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Yorodumi- PDB-7kv6: Surface glycan-binding protein B from Bacteroides fluxus in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7kv6 | ||||||
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Title | Surface glycan-binding protein B from Bacteroides fluxus in complex with mixed-linkage glucotriose | ||||||
Components | PKD domain protein | ||||||
Keywords | SUGAR BINDING PROTEIN / CBM / lectin | ||||||
Function / homology | Polycystic kidney disease (PKD) domain profile. / PKD domain / PKD domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin-like fold / GUANIDINE / PKD domain protein Function and homology information | ||||||
Biological species | Bacteroides fluxus YIT 12057 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å | ||||||
Authors | Tamura, K. / Brumer, H. / Van Petegem, F. | ||||||
Funding support | Canada, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2021 Title: Distinct protein architectures mediate species-specific beta-glucan binding and metabolism in the human gut microbiota. Authors: Tamura, K. / Dejean, G. / Van Petegem, F. / Brumer, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7kv6.cif.gz | 110.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7kv6.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7kv6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kv/7kv6 ftp://data.pdbj.org/pub/pdb/validation_reports/kv/7kv6 | HTTPS FTP |
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-Related structure data
Related structure data | 7kv1C 7kv2C 7kv3C 7kv4C 7kv5C 7kv7C 7kwbC 7kwcC C: citing same article (ref.) |
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Similar 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: 31185.545 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides fluxus YIT 12057 (bacteria) Gene: HMPREF9446_00613 / Production host: Escherichia coli (E. coli) / References: UniProt: F3PPH3 | ||||
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#2: Polysaccharide | beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||||
#3: Chemical | #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: 2.75 Å3/Da / Density % sol: 55.35 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion Details: 0.1 M MES pH6.6, 0.2 M ammonium sulfate, 20 % (w/v) PEG5000MME, 0.1M guanidine hydrochloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 18, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→74.19 Å / Num. obs: 43047 / % possible obs: 95.5 % / Redundancy: 11.8 % / CC1/2: 0.999 / Net I/σ(I): 34.4 |
Reflection shell | Resolution: 1.61→1.64 Å / Num. unique obs: 2197 / CC1/2: 0.907 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.6→74.189 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.967 / Cross valid method: FREE R-VALUE / ESU R: 0.08 / ESU R Free: 0.081 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.631 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→74.189 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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