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Yorodumi- PDB-8yk1: Blood group B alpha-1,3-galactosidase AgaBb from Bifidobacterium ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8yk1 | |||||||||
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Title | Blood group B alpha-1,3-galactosidase AgaBb from Bifidobacterium bifidum, construct 23-844 | |||||||||
Components | Alpha-galactosidase | |||||||||
Keywords | HYDROLASE / Blood group B antigen / Glycoside hydrolase / ligand free | |||||||||
Function / homology | Function and homology information Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / metabolic process / hydrolase activity, acting on glycosyl bonds / membrane Similarity search - Function | |||||||||
Biological species | Bifidobacterium bifidum JCM 1254 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å | |||||||||
Authors | Kashima, T. / Ashida, H. / Fushinobu, S. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: J.Appl.Glyosci. / Year: 2024 Title: Crystal Structure of Bifidobacterium bifidum Glycoside Hydrolase Family 110 alpha-Galactosidase Specific for Blood Group B Antigen Authors: Kashima, T. / Akama, M. / Wakinaka, T. / Arakawa, T. / Ashida, H. / Fushinobu, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8yk1.cif.gz | 584.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8yk1.ent.gz | 382.8 KB | Display | PDB format |
PDBx/mmJSON format | 8yk1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8yk1_validation.pdf.gz | 454.3 KB | Display | wwPDB validaton report |
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Full document | 8yk1_full_validation.pdf.gz | 468.4 KB | Display | |
Data in XML | 8yk1_validation.xml.gz | 85.9 KB | Display | |
Data in CIF | 8yk1_validation.cif.gz | 124.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yk/8yk1 ftp://data.pdbj.org/pub/pdb/validation_reports/yk/8yk1 | HTTPS FTP |
-Related structure data
Related structure data | 8yk2C 8yk3C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 88378.852 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bifidobacterium bifidum JCM 1254 (bacteria) Gene: agabb, GBA83_07165 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 (DE3) References: UniProt: L8B3G2, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.47 Å3/Da / Density % sol: 50.16 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 10% (w/v) PEG 3350, 0.1M sodium iodide (seed condition: 10% (w/v) PEG 6000, 0.1M citric acid pH 5.0) |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.052 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Feb 27, 2022 |
Radiation | Monochromator: Cryo-cooled channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.052 Å / Relative weight: 1 |
Reflection | Resolution: 2.02→48.59 Å / Num. obs: 161615 / % possible obs: 98.2 % / Redundancy: 7.1 % / Biso Wilson estimate: 25.12 Å2 / CC1/2: 1 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 2.02→2.06 Å / Mean I/σ(I) obs: 2.7 / Num. unique obs: 5145 / CC1/2: 0.88 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.02→48.59 Å / SU ML: 0.2156 / Cross valid method: FREE R-VALUE / σ(F): 1.95 / Phase error: 21.069 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.87 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.02→48.59 Å
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Refine LS restraints |
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LS refinement shell |
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