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Yorodumi- PDB-7all: A single sulfatase is required for metabolism of colonic mucin O-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7all | ||||||
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Title | A single sulfatase is required for metabolism of colonic mucin O-glycans and intestinal colonization by a symbiotic human gut bacterium (BT4683-S1_4) | ||||||
Components | Arylsulfatase | ||||||
Keywords | HYDROLASE / Carbohydrate sulfatase / Mucin / Microbiome / Bacteroides | ||||||
Function / homology | arylsulfatase activity / Sulfatases signature 2. / Sulfatase, conserved site / Sulfatase, N-terminal / Sulfatase / Alkaline-phosphatase-like, core domain superfamily / N-acetyl-alpha-lactosamine / IODIDE ION / Arylsulfatase Function and homology information | ||||||
Biological species | Bacteroides thetaiotaomicron (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å | ||||||
Authors | Sofia de Jesus Vaz Luis, A. / Martens, E.C. / Basle, A. / Cartmell, A. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Nature / Year: 2021 Title: A single sulfatase is required to access colonic mucin by a gut bacterium. Authors: Luis, A.S. / Jin, C. / Pereira, G.V. / Glowacki, R.W.P. / Gugel, S.R. / Singh, S. / Byrne, D.P. / Pudlo, N.A. / London, J.A. / Basle, A. / Reihill, M. / Oscarson, S. / Eyers, P.A. / Czjzek, ...Authors: Luis, A.S. / Jin, C. / Pereira, G.V. / Glowacki, R.W.P. / Gugel, S.R. / Singh, S. / Byrne, D.P. / Pudlo, N.A. / London, J.A. / Basle, A. / Reihill, M. / Oscarson, S. / Eyers, P.A. / Czjzek, M. / Michel, G. / Barbeyron, T. / Yates, E.A. / Hansson, G.C. / Karlsson, N.G. / Cartmell, A. / Martens, E.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7all.cif.gz | 129.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7all.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7all.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7all_validation.pdf.gz | 760.1 KB | Display | wwPDB validaton report |
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Full document | 7all_full_validation.pdf.gz | 760.1 KB | Display | |
Data in XML | 7all_validation.xml.gz | 21.6 KB | Display | |
Data in CIF | 7all_validation.cif.gz | 32.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/al/7all ftp://data.pdbj.org/pub/pdb/validation_reports/al/7all | HTTPS FTP |
-Related structure data
Related structure data | 7an1C 7anaC 7anbC 7oqdC 1hdhS 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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Unit cell |
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-Components
#1: Protein | Mass: 59468.293 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482) (bacteria) Strain: ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482 / Gene: BT_4683 / Production host: Escherichia coli (E. coli) / References: UniProt: Q89YP8 | ||||
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#2: Polysaccharide | beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose | ||||
#3: Chemical | ChemComp-CA / | ||||
#4: Chemical | ChemComp-IOD / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.65 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 20 % PEG 3350, 0.2 M sodium iodide and BTP pH 8.5 25mg/ml |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.98 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 15, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.63→66.585 Å / Num. obs: 62376 / % possible obs: 99.9 % / Redundancy: 1.9 % / CC1/2: 0.999 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 1.63→1.66 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 3024 / CC1/2: 0.795 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1HDH Resolution: 1.63→66.585 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.954 / WRfactor Rfree: 0.196 / WRfactor Rwork: 0.17 / SU B: 2.437 / SU ML: 0.078 / Average fsc free: 0.8918 / Average fsc work: 0.8974 / Cross valid method: FREE R-VALUE / ESU R: 0.094 / ESU R Free: 0.09 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: 22.124 Å2
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Refinement step | Cycle: LAST / Resolution: 1.63→66.585 Å
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Refine LS restraints |
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LS refinement shell |
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