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Yorodumi- PDB-8axs: Sialidases and Fucosidases of Akkermansia muciniphila are key for... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8axs | |||||||||
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Title | Sialidases and Fucosidases of Akkermansia muciniphila are key for rapid growth on colonic mucin and nutrient sharing amongst mucin-associated human gut microbiota | |||||||||
Components | (Exo-alpha-sialidase) x 2 | |||||||||
Keywords | HYDROLASE / Sialidase / Neuraminidase | |||||||||
Function / homology | BNR repeat-like domain / Sialidase / Sialidase superfamily / 2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID / IMIDAZOLE / N-acetyl-beta-neuraminic acid / Exo-alpha-sialidase Function and homology information | |||||||||
Biological species | Akkermansia muciniphila (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | |||||||||
Authors | Sakanaka, H. / Nielsen, T.S. / Pichler, M.J. / Nordberg Karlsson, E. / Abou Hachem, M. / Morth, J.P. | |||||||||
Funding support | Denmark, Iraq, 2items
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Citation | Journal: Nat Commun / Year: 2023 Title: Sialidases and fucosidases of Akkermansia muciniphila are crucial for growth on mucin and nutrient sharing with mucus-associated gut bacteria. Authors: Shuoker, B. / Pichler, M.J. / Jin, C. / Sakanaka, H. / Wu, H. / Gascuena, A.M. / Liu, J. / Nielsen, T.S. / Holgersson, J. / Nordberg Karlsson, E. / Juge, N. / Meier, S. / Morth, J.P. / ...Authors: Shuoker, B. / Pichler, M.J. / Jin, C. / Sakanaka, H. / Wu, H. / Gascuena, A.M. / Liu, J. / Nielsen, T.S. / Holgersson, J. / Nordberg Karlsson, E. / Juge, N. / Meier, S. / Morth, J.P. / Karlsson, N.G. / Abou Hachem, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8axs.cif.gz | 588.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8axs.ent.gz | 388.6 KB | Display | PDB format |
PDBx/mmJSON format | 8axs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8axs_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 8axs_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 8axs_validation.xml.gz | 56.2 KB | Display | |
Data in CIF | 8axs_validation.cif.gz | 88.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ax/8axs ftp://data.pdbj.org/pub/pdb/validation_reports/ax/8axs | HTTPS FTP |
-Related structure data
Related structure data | 8axiC 8axtC 8ayrC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 64362.559 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Akkermansia muciniphila (bacteria) / Gene: HXS70_08015 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7G6DVF6 |
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#2: Protein | Mass: 64278.441 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Akkermansia muciniphila (bacteria) / Gene: HXS70_08015 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7G6DVF6 |
-Sugars , 2 types, 4 molecules
#3: Sugar | #9: Sugar | ChemComp-DAN / | |
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-Non-polymers , 6 types, 1430 molecules
#4: Chemical | ChemComp-IMD / | ||||||||
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#5: Chemical | ChemComp-EDO / #6: Chemical | ChemComp-CL / #7: Chemical | #8: Chemical | ChemComp-SO4 / | #10: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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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: 2.48 Å3/Da / Density % sol: 50.35 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 5.5 / Details: 18% PEG 3350,0.1 M BIS TRIS, 0.2 M MgCl2 / PH range: 5 - 6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.976254 Å |
Detector | Type: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: May 5, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976254 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→59.135 Å / Num. obs: 308465 / % possible obs: 99.7 % / Redundancy: 5.5 % / Biso Wilson estimate: 16.71 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.069 / Rsym value: 0.066 / Net I/σ(I): 12.14 |
Reflection shell | Resolution: 1.3→1.33 Å / Redundancy: 4 % / Mean I/σ(I) obs: 0.8 / Num. unique obs: 22149 / CC1/2: 0.44 / Rrim(I) all: 1 / Rsym value: 1.7 / % possible all: 97.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: alphafold model Resolution: 1.3→50.25 Å / SU ML: 0.1984 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.893 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.41 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.3→50.25 Å
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Refine LS restraints |
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LS refinement shell |
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