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Yorodumi- PDB-7oza: Sulfated host glycan recognition by carbohydrate sulfatases of th... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7oza | ||||||
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Title | Sulfated host glycan recognition by carbohydrate sulfatases of the human gut microbiota (BT3796_S1_16) | ||||||
Components | Putative secreted sulfatase ydeN | ||||||
Keywords | HYDROLASE / Host glycans / sulfation / carbohydrate sulfatases / microbiota | ||||||
Function / homology | arylsulfatase activity / Sulfatases signature 1. / Sulfatase, conserved site / Sulfatase, N-terminal / Sulfatase / Alkaline-phosphatase-like, core domain superfamily / 4-O-sulfo-beta-D-galactopyranose / Putative secreted sulfatase ydeN Function and homology information | ||||||
Biological species | Bacteroides thetaiotaomicron VPI-5482 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 | 7oza.cif.gz | 401.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7oza.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7oza.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7oza_validation.pdf.gz | 663.7 KB | Display | wwPDB validaton report |
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Full document | 7oza_full_validation.pdf.gz | 666.5 KB | Display | |
Data in XML | 7oza_validation.xml.gz | 20.5 KB | Display | |
Data in CIF | 7oza_validation.cif.gz | 35.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oz/7oza ftp://data.pdbj.org/pub/pdb/validation_reports/oz/7oza | HTTPS FTP |
-Related structure data
Related structure data | 7oz8C 7oz9C 7ozcC 7ozeC 7p24C 7p26C 7an1S 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: GLU / End label comp-ID: GLU / Auth seq-ID: 31 - 516 / Label seq-ID: 35 - 520
NCS ensembles : (Details: Local NCS retraints between domains: 1 2) |
-Components
-Protein / Sugars , 2 types, 4 molecules AAACCC
#1: Protein | Mass: 58722.207 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria) Gene: BT_3796 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: Q8A171 #3: Sugar | |
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-Non-polymers , 6 types, 762 molecules
#2: Chemical | ChemComp-P6G / | ||||||||
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#4: Chemical | #5: Chemical | #6: Chemical | ChemComp-15P / | #7: Chemical | ChemComp-CL / | #8: Water | ChemComp-HOH / | |
-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: 2.26 Å3/Da / Density % sol: 45.53 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 20 mg/ml BT3796S1_16 with 10mM 4S-GalNAc was crystallised in 20 % PEG 6000, 0.2 M magnesium chloride and 0.1 MES pH 6.0. |
-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: 1.5→81.613 Å / Num. obs: 166081 / % possible obs: 99.7 % / Redundancy: 1.9 % / CC1/2: 0.996 / Net I/σ(I): 7 |
Reflection shell | Resolution: 1.5→1.53 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 8213 / CC1/2: 0.577 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7AN1 Resolution: 1.5→81.613 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.966 / WRfactor Rfree: 0.179 / WRfactor Rwork: 0.144 / SU B: 3.784 / SU ML: 0.058 / Average fsc free: 0.9439 / Average fsc work: 0.9534 / Cross valid method: FREE R-VALUE / ESU R: 0.071 / ESU R Free: 0.063 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: 17.155 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→81.613 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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