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Yorodumi- PDB-7kv3: Surface glycan-binding protein A from Bacteroides thetaiotaomicro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7kv3 | ||||||
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Title | Surface glycan-binding protein A from Bacteroides thetaiotaomicron in complex with laminarihexaose | ||||||
Components | RagB/SusD family nutrient uptake outer membrane protein | ||||||
Keywords | SUGAR BINDING PROTEIN / SusD / Tetratricopeptide repeat / CBM | ||||||
Function / homology | RagB/SusD domain / SusD family / cell outer membrane / Tetratricopeptide-like helical domain superfamily / beta-cellohexaose / RagB/SusD family nutrient uptake outer membrane protein Function and homology information | ||||||
Biological species | Bacteroides thetaiotaomicron (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 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 | 7kv3.cif.gz | 191.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7kv3.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7kv3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kv/7kv3 ftp://data.pdbj.org/pub/pdb/validation_reports/kv/7kv3 | HTTPS FTP |
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-Related structure data
Related structure data | 7kv1C 7kv2C 7kv4C 7kv5C 7kv6C 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: 59352.117 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria) Gene: DW011_12550, DW780_14665, DWY18_18425, GAN67_20195, GAN98_19115 Production host: Escherichia coli (E. coli) / References: UniProt: A0A173VPY3 |
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#2: Polysaccharide | beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D- ...beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose |
#3: Chemical | ChemComp-SO4 / |
#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: 2.28 Å3/Da / Density % sol: 46.11 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion Details: 0.1 M bis-tris pH 6.5, 0.2 M lithium sulfate, 25 % (w/v) PEG3350 |
-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: 0.97946 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: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→39.45 Å / Num. obs: 33221 / % possible obs: 99 % / Redundancy: 7 % / CC1/2: 0.992 / Net I/σ(I): 8 |
Reflection shell | Resolution: 2.05→2.11 Å / Num. unique obs: 1639 / CC1/2: 0.668 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.05→39.447 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.933 / Cross valid method: FREE R-VALUE / ESU R: 0.173 / ESU R Free: 0.155 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: 20.868 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→39.447 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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