+Open data
-Basic information
Entry | Database: PDB / ID: 6bjl | ||||||
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Title | Human ABO(H) blood group glycosyltransferase GTB D302L mutant | ||||||
Components | ABO blood group (Transferase A, alpha 1-3-N-acetylgalactosaminyltransferase transferase B, alpha 1-3-galactosyltransferase) | ||||||
Keywords | TRANSFERASE / Blood group transferases / glycosyltransferases / enzymes | ||||||
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 / hexosyltransferase activity / lipid glycosylation / Golgi cisterna membrane / protein glycosylation / antigen 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 / hexosyltransferase activity / 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: 1.69 Å | ||||||
Authors | Gagnon, S.M.L. / Legg, M.S.G. / Evans, S.V. | ||||||
Funding support | Canada, 1items
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Citation | Journal: Glycobiology / Year: 2018 Title: Conserved residues Arg188 and Asp302 are critical for active site organization and catalysis in human ABO(H) blood group A and B glycosyltransferases. Authors: Gagnon, S.M.L. / Legg, M.S.G. / Polakowski, R. / Letts, J.A. / Persson, M. / Lin, S. / Zheng, R.B. / Rempel, B. / Schuman, B. / Haji-Ghassemi, 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 | 6bjl.cif.gz | 75.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6bjl.ent.gz | 54.1 KB | Display | PDB format |
PDBx/mmJSON format | 6bjl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bj/6bjl ftp://data.pdbj.org/pub/pdb/validation_reports/bj/6bjl | HTTPS FTP |
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-Related structure data
Related structure data | 6bjiC 6bjjC 6bjkC 6bjmC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 32928.113 Da / Num. of mol.: 1 / Fragment: UNP residues 54-335 / Mutation: D302L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ABO / Production host: Escherichia coli (E. coli) / References: UniProt: D3HIC2, UniProt: P16442*PLUS |
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#2: Chemical | ChemComp-GOL / |
#3: 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: 2.27 Å3/Da / Density % sol: 45.78 % |
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Crystal grow | Temperature: 277 K / Method: small tubes Details: Spontaneous crystals were recovered from concentrated stocks of GTB/D302L (40-50 mg/mL) stored in 50 mM MOPS, pH 7.00, 0.1 M sodium chloride, 1 mM DTT, 5 mM manganese chloride, and kept at 277 K. |
-Data collection
Diffraction | Mean temperature: 113 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SEALED TUBE / Type: RIGAKU / Wavelength: 1.5418 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 27, 2006 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.69→19.61 Å / Num. obs: 34748 / % possible obs: 98.3 % / Redundancy: 4.71 % / Rmerge(I) obs: 0.046 / Rrim(I) all: 0.046 / Χ2: 0.96 / Net I/σ(I): 15.1 / Num. measured all: 164960 / Scaling rejects: 1238 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1LZ7 Resolution: 1.69→75.59 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.948 / SU ML: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.1 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 66.7 Å2 / Biso mean: 23.618 Å2 / Biso min: 13.34 Å2
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Refinement step | Cycle: final / Resolution: 1.69→75.59 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.69→1.734 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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