+Open data
-Basic information
Entry | Database: PDB / ID: 3sx5 | ||||||
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Title | Crystal structure of AABB+UDP+Gal with MPD as the cryoprotectant | ||||||
Components | Histo-blood group ABO system transferase | ||||||
Keywords | TRANSFERASE / retaining glycosyltransferase / glycoprotein / blood group antigen / ABO Rossmann fold / metal-binding / manganese | ||||||
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 / molecular replacement / Resolution: 1.43 Å | ||||||
Authors | Johal, A.R. / Evans, S.V. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2012 Title: Sequence-dependent effects of cryoprotectants on the active sites of the human ABO(H) blood group A and B glycosyltransferases. Authors: Johal, A.R. / Schuman, B. / Alfaro, J.A. / Borisova, S. / Seto, N.O. / 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 | 3sx5.cif.gz | 83.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3sx5.ent.gz | 59.7 KB | Display | PDB format |
PDBx/mmJSON format | 3sx5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sx/3sx5 ftp://data.pdbj.org/pub/pdb/validation_reports/sx/3sx5 | HTTPS FTP |
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-Related structure data
Related structure data | 3sx3C 3sx7C 3sx8C 3sxaC 3sxbC 3sxcC 3sxdC 3sxeC 3sxgC 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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1 |
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2 |
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Unit cell |
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-Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 34226.559 Da / Num. of mol.: 1 Fragment: Histo-blood group B transferase (UNP residues 64-354) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ABO / Plasmid: PCQ DELTA 1AC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 GOLD References: UniProt: P16442, fucosylgalactoside 3-alpha-galactosyltransferase |
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#3: Sugar | ChemComp-GAL / |
-Non-polymers , 4 types, 261 molecules
#2: Chemical | ChemComp-UDP / |
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#4: Chemical | ChemComp-PEG / |
#5: Chemical | ChemComp-MN / |
#6: Water | ChemComp-HOH / |
-Details
Sequence details | MUTATIONS L266M AND G268A ARE B GROUP TRANSFERAS |
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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: 2.28 Å3/Da / Density % sol: 46.01 % |
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Crystal grow | Temperature: 298 K / pH: 7 Details: 1% PEG4000, 5% MPD, 100 mM ammonium sulfate, 70 mM sodium chloride, 50 mM ADA, pH 7.6, 30 mM sodium acetate, pH 4.6, 5 mM manganese chloride, with 20% MPD as cryoprotectant, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-002 / Wavelength: 1.54 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Nov 9, 2007 / Details: OSMIC BLUE MIRRORS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.43→74.953 Å / Num. obs: 55579 / % possible obs: 95.6 % / Redundancy: 4.24 % / Rmerge(I) obs: 0.031 / Χ2: 0.95 / Net I/σ(I): 20.7 / Scaling rejects: 1783 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1LZ7 Resolution: 1.43→20 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.958 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 0.996 / SU ML: 0.039 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 67.25 Å2 / Biso mean: 20.3719 Å2 / Biso min: 8.32 Å2
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Refinement step | Cycle: LAST / Resolution: 1.43→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.43→1.467 Å / Total num. of bins used: 20
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