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- PDB-7v6i: Crystal structure of lacto-N-biosidase BsaX from Bifidobacterium ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7v6i | |||||||||
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Title | Crystal structure of lacto-N-biosidase BsaX from Bifidobacterium saguini, lacto-N-biose complex | |||||||||
![]() | Lacto-N-biosidase | |||||||||
![]() | HYDROLASE / Glycoside hydrolase / lacto-N-biosidase / lacto-N-biose complex | |||||||||
Function / homology | Parallel beta-helix repeat / Parallel beta-helix repeats / Pectin lyase fold/virulence factor / membrane => GO:0016020 / Immunoglobulin-like fold / Uncharacterized protein![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Yamada, C. / Fushinobu, S. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structures of glycoside hydrolase family 136 lacto-N-biosidases from monkey gut- and human adult gut bacteria. Authors: Yamada, C. / Katayama, T. / Fushinobu, S. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 133.1 KB | Display | ![]() |
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PDB format | ![]() | 98.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 785.2 KB | Display | ![]() |
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Full document | ![]() | 790.4 KB | Display | |
Data in XML | ![]() | 23.2 KB | Display | |
Data in CIF | ![]() | 32.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7v6mC ![]() 5gqfS 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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Unit cell |
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Components
#1: Protein | Mass: 68053.273 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: BISA_2023 / Plasmid: pET23b / Production host: ![]() ![]() |
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#2: Polysaccharide | beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.02 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.5M ammonium sulfate, 0.1M sodium acetate (pH 4.6), 30% (w/v) PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 22, 2018 |
Radiation | Monochromator: Numerical link type Si(111) double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.51→49.08 Å / Num. obs: 20374 / % possible obs: 100 % / Redundancy: 10 % / Biso Wilson estimate: 15.86 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.184 / Rpim(I) all: 0.061 / Rrim(I) all: 0.194 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 2.51→2.61 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.695 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 2262 / CC1/2: 0.913 / Rpim(I) all: 0.228 / Rrim(I) all: 0.732 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5GQF Resolution: 2.51→49.08 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.897 / SU B: 8.99 / SU ML: 0.199 / Cross valid method: THROUGHOUT / ESU R: 1.391 / ESU R Free: 0.287 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.598 Å2
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Refinement step | Cycle: 1 / Resolution: 2.51→49.08 Å
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Refine LS restraints |
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