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Yorodumi- PDB-7oze: Sulfated host glycan recognition by carbohydrate sulfatases of th... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7oze | ||||||
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Title | Sulfated host glycan recognition by carbohydrate sulfatases of the human gut microbiota (BT1624-S1_15) | ||||||
Components | Putative secreted 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: 2.7 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 | 7oze.cif.gz | 389.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7oze.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7oze.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7oze_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 7oze_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 7oze_validation.xml.gz | 66.5 KB | Display | |
Data in CIF | 7oze_validation.cif.gz | 91.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oz/7oze ftp://data.pdbj.org/pub/pdb/validation_reports/oz/7oze | HTTPS FTP |
-Related structure data
Related structure data | 7oz8C 7oz9C 7ozaC 7ozcC 7p24C 7p26C 6s20S 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: LEU / End label comp-ID: LEU / Auth seq-ID: 29 - 515 / Label seq-ID: 27 - 513
NCS ensembles :
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-Components
#1: Protein | Mass: 56125.184 Da / Num. of mol.: 4 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_1624 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q8A7A1 #2: Sugar | ChemComp-G6S / #3: Chemical | ChemComp-CA / #4: Water | ChemComp-HOH / | 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: 2.32 Å3/Da / Density % sol: 47.01 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 20 mg/ml BT1624-S1_15 with 10 mM 6S-GalNAc crystallised in 20 % PEG 6000, 0.2 M ammonium chloride and 0.1 M sodium acetate pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 18, 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: 2.7→50.54 Å / Num. obs: 56316 / % possible obs: 100 % / Redundancy: 3.7 % / CC1/2: 0.927 / Net I/σ(I): 3 |
Reflection shell | Resolution: 2.7→2.78 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4596 / CC1/2: 0.662 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6S20 Resolution: 2.7→50.5 Å / Cor.coef. Fo:Fc: 0.88 / Cor.coef. Fo:Fc free: 0.837 / SU B: 17.056 / SU ML: 0.34 / Cross valid method: FREE R-VALUE / ESU R Free: 0.387 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: 16.837 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→50.5 Å
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Refine LS restraints |
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