i_validation.cif.gz | 22.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i0/3i0i ftp://data.pdbj.org/pub/pdb/validation_reports/i0/3i0i | HTTPS FTP |
-Related structure data
Related structure data | 3i0cC 3i0dC 3i0eC 3i0fC 3i0gC 3i0hC 3i0jC 3i0kC 3i0lC 1lz7S 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: 33405.320 Da / Num. of mol.: 1 / Fragment: UNP residues 59 to 344 / Mutation: C80S/C196S/C209S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GTB / Plasmid: pCW(delta)lac / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q70V26, UniProt: P16442*PLUS, fucosylgalactoside 3-alpha-galactosyltransferase |
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#2: Chemical | ChemComp-UDP / |
#3: Water | ChemComp-HOH / |
Sequence details | AUTHORS STATE THAT GLU 355 IS THE BIOLOGICAL |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.3 % |
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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: ROTATING ANODE / Type: RIGAKU MICROMAX-002 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 | Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.49→19.94 Å / Num. obs: 49738 / % possible obs: 96.7 % / Redundancy: 4.35 % / Rmerge(I) obs: 0.035 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1LZ7 Resolution: 1.9→19.94 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.927 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.816 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.146 / 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: 22.772 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→19.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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