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Yorodumi- PDB-6b52: Schistosoma haematobium (Blood Fluke) Sulfotransferase/Oxamniquin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6b52 | ||||||
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Title | Schistosoma haematobium (Blood Fluke) Sulfotransferase/Oxamniquine Complex, Y54F Mutant | ||||||
Components | Sulfotransferase | ||||||
Keywords | TRANSFERASE / sulfotransferase / parasite / helminth | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Schistosoma haematobium (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Taylor, A.B. | ||||||
Funding support | United States, 1items
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Citation | Journal: Int.J.Parasitol. / Year: 2020 Title: Why does oxamniquine kill Schistosoma mansoni and not S. haematobium and S. japonicum? Authors: Rugel, A.R. / Guzman, M.A. / Taylor, A.B. / Chevalier, F.D. / Tarpley, R.S. / McHardy, S.F. / Cao, X. / Holloway, S.P. / Anderson, T.J.C. / Hart, P.J. / LoVerde, P.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6b52.cif.gz | 71.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6b52.ent.gz | 50.1 KB | Display | PDB format |
PDBx/mmJSON format | 6b52.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6b52_validation.pdf.gz | 1015.2 KB | Display | wwPDB validaton report |
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Full document | 6b52_full_validation.pdf.gz | 1023.2 KB | Display | |
Data in XML | 6b52_validation.xml.gz | 12.8 KB | Display | |
Data in CIF | 6b52_validation.cif.gz | 18.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b5/6b52 ftp://data.pdbj.org/pub/pdb/validation_reports/b5/6b52 | HTTPS FTP |
-Related structure data
Related structure data | 6b4xC 6b4yC 6b4zC 6b50C 6b51C 6b53C 6b54C 5tivS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-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
#1: Protein | Mass: 29246.564 Da / Num. of mol.: 1 / Mutation: Y54F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schistosoma haematobium (invertebrata) / Gene: MS3_07706 / Plasmid: pAG8H / Production host: Escherichia coli BL21 (bacteria) References: UniProt: A0A094ZWQ2, Transferases; Transferring sulfur-containing groups; Sulfotransferases |
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#2: Chemical | ChemComp-A3P / |
#3: Chemical | ChemComp-OAQ / {( |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.08 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 0.06 M (magnesium chloride, calcium chloride), 0.1 M (Tris, Bicine), pH 8.5, 37.5% (MPD, PEG1000, PEG3350) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9789 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 5, 2014 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→70.15 Å / Num. obs: 25230 / % possible obs: 99.9 % / Redundancy: 7 % / Biso Wilson estimate: 31.7 Å2 / Rpim(I) all: 0.021 / Rsym value: 0.049 / Net I/σ(I): 20 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 4.5 / Num. unique obs: 3611 / Rpim(I) all: 0.166 / Rsym value: 0.374 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 5TIV Resolution: 1.8→70.154 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.41 / Phase error: 29.33 / 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: 1.8→70.154 Å
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Refine LS restraints |
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LS refinement shell |
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