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Open data
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Basic information
| Entry | Database: PDB / ID: 2y7a | ||||||
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| Title | Crystal structure of unliganded GTB P156L | ||||||
Components | ABO GLYCOSYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / ABO BLOOD GROUP | ||||||
| Function / homology | Function and homology informationfucosylgalactoside 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 / : / Golgi cisterna membrane / : / 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 / : / Golgi cisterna membrane / : / antigen binding / manganese ion binding / vesicle / carbohydrate metabolic process / Golgi membrane / nucleotide binding / Golgi apparatus / extracellular region / metal ion binding / membrane Similarity search - Function | ||||||
| Biological species | HOMO SAPIENS (human) | ||||||
| Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.06 Å | ||||||
Authors | Weadge, J. / Palcic, M.M. / Henriksen, A. | ||||||
Citation | Journal: To be PublishedTitle: Structural and Biochemical Characterization of the Human Blood Group a and B Galactosyltransferases Possessing the Pro156Leu Mutation Authors: Weadge, J. / Palcic, M.M. / Henriksen, A. #1: Journal: J.Mol.Biol. / Year: 2010Title: 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.L. / Borisova, S.N. / Palcic, M.M. / Evans, S.V. | ||||||
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 2y7a.cif.gz | 465.9 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb2y7a.ent.gz | 385.9 KB | Display | PDB format |
| PDBx/mmJSON format | 2y7a.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y7/2y7a ftp://data.pdbj.org/pub/pdb/validation_reports/y7/2y7a | HTTPS FTP |
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-Related structure data
| Related structure data | ![]() 1zizS S: Starting model for refinement |
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| Similar structure data |
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Links
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Assembly
| Deposited unit | ![]()
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| 3 | ![]()
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| Unit cell |
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Components
| #1: Protein | Mass: 34676.098 Da / Num. of mol.: 4 / Fragment: RESIDUES 54-344 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ![]() References: UniProt: Q70V26, UniProt: P16442*PLUS, fucosylgalactoside 3-alpha-galactosyltransferase #2: Chemical | ChemComp-MN / | #3: Chemical | ChemComp-UDP / | #4: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, PRO 146 TO LEU ENGINEERED RESIDUE IN CHAIN B, PRO 146 TO LEU ...ENGINEERED | Sequence details | N-TERMINAL DISCREPANC | |
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-Experimental details
-Experiment
| Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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Sample preparation
| Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.8 % / Description: NONE |
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| Crystal grow | pH: 7 Details: 5 MM MOPS PH 7, 1 MM MNCL2, 1 MM DTT, 0.1 M AMSO4, 10% (W/V) PEG 3350. |
-Data collection
| Diffraction | Mean temperature: 100 K | |||||||||||||||
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| Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 | |||||||||||||||
| Detector | Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Details: MIRRORS | |||||||||||||||
| Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
| Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||
| Reflection twin |
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| Reflection | Resolution: 2.06→143.76 Å / Num. obs: 75523 / % possible obs: 93.2 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 29.955 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.6 | |||||||||||||||
| Reflection shell | Resolution: 2.06→2.16 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.6 / % possible all: 77.6 |
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Processing
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| Refinement | Method to determine structure: MOLECULAR REPLACEMENTStarting model: PDB ENTRY 1ZIZ Resolution: 2.06→143.76 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.92 / SU B: 9.629 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.049 / ESU R Free: 0.039 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS AND SIDECHAINS WERE NOT MODELED.
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Displacement parameters | Biso mean: 39.362 Å2
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| Refinement step | Cycle: LAST / Resolution: 2.06→143.76 Å
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| Refine LS restraints |
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HOMO SAPIENS (human)
X-RAY DIFFRACTION
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