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Yorodumi- PDB-8j0p: Chitin binding SusD-like protein AqSusD from a marine Bacteroidetes -
+Open data
-Basic information
Entry | Database: PDB / ID: 8j0p | ||||||
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Title | Chitin binding SusD-like protein AqSusD from a marine Bacteroidetes | ||||||
Components | Chitin binding SusD-like protein | ||||||
Keywords | SUGAR BINDING PROTEIN / SusD-like protein | ||||||
Biological species | Aquimarina (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Yang, J. | ||||||
Funding support | 1items
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Citation | Journal: Febs J. / Year: 2024 Title: Structural insights of a SusD-like protein in marine Bacteroidetes bacteria reveal the molecular basis for chitin recognition and acquisition. Authors: Yang, J. / Zhang, L. / Lin, S. / Li, W. / Liu, C. / Yan, J. / Li, S. / Long, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8j0p.cif.gz | 116.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8j0p.ent.gz | 86.6 KB | Display | PDB format |
PDBx/mmJSON format | 8j0p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8j0p_validation.pdf.gz | 420.4 KB | Display | wwPDB validaton report |
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Full document | 8j0p_full_validation.pdf.gz | 423.3 KB | Display | |
Data in XML | 8j0p_validation.xml.gz | 21.1 KB | Display | |
Data in CIF | 8j0p_validation.cif.gz | 31.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j0/8j0p ftp://data.pdbj.org/pub/pdb/validation_reports/j0/8j0p | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 58166.992 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquimarina (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.97 % |
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Crystal grow | Temperature: 293 K / Method: evaporation Details: 0.2 M magnesium chloride, 0.1 M Tris-HCl pH8.5, and 20% (w/v) PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54184 Å |
Detector | Type: DECTRIS PILATUS3 R 200K-A / Detector: PIXEL / Date: Dec 2, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54184 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→19.01 Å / Num. obs: 21313 / % possible obs: 99.6 % / Redundancy: 5.1 % / CC1/2: 0.984 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 2.4→2.49 Å / Num. unique obs: 2225 / CC1/2: 0.771 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→19.01 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.47 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→19.01 Å
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Refine LS restraints |
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LS refinement shell |
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