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- PDB-7oz9: Sulfated host glycan recognition by carbohydrate sulfatases of th... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7oz9 | ||||||
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Title | Sulfated host glycan recognition by carbohydrate sulfatases of the human gut microbiota (BT3057-S1_16) | ||||||
![]() | N-acetylgalactosamine-6-sulfatase![]() | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cartmell, A. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 216.7 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7oz8C ![]() 7ozaC ![]() 7ozcC ![]() 7ozeC ![]() 7p24C ![]() 7p26C ![]() 7an1S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | ![]() Mass: 57028.387 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482 / Gene: BT_3057 Production host: ![]() ![]() ![]() References: UniProt: Q8A397 #2: Sugar | #3: Sugar | #4: Chemical | #5: Water | ChemComp-HOH / | ![]() Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.83 % |
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Crystal grow![]() | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 35 mg/ml BT3057S1_16 with 10 mM 4S-GalNAc was crystallised in 20 % PEG 3350 and 0.2 M sodium nitrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
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![]() |
Reflection | Resolution: 1.907→65.52 Å / Num. obs: 85409 / % possible obs: 99.6 % / Redundancy: 1.9 % / CC1/2: 0.992 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 1.91→1.94 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4269 / CC1/2: 0.39 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 7AN1 Resolution: 1.907→65.52 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.932 / WRfactor Rfree: 0.223 / WRfactor Rwork: 0.183 / SU B: 3.73 / SU ML: 0.105 / Average fsc free: 0.9126 / Average fsc work: 0.9213 / Cross valid method: FREE R-VALUE / ESU R: 0.146 / ESU R Free: 0.137 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: 23.895 Å2
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Refinement step | Cycle: LAST / Resolution: 1.907→65.52 Å
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Refine LS restraints |
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LS refinement shell |
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