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Yorodumi- PDB-2o1h: Naturally occurring mutation of Humna ABO(H) Galactosyltransferas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2o1h | ||||||
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Title | Naturally occurring mutation of Humna ABO(H) Galactosyltransferase in complex with UDP: GTB/M214T_UDP | ||||||
Components | ABO glycosyltransferase | ||||||
Keywords | TRANSFERASE / Glycosyltransferase / galactosyltransferase / GTB / blood type subgroup / DXD | ||||||
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: 1.67 Å | ||||||
Authors | Letts, J.A. / Borisova, S.N. / Evans, S.V. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 Title: Structural effects of naturally occurring human blood group B galactosyltransferase mutations adjacent to the DXD motif. Authors: Persson, M. / Letts, J.A. / Hosseini-Maaf, B. / Borisova, S.N. / Palcic, M.M. / Evans, S.V. / Olsson, M.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2o1h.cif.gz | 78.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2o1h.ent.gz | 55.5 KB | Display | PDB format |
PDBx/mmJSON format | 2o1h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o1/2o1h ftp://data.pdbj.org/pub/pdb/validation_reports/o1/2o1h | HTTPS FTP |
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-Related structure data
Related structure data | 2o1fC 2o1gC 1lz7S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 34496.754 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ABO / Plasmid: pCWdeltalac / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q70V27, UniProt: P16442*PLUS | ||||||
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#2: Chemical | ChemComp-HG / #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: 2.28 Å3/Da / Density % sol: 46.08 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: ADA, manganese chloride, ammonium sulfate, MPD, glycerol, PEG 4000,, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-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: Apr 27, 2006 |
Radiation | Monochromator: Osmic "Blue" confocal x-ray mirrors with power levels of 30 watts Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.67→20 Å / Num. all: 36659 / Num. obs: 36659 / % possible obs: 100 % / Redundancy: 6.71 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 1.67→1.73 Å / Redundancy: 6.33 % / Rmerge(I) obs: 0.299 / Mean I/σ(I) obs: 4.9 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1lz7 Resolution: 1.67→20 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.637 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.093 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.584 Å2
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Refinement step | Cycle: LAST / Resolution: 1.67→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.67→1.713 Å / Total num. of bins used: 20
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