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Yorodumi- PDB-5m7b: Blood group synthase AAGlyB in complex with UDP and cryoprotected... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5m7b | ||||||
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Title | Blood group synthase AAGlyB in complex with UDP and cryoprotected with glycerol | ||||||
Components | Histo-blood group ABO system transferase | ||||||
Keywords | TRANSFERASE / blood group synthase / glycosyltransferase / dual-specificity / cis-AB mutant | ||||||
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 / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.5 Å | ||||||
Authors | Rocha, J. / Royant, A. | ||||||
Funding support | France, 1items
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Citation | Journal: To be published Title: Blood group synthase AAGlyB in complex with UDP and cryoprotected with glycerol Authors: Rocha, J. / Batot, G.O. / Palcic, M.M. / Breton, C. / Royant, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5m7b.cif.gz | 90.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5m7b.ent.gz | 65.7 KB | Display | PDB format |
PDBx/mmJSON format | 5m7b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m7/5m7b ftp://data.pdbj.org/pub/pdb/validation_reports/m7/5m7b | HTTPS FTP |
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-Related structure data
Related structure data | 3zggS 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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 34654.008 Da / Num. of mol.: 1 / Mutation: L266G, G268A 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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-Non-polymers , 5 types, 323 molecules
#2: Chemical | ChemComp-MN / | ||||
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#3: Chemical | ChemComp-UDP / | ||||
#4: Chemical | #5: Chemical | #6: 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: 2.26 Å3/Da / Density % sol: 45.47 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: MOPS buffer, manganese chloride, ammonium sulfate, PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9762 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 3, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→42.13 Å / Num. obs: 50377 / % possible obs: 99.6 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.649 / % possible all: 96.4 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 3ZGG Resolution: 1.5→40 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.289 / SU ML: 0.046 / Cross valid method: FREE R-VALUE / ESU R: 0.064 / ESU R Free: 0.066 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.338 Å2
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Refinement step | Cycle: 1 / Resolution: 1.5→40 Å
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Refine LS restraints |
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