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Yorodumi- PDB-7p26: Sulfated host glycan recognition by carbohydrate sulfatases of th... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7p26 | ||||||
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Title | Sulfated host glycan recognition by carbohydrate sulfatases of the human gut microbiota (BT4631_S1_15) | ||||||
Components | Putative arylsulfatase | ||||||
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: 1.35 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 | 7p26.cif.gz | 232.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7p26.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7p26.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7p26_validation.pdf.gz | 788.1 KB | Display | wwPDB validaton report |
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Full document | 7p26_full_validation.pdf.gz | 789 KB | Display | |
Data in XML | 7p26_validation.xml.gz | 24.9 KB | Display | |
Data in CIF | 7p26_validation.cif.gz | 39.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p2/7p26 ftp://data.pdbj.org/pub/pdb/validation_reports/p2/7p26 | HTTPS FTP |
-Related structure data
Related structure data | 7oz8C 7oz9C 7ozaC 7ozcC 7ozeSC 7p24C 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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules AAA
#1: Protein | Mass: 57253.625 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_4631 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q89YV0 |
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-Non-polymers , 5 types, 604 molecules
#2: Chemical | ChemComp-15P / | ||
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#3: Chemical | ChemComp-P4K / | ||
#4: Chemical | ChemComp-CA / | ||
#5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
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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: 2.81 Å3/Da / Density % sol: 56.19 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 80 mg/ml BT4631 with 10 mM 6S-Gal was crystallised in 20 % PEG 10K and 0.1 M Bicine pH8.5. |
-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: 0.9786 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 12, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→109.57 Å / Num. obs: 140145 / % possible obs: 98.8 % / Redundancy: 12.4 % / CC1/2: 0.999 / Net I/σ(I): 25.4 |
Reflection shell | Resolution: 1.35→1.37 Å / Mean I/σ(I) obs: 4.5 / Num. unique obs: 6050 / CC1/2: 0.955 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7OZE Resolution: 1.35→80.274 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.971 / WRfactor Rfree: 0.139 / WRfactor Rwork: 0.123 / SU B: 1.011 / SU ML: 0.019 / Average fsc free: 0.9798 / Average fsc work: 0.9824 / Cross valid method: FREE R-VALUE / ESU R: 0.039 / ESU R Free: 0.036 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: 14.129 Å2
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Refinement step | Cycle: LAST / Resolution: 1.35→80.274 Å
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Refine LS restraints |
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LS refinement shell |
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