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Yorodumi- PDB-7ana: A single sulfatase is required for metabolism of colonic mucin O-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ana | ||||||
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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 (BT1622-S1_20) | ||||||
Components | N-acetylgalactosamine-6-sulfatase | ||||||
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 / 2-acetamido-2-deoxy-alpha-D-galactopyranose / 2-acetamido-2-deoxy-beta-D-galactopyranose / N-acetylgalactosamine-6-sulfatase Function and homology information | ||||||
Biological species | Bacteroides thetaiotaomicron VPI-5482 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / 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 | 7ana.cif.gz | 372.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ana.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7ana.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ana_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7ana_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7ana_validation.xml.gz | 34.8 KB | Display | |
Data in CIF | 7ana_validation.cif.gz | 48.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/an/7ana ftp://data.pdbj.org/pub/pdb/validation_reports/an/7ana | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: PHE / End label comp-ID: PHE / Auth seq-ID: 26 - 500 / Label seq-ID: 29 - 503
NCS ensembles : (Details: Local NCS retraints between domains: 1 2) |
-Components
-Protein , 1 types, 2 molecules AAABBB
#1: Protein | Mass: 56825.832 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria) Gene: BT_1622 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8A7A3 |
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-Sugars , 2 types, 3 molecules
#2: Sugar | #4: Sugar | ChemComp-NGA / | |
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-Non-polymers , 3 types, 170 molecules
#3: Chemical | #5: Chemical | ChemComp-EDO / | #6: Water | ChemComp-HOH / | |
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-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: 2.98 Å3/Da / Density % sol: 58.66 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 20 % PEG 3350, 0.2 M sodium citrate 30 mg/ml BT1622 with 100 mM GalNAc. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 2, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→70.221 Å / Num. obs: 62514 / % possible obs: 100 % / Redundancy: 1.9 % / CC1/2: 0.999 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 2.3→2.36 Å / Num. unique obs: 4532 / CC1/2: 0.84 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: BT1624 Resolution: 2.3→70.221 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.94 / WRfactor Rfree: 0.227 / WRfactor Rwork: 0.208 / SU B: 14.473 / SU ML: 0.167 / Average fsc free: 0.9133 / Average fsc work: 0.9177 / Cross valid method: FREE R-VALUE / ESU R: 0.26 / ESU R Free: 0.199 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: 58.047 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→70.221 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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