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- PDB-7an1: A single sulfatase is required for metabolism of colonic mucin O-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7an1 | ||||||
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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) | ||||||
![]() | Arylsulfatase | ||||||
![]() | 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 / Arylsulfatase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sofia de Jesus Vaz Luis, A. / Basle, A. / Martens, E.C. / Cartmell, A. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 217.7 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 765.1 KB | Display | ![]() |
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Full document | ![]() | 766.9 KB | Display | |
Data in XML | ![]() | 22.4 KB | Display | |
Data in CIF | ![]() | 34.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7allC ![]() 7anaC ![]() 7anbC ![]() 7oqdC ![]() 1fsuS 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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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.) ![]() Strain: ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482 / Gene: BT_1636 / Production host: ![]() ![]() |
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#2: Polysaccharide | beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#3: Chemical | ChemComp-CA / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.65 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: BT1636 (20 mg/ml) with 20 mM LacNAc crystallised in 40 % MPD and 0.2 M sodium cacodylate pH 6.5. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 8, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→51.709 Å / Num. obs: 107725 / % possible obs: 99.1 % / Redundancy: 7 % / CC1/2: 0.997 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 1.5→1.53 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 5296 / CC1/2: 0.656 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1FSU Resolution: 1.5→51.708 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.973 / WRfactor Rfree: 0.172 / WRfactor Rwork: 0.143 / SU B: 3.819 / SU ML: 0.057 / Average fsc free: 0.9433 / Average fsc work: 0.957 / Cross valid method: FREE R-VALUE / ESU R: 0.057 / ESU R Free: 0.053 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: 24.081 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→51.708 Å
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Refine LS restraints |
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LS refinement shell |
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