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Yorodumi- PDB-8i5k: Crystal structure of chitin oligosaccharide binding protein from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8i5k | ||||||
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Title | Crystal structure of chitin oligosaccharide binding protein from Vibrio cholera in complex with chitotriose. | ||||||
Components | ABC transporter substrate-binding protein | ||||||
Keywords | SUGAR BINDING PROTEIN / chitin oligosaccharide / periplasmic / solute binding protein | ||||||
Function / homology | Function and homology information ATP-binding cassette (ABC) transporter complex / transmembrane transport / outer membrane-bounded periplasmic space Similarity search - Function | ||||||
Biological species | Vibrio cholerae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.219 Å | ||||||
Authors | Ohnuma, T. / Takeshita, D. | ||||||
Funding support | 1items
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Citation | Journal: Sci Rep / Year: 2023 Title: Periplasmic chitooligosaccharide-binding protein requires a three-domain organization for substrate translocation. Authors: Ohnuma, T. / Tsujii, J. / Kataoka, C. / Yoshimoto, T. / Takeshita, D. / Lampela, O. / Juffer, A.H. / Suginta, W. / Fukamizo, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8i5k.cif.gz | 136.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8i5k.ent.gz | 101.2 KB | Display | PDB format |
PDBx/mmJSON format | 8i5k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8i5k_validation.pdf.gz | 768.2 KB | Display | wwPDB validaton report |
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Full document | 8i5k_full_validation.pdf.gz | 769.5 KB | Display | |
Data in XML | 8i5k_validation.xml.gz | 25.7 KB | Display | |
Data in CIF | 8i5k_validation.cif.gz | 39.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i5/8i5k ftp://data.pdbj.org/pub/pdb/validation_reports/i5/8i5k | HTTPS FTP |
-Related structure data
Related structure data | 8i5jC 4gfbS S: Starting model for refinement 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 60977.188 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae (bacteria) Gene: appA_1, appA, D6U24_16190, ERS013201_01979, ERS013202_02445, EYB64_10090, F0H40_11710, F0M16_04225, FLM12_17525 Production host: Escherichia coli (E. coli) / References: UniProt: A0A085SLP2 |
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#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose |
#3: Chemical | ChemComp-MG / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.17 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.9 Details: 0.2 M Magnesium chloride hexahydrate, 20% w/v Polyethylene glycol 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-17A / Wavelength: 0.98 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 22, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.219→19.307 Å / Num. obs: 237875 / % possible obs: 84.8 % / Redundancy: 3.45 % / CC1/2: 0.996 / Net I/σ(I): 8.82 |
Reflection shell | Resolution: 1.22→1.28 Å / Num. unique obs: 18620 / CC1/2: 0.507 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4GFB Resolution: 1.219→19.307 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.22 / Phase error: 21.8 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.219→19.307 Å
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Refine LS restraints |
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LS refinement shell |
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