+Open data
-Basic information
Entry | Database: PDB / ID: 5bxc | ||||||||||||
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Title | Crystal structure of GTA + UDP + DI | ||||||||||||
Components | Histo-blood group ABO system transferase | ||||||||||||
Keywords | TRANSFERASE / Glycosyltransferase Deoxyinhibitor ABO(H) Blood-Group System Complex | ||||||||||||
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 Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||||||||
Authors | Gagnon, S. | ||||||||||||
Funding support | Canada, 3items
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Citation | Journal: J.Biol.Chem. / Year: 2015 Title: High Resolution Structures of the Human ABO(H) Blood Group Enzymes in Complex with Donor Analogs Reveal That the Enzymes Utilize Multiple Donor Conformations to Bind Substrates in a Stepwise Manner. Authors: Gagnon, S.M. / Meloncelli, P.J. / Zheng, R.B. / Haji-Ghassemi, O. / Johal, A.R. / Borisova, S.N. / Lowary, T.L. / 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 | 5bxc.cif.gz | 88.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5bxc.ent.gz | 62.8 KB | Display | PDB format |
PDBx/mmJSON format | 5bxc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bx/5bxc ftp://data.pdbj.org/pub/pdb/validation_reports/bx/5bxc | HTTPS FTP |
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-Related structure data
Related structure data | 5c1gC 5c1hC 5c1lC 5c36C 5c38C 5c3aC 5c3bC 5c3dC 5c47C 5c48C 5c49C 5c4bC 5c4cC 5c4dC 5c4eC 5c4fC 5c8rC 1lz0S C: citing same article (ref.) S: Starting model for refinement |
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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: 34694.008 Da / Num. of mol.: 1 / Fragment: UNP residues 64-354 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ABO / Production host: Escherichia coli (E. coli) References: UniProt: P16442, glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase, fucosylgalactoside 3-alpha-galactosyltransferase |
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#2: Chemical | ChemComp-DA8 / |
#3: Chemical | ChemComp-MN / |
#4: Chemical | ChemComp-UDP / |
#5: 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: 45.77 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 1 % PEG 4000, 4.5-5 % 2-methyl-2,4-pentanediol (MPD), 100 mM ammonium sulfate, 70 mM sodium chloride, 50 mM N-[2-acetamido]-2-iminodiacetic acid (ADA), 30 mM sodium acetate, 5-8 mM cobalt chloride, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 25, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→74.33 Å / Num. obs: 59210 / % possible obs: 95.1 % / Redundancy: 4.07 % / Rmerge(I) obs: 0.033 / Net I/σ(I): 20.4 |
Reflection shell | Highest resolution: 1.4 Å / Redundancy: 2.54 % / Rmerge(I) obs: 0.307 / Mean I/σ(I) obs: 3.1 / % possible all: 81.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1LZ0 Resolution: 1.4→74.33 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.961 / SU B: 0.998 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.065 / 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 mean: 19.449 Å2
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Refinement step | Cycle: 1 / Resolution: 1.4→74.33 Å
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