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- PDB-6e9b: Bacteroides ovatus mixed-linkage glucan utilization locus (MLGUL)... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6e9b | |||||||||
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Title | Bacteroides ovatus mixed-linkage glucan utilization locus (MLGUL) SGBP-B in complex with mixed-linkage heptasaccharide | |||||||||
![]() | Mixed-linkage glucan utilization locus (MLGUL) SGBP-B | |||||||||
![]() | SUGAR BINDING PROTEIN / tetratricopeptide repeat / outer membrane protein / binding protein | |||||||||
Function / homology | Immunoglobulin-like fold / PKD domain-containing protein![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Tamura, K. / Gardill, B.R. / Brumer, H. / Van Petegem, F. | |||||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 295.4 KB | Display | ![]() |
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PDB format | ![]() | 235.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 679.2 KB | Display | ![]() |
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Full document | ![]() | 704.2 KB | Display | |
Data in XML | ![]() | 53.7 KB | Display | |
Data in CIF | ![]() | 73.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6dmfC ![]() 6e57SC ![]() 6e60C ![]() 6e61C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 45678.328 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 8483 / DSM 1896 / JCM 5824 / NCTC 11153 / Gene: BACOVA_02744 / Production host: ![]() ![]() #2: Polysaccharide | beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-4)-beta-D- ...beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.9 Å3/Da / Density % sol: 71.59 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 4.2 Details: 0.2M lithium sulfate, 0.1M phosphate-citrate, 20% (w/v) PEG1000 Temp details: room temperature |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Feb 8, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 3.15→50 Å / Num. obs: 50094 / % possible obs: 99.8 % / Redundancy: 7.42 % / CC1/2: 0.999 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 3.15→3.34 Å / Redundancy: 7.44 % / Mean I/σ(I) obs: 1.73 / Num. unique obs: 7894 / CC1/2: 0.651 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]()
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Displacement parameters | Biso max: 207.63 Å2 / Biso mean: 100.53 Å2 / Biso min: 30.95 Å2
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Refine analyze | Luzzati coordinate error obs: 0.46 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.15→34.33 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.15→3.18 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
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