+Open data
-Basic information
Entry | Database: PDB / ID: 8in3 | ||||||||||||
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Title | Eisenia hydrolysis-enhancing protein from Aplysia kurodai | ||||||||||||
Components | 25 kDa polyphenol-binding protein | ||||||||||||
Keywords | UNKNOWN FUNCTION / EHEP | ||||||||||||
Function / homology | Chitin-binding domain type 2 / Chitin binding domain / Chitin binding Peritrophin-A domain / Chitin-binding type-2 domain profile. / Chitin binding domain superfamily / chitin binding / extracellular region / 25 kDa polyphenol-binding protein Function and homology information | ||||||||||||
Biological species | Aplysia kurodai (Kuroda's sea hare) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.15 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 | 8in3.cif.gz | 118.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8in3.ent.gz | 80.9 KB | Display | PDB format |
PDBx/mmJSON format | 8in3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/in/8in3 ftp://data.pdbj.org/pub/pdb/validation_reports/in/8in3 | HTTPS FTP |
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-Related structure data
Related structure data | 8in1C 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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Unit cell |
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-Components
#1: Protein | Mass: 24669.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Aplysia kurodai (Kuroda's sea hare) / References: UniProt: A0A1B4XTR1 | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.86 Å3/Da / Density % sol: 33.77 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.0 M sodium acetate, 0.1 M imidazole (pH 6.5) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 12, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.15→50 Å / Num. obs: 60994 / % possible obs: 93.41 % / Redundancy: 6.6 % / Biso Wilson estimate: 8.81 Å2 / CC1/2: 0.999 / Net I/σ(I): 19.28 |
Reflection shell | Resolution: 1.15→1.195 Å / Num. unique obs: 4888 / CC1/2: 0.704 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.15→35.62 Å / SU ML: 0.1373 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.0217 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: 13.04 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.15→35.62 Å
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Refine LS restraints |
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LS refinement shell |
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