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Yorodumi- PDB-8yk3: Blood group B alpha-1,3-galactosidase AgaBb from Bifidobacterium ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8yk3 | |||||||||
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Title | Blood group B alpha-1,3-galactosidase AgaBb from Bifidobacterium bifidum, construct T7-tag_24-673 | |||||||||
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 / 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: 3.5 Å | |||||||||
Authors | Kashima, T. / Ashida, H. / Fushinobu, S. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: J Appl Glycosci (1999) / 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 | 8yk3.cif.gz | 299.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8yk3.ent.gz | 193.1 KB | Display | PDB format |
PDBx/mmJSON format | 8yk3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8yk3_validation.pdf.gz | 1012.6 KB | Display | wwPDB validaton report |
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Full document | 8yk3_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 8yk3_validation.xml.gz | 43.9 KB | Display | |
Data in CIF | 8yk3_validation.cif.gz | 60.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yk/8yk3 ftp://data.pdbj.org/pub/pdb/validation_reports/yk/8yk3 | HTTPS FTP |
-Related structure data
Related structure data | 8yk1C 8yk2C 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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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 72590.352 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bifidobacterium bifidum JCM 1254 (bacteria) Gene: agabb, GBA83_07165 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 References: UniProt: L8B3G2, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds #2: Sugar | #3: Chemical | #4: Chemical | ChemComp-MES / | Has ligand of interest | Y | |
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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: 2.95 Å3/Da / Density % sol: 58.26 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 15% (w/v) PEG 20000, 0.1M MES-NaOH pH 6.5 (Seed condition: 10% (w/v) PEG 6000, 0.1M citric acid pH 5.0, 4 degrees celsius) |
-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: 1.08 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 29, 2020 |
Radiation | Monochromator: Cryo-cooled channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→47.88 Å / Num. obs: 20905 / % possible obs: 99.9 % / Redundancy: 3.4 % / Biso Wilson estimate: 19.82 Å2 / CC1/2: 0.76 / Net I/σ(I): 2.9 |
Reflection shell | Resolution: 3.5→3.83 Å / Num. unique obs: 4934 / CC1/2: 0.35 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→47.88 Å / SU ML: 0.5648 / Cross valid method: FREE R-VALUE / σ(F): 1.95 / Phase error: 27.7232 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: 17.8 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.5→47.88 Å
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Refine LS restraints |
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LS refinement shell |
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