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Yorodumi- PDB-7p24: Sulfated host glycan recognition by carbohydrate sulfatases of th... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7p24 | ||||||
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Title | Sulfated host glycan recognition by carbohydrate sulfatases of the human gut microbiota (BT3177_S1_11) | ||||||
Components | Mucin-desulfating sulfatase | ||||||
Keywords | HYDROLASE / Host glycans / sulfation / carbohydrate sulfatases / microbiota | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bacteroides thetaiotaomicron (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.97 Å | ||||||
Authors | Cartmell, A. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Nat.Chem.Biol. / Year: 2022 Title: Sulfated glycan recognition by carbohydrate sulfatases of the human gut microbiota. Authors: Luis, A.S. / Basle, A. / Byrne, D.P. / Wright, G.S.A. / London, J.A. / Jin, C. / Karlsson, N.G. / Hansson, G.C. / Eyers, P.A. / Czjzek, M. / Barbeyron, T. / Yates, E.A. / Martens, E.C. / Cartmell, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7p24.cif.gz | 241.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7p24.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7p24.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7p24_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7p24_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7p24_validation.xml.gz | 24.7 KB | Display | |
Data in CIF | 7p24_validation.cif.gz | 39.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p2/7p24 ftp://data.pdbj.org/pub/pdb/validation_reports/p2/7p24 | HTTPS FTP |
-Related structure data
Related structure data | 7oz8C 7oz9C 7ozaC 7ozcC 7ozeC 7p26C 5g2vS S: Starting model for refinement 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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Unit cell |
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-Components
#1: Protein | Mass: 61037.914 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_3177 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q8A2X8 |
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#2: Sugar | ChemComp-NGS / |
#3: Sugar | ChemComp-NGY / |
#4: Chemical | ChemComp-CA / |
#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: 2.3 Å3/Da / Density % sol: 46.48 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 20 mg/ml BT3177S1_11 with 10 mM 6S-GlcNAc crystallised in 50 % precipitant mix 1 (40% v/v PEG 500, MME; 20 % w/v PEG 20000), 0.1 M carboxcylic acids (0.2M Sodium formate; 0.2M Ammonium ...Details: 20 mg/ml BT3177S1_11 with 10 mM 6S-GlcNAc crystallised in 50 % precipitant mix 1 (40% v/v PEG 500, MME; 20 % w/v PEG 20000), 0.1 M carboxcylic acids (0.2M Sodium formate; 0.2M Ammonium acetate; 0.2M Sodium citrate tribasic dihydrate; 0.2M Sodium potassium tartrate tetrahydrate; 0.2M Sodium oxamate) and 0.1 M buffer system 3 pH 8.5 (Tris (base); BICINE). |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 18, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9159 Å / Relative weight: 1 |
Reflection | Resolution: 0.97→35.856 Å / Num. obs: 298423 / % possible obs: 91.9 % / Redundancy: 1.9 % / CC1/2: 0.996 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 0.97→0.99 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 12666 / CC1/2: 0.596 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5G2V Resolution: 0.97→35.856 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.981 / WRfactor Rfree: 0.141 / WRfactor Rwork: 0.126 / SU B: 0.705 / SU ML: 0.016 / Average fsc free: 0.9606 / Average fsc work: 0.9634 / Cross valid method: FREE R-VALUE / ESU R: 0.018 / ESU R Free: 0.019 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: 11.374 Å2
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Refinement step | Cycle: LAST / Resolution: 0.97→35.856 Å
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Refine LS restraints |
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LS refinement shell |
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