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Yorodumi- PDB-7sno: Structure of Bacple_01701(H214N), a 6-O-galactose porphyran sulfatase -
+Open data
-Basic information
Entry | Database: PDB / ID: 7sno | ||||||
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Title | Structure of Bacple_01701(H214N), a 6-O-galactose porphyran sulfatase | ||||||
Components | Arylsulfatase | ||||||
Keywords | HYDROLASE / 6-O-galactose porphyran sulfatase | ||||||
Function / homology | Function and homology information Hydrolases; Acting on ester bonds; Sulfuric-ester hydrolases / sulfuric ester hydrolase activity Similarity search - Function | ||||||
Biological species | Phocaeicola plebeius DSM 17135 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Ulaganathan, T. / Cygler, M. | ||||||
Funding support | Canada, 1items
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Citation | Journal: Biorxiv / Year: 2023 Title: The porphyran degradation system of the human gut microbiota is complete, phylogenetically diverse and geographically structured across Asian populations Authors: Mathieu, S. / Touvrey, M. / Poulet, L. / Drouillard, S. / Ulaganathan, T.S. / Segurel, L. / Cygler, M. / Helbert, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7sno.cif.gz | 231.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7sno.ent.gz | 182.9 KB | Display | PDB format |
PDBx/mmJSON format | 7sno.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7sno_validation.pdf.gz | 814.1 KB | Display | wwPDB validaton report |
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Full document | 7sno_full_validation.pdf.gz | 821.8 KB | Display | |
Data in XML | 7sno_validation.xml.gz | 23.9 KB | Display | |
Data in CIF | 7sno_validation.cif.gz | 33.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sn/7sno ftp://data.pdbj.org/pub/pdb/validation_reports/sn/7sno | HTTPS FTP |
-Related structure data
Related structure data | 7snjSC 7snkC 8ep4C 8ew1C 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 / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 62621.336 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Phocaeicola plebeius DSM 17135 (bacteria) Gene: BACPLE_01701 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: B5CYA4, Hydrolases; Acting on ester bonds; Sulfuric-ester hydrolases |
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#2: Polysaccharide | 6-O-sulfo-alpha-L-galactopyranose-(1-3)-beta-D-galactopyranose-(1-4)-6-O-sulfo-alpha-L- ...6-O-sulfo-alpha-L-galactopyranose-(1-3)-beta-D-galactopyranose-(1-4)-6-O-sulfo-alpha-L-galactopyranose-(1-3)-beta-D-galactopyranose Type: oligosaccharide / Mass: 826.704 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source |
-Non-polymers , 6 types, 237 molecules
#3: Chemical | #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-PG4 / | #6: Chemical | ChemComp-PGE / | #7: Chemical | ChemComp-NA / | #8: Water | ChemComp-HOH / | |
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-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: 2.54 Å3/Da / Density % sol: 51.51 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 40% PEG 400, 100mM Sodium Citrate pH 5.5, 30% MPD |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 16, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 37128 / % possible obs: 100 % / Redundancy: 10.1 % / CC1/2: 0.99 / Net I/σ(I): 10.24 |
Reflection shell | Resolution: 2.1→2.22 Å / Mean I/σ(I) obs: 1.38 / Num. unique obs: 57365 / CC1/2: 0.71 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7SNJ Resolution: 2.1→44.66 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.79 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→44.66 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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