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Yorodumi- PDB-7oqd: A single sulfatase is required for metabolism of colonic mucin O-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7oqd | ||||||
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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 (BT1636-S1_20) | ||||||
Components | Arylsulfatase | ||||||
Keywords | HYDROLASE / Carbohydrate sulfatase / mucin / microbiome / bacteroides | ||||||
Function / homology | Sulfatases signature 1. / Sulfatase, conserved site / sulfuric ester hydrolase activity / Sulfatase, N-terminal / Sulfatase / Alkaline-phosphatase-like, core domain superfamily / 3-O-sulfo-beta-D-galactopyranose / Arylsulfatase Function and homology information | ||||||
Biological species | Bacteroides thetaiotaomicron (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Sofia de Jesus Vaz Luis, A. / Basle, A. / Martens, E.C. / 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 | 7oqd.cif.gz | 120.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7oqd.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7oqd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oq/7oqd ftp://data.pdbj.org/pub/pdb/validation_reports/oq/7oqd | HTTPS FTP |
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-Related structure data
Related structure data | 7allC 7an1SC 7anaC 7anbC 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: 58029.316 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_1636 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q8A789 |
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#2: Sugar | ChemComp-SGA / |
#3: Chemical | ChemComp-CA / |
#4: 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: 2.37 Å3/Da / Density % sol: 48.05 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 40 % MPD, 0.1 M sodium cacodylate with a protein concentration of 20 mg/ml and the ligand concentration (3S-LewisA) of 20 mM. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: LIQUID ANODE / Type: BRUKER METALJET / Wavelength: 1.34 Å |
Detector | Type: Bruker PHOTON III / Detector: PIXEL / Date: May 29, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.34 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→18.523 Å / Num. obs: 24826 / % possible obs: 98.8 % / Redundancy: 4 % / CC1/2: 0.968 / Net I/σ(I): 4.8 |
Reflection shell | Resolution: 2.3→2.38 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2444 / CC1/2: 0.76 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7AN1 Resolution: 2.3→18.52 Å / Cor.coef. Fo:Fc: 0.886 / Cor.coef. Fo:Fc free: 0.837 / SU B: 10.917 / SU ML: 0.263 / Cross valid method: FREE R-VALUE / ESU R: 0.42 / ESU R Free: 0.282 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: 19.149 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→18.52 Å
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Refine LS restraints |
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LS refinement shell |
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