+Open data
-Basic information
Entry | Database: PDB / ID: 8in1 | ||||||||||||
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Title | beta-glucosidase protein from Aplysia kurodai | ||||||||||||
Components | Beta-Glucosidase | ||||||||||||
Keywords | HYDROLASE / glucosidase | ||||||||||||
Function / homology | Function and homology information hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process Similarity search - Function | ||||||||||||
Biological species | Aplysia kurodai (Kuroda's sea hare) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||||||||
Authors | Sun, X.M. / Ye, Y.X. / Kato, K. / Yu, J. / Yao, M. | ||||||||||||
Funding support | Japan, 3items
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Citation | Journal: Elife / Year: 2023 Title: Structural basis of EHEP-mediated offense against phlorotannin-induced defense from brown algae to protect aku BGL activity. Authors: Sun, X. / Ye, Y. / Sakurai, N. / Wang, H. / Kato, K. / Yu, J. / Yuasa, K. / Tsuji, A. / Yao, M. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8in1.cif.gz | 906.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8in1.ent.gz | 627.5 KB | Display | PDB format |
PDBx/mmJSON format | 8in1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/in/8in1 ftp://data.pdbj.org/pub/pdb/validation_reports/in/8in1 | HTTPS FTP |
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-Related structure data
Related structure data | 8in3C 8in4C 8in6C 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
-Protein / Non-polymers , 2 types, 98 molecules AB
#1: Protein | Mass: 112560.016 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Aplysia kurodai (Kuroda's sea hare) / References: UniProt: A0A1V1FXL2 #7: Water | ChemComp-HOH / | |
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-Sugars , 5 types, 6 molecules
#2: Polysaccharide | Type: oligosaccharide / Mass: 878.823 Da / Num. of mol.: 2 / Source method: isolated from a natural source #3: Polysaccharide | alpha-L-fucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose | #4: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose | #5: Polysaccharide | alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta- ...alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose | #6: Sugar | ChemComp-NAG / | |
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-Details
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: 2.77 Å3/Da / Density % sol: 55.54 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M sodium acetate pH 4.5, and 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Oct 31, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→49.65 Å / Num. obs: 64457 / % possible obs: 99.86 % / Redundancy: 10.7 % / Biso Wilson estimate: 42.39 Å2 / CC1/2: 0.995 / Net I/σ(I): 10.69 |
Reflection shell | Resolution: 2.7→2.8 Å / Mean I/σ(I) obs: 2.57 / Num. unique obs: 6309 / CC1/2: 0.842 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→49.65 Å / SU ML: 0.3747 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.7301 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.43 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→49.65 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 49.8074712124 Å / Origin y: 42.3099619723 Å / Origin z: 132.950302095 Å
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Refinement TLS group | Selection details: all |