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Yorodumi- PDB-6e61: Bacteroides ovatus mixed-linkage glucan utilization locus (MLGUL)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6.0E+61 | |||||||||
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Title | Bacteroides ovatus mixed-linkage glucan utilization locus (MLGUL) SGBP-A in complex with mixed-linkage heptasaccharide | |||||||||
Components | mixed-linkage glucan utilization locus (MLGUL) SGBP-B | |||||||||
Keywords | SUGAR BINDING PROTEIN / tetratricopeptide repeat / outer membrane protein / binding protein | |||||||||
Function / homology | SusD-like 2 / Starch-binding associating with outer membrane / Prokaryotic membrane lipoprotein lipid attachment site profile. / Tetratricopeptide-like helical domain superfamily / SusD/RagB family nutrient-binding outer membrane lipoprotein Function and homology information | |||||||||
Biological species | Bacteroides ovatus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å | |||||||||
Authors | Tamura, K. / Gardill, B.R. / Brumer, H. / Van Petegem, F. | |||||||||
Citation | Journal: Cell.Mol.Life Sci. / Year: 2019 Title: Surface glycan-binding proteins are essential for cereal beta-glucan utilization by the human gut symbiont Bacteroides ovatus. Authors: Tamura, K. / Foley, M.H. / Gardill, B.R. / Dejean, G. / Schnizlein, M. / Bahr, C.M.E. / Louise Creagh, A. / van Petegem, F. / Koropatkin, N.M. / Brumer, H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6e61.cif.gz | 227.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6e61.ent.gz | 179.6 KB | Display | PDB format |
PDBx/mmJSON format | 6e61.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e6/6e61 ftp://data.pdbj.org/pub/pdb/validation_reports/e6/6e61 | HTTPS FTP |
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-Related structure data
Related structure data | 6dmfC 6e57C 6e60C 6e9bC 6dk2S S: Starting model for refinement 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 62693.426 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides ovatus (bacteria) / Strain: ATCC 8483 / DSM 1896 / JCM 5824 / NCTC 11153 / Gene: BACOVA_02743 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A7LY27 #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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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: 2.68 Å3/Da / Density % sol: 54.07 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2M magnesium chloride, 0.1M HEPES, 25% (w/v) PEG3350 Temp details: room temperature |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-3 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 3, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.51→50 Å / Num. obs: 43053 / % possible obs: 98.6 % / Redundancy: 6.49 % / CC1/2: 0.997 / Net I/σ(I): 14.61 |
Reflection shell | Resolution: 2.51→2.66 Å / Redundancy: 5.37 % / Mean I/σ(I) obs: 3.51 / Num. unique obs: 6405 / CC1/2: 0.887 / % possible all: 92.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6DK2 Resolution: 2.51→39.65 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.907 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.541 / ESU R Free: 0.264 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 84.68 Å2 / Biso mean: 28.427 Å2 / Biso min: 7.17 Å2
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Refinement step | Cycle: final / Resolution: 2.51→39.65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.511→2.576 Å / Total num. of bins used: 20
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