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- PDB-7kv7: Surface glycan-binding protein B from Bacteroides fluxus in compl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7kv7 | ||||||
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Title | Surface glycan-binding protein B from Bacteroides fluxus in complex with laminaritriose | ||||||
![]() | PKD domain protein | ||||||
![]() | 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 Similarity search - Domain/homology | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tamura, K. / Brumer, H. / Van Petegem, F. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 203.4 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 27.1 KB | Display | |
Data in CIF | ![]() | 42.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7kv1C ![]() 7kv2C ![]() 7kv3C ![]() 7kv4C ![]() 7kv5C ![]() 7kv6C ![]() 7kwbC ![]() 7kwcC 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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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.) ![]() Gene: HMPREF9446_00613 / Production host: ![]() ![]() |
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-Sugars , 2 types, 4 molecules ![](data/chem/img/BGC.gif)
#2: Polysaccharide | beta-D-glucopyranose-(1-3)-beta-D-glucopyranose |
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#4: Sugar |
-Non-polymers , 5 types, 650 molecules ![](data/chem/img/LYS.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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