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Yorodumi- PDB-7kv7: Surface glycan-binding protein B from Bacteroides fluxus in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7kv7 | ||||||
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Title | Surface glycan-binding protein B from Bacteroides fluxus in complex with laminaritriose | ||||||
Components | PKD domain protein | ||||||
Keywords | SUGAR BINDING PROTEIN / CBM / lectin | ||||||
Function / homology | Function and homology information Polycystic kidney disease (PKD) domain profile. / PKD domain / PKD domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin-like fold Similarity search - Domain/homology | ||||||
Biological species | Bacteroides fluxus YIT 12057 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.76 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 | 7kv7.cif.gz | 203.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7kv7.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7kv7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kv/7kv7 ftp://data.pdbj.org/pub/pdb/validation_reports/kv/7kv7 | HTTPS FTP |
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-Related structure data
Related structure data | 7kv1C 7kv2C 7kv3C 7kv4C 7kv5C 7kv6C 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
-Protein , 1 types, 2 molecules AAABBB
#1: Protein | Mass: 31185.545 Da / Num. of mol.: 2 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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-Sugars , 2 types, 4 molecules
#2: Polysaccharide | beta-D-glucopyranose-(1-3)-beta-D-glucopyranose |
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#4: Sugar |
-Non-polymers , 5 types, 650 molecules
#3: Chemical | ChemComp-LYS / | ||||
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#5: Chemical | ChemComp-PEG / | ||||
#6: Chemical | #7: Chemical | ChemComp-EDO / | #8: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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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: 2.55 Å3/Da / Density % sol: 51.76 % |
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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, 0.1 M 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: 1.76→37.38 Å / Num. obs: 57885 / % possible obs: 93.5 % / Redundancy: 6.8 % / CC1/2: 0.999 / Net I/σ(I): 21.6 |
Reflection shell | Resolution: 1.76→1.79 Å / Num. unique obs: 2864 / CC1/2: 0.972 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.76→35.664 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.945 / WRfactor Rfree: 0.207 / WRfactor Rwork: 0.163 / Average fsc free: 0.9398 / Average fsc work: 0.9499 / Cross valid method: FREE R-VALUE / ESU R: 0.103 / ESU R Free: 0.107 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: 24.287 Å2
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Refinement step | Cycle: LAST / Resolution: 1.76→35.664 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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