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Yorodumi- PDB-6b50: Schistosoma mansoni (Blood Fluke) Sulfotransferase/Oxamniquine Co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6b50 | ||||||
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Title | Schistosoma mansoni (Blood Fluke) Sulfotransferase/Oxamniquine Complex, T157S Mutant | ||||||
Components | Sulfotransferase oxamniquine resistance protein | ||||||
Keywords | TRANSFERASE / sulfotransferase / parasite / drug resistance | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Schistosoma mansoni (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 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 | 6b50.cif.gz | 72.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6b50.ent.gz | 50.4 KB | Display | PDB format |
PDBx/mmJSON format | 6b50.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6b50_validation.pdf.gz | 1000.5 KB | Display | wwPDB validaton report |
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Full document | 6b50_full_validation.pdf.gz | 1001.2 KB | Display | |
Data in XML | 6b50_validation.xml.gz | 12.8 KB | Display | |
Data in CIF | 6b50_validation.cif.gz | 17.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b5/6b50 ftp://data.pdbj.org/pub/pdb/validation_reports/b5/6b50 | HTTPS FTP |
-Related structure data
Related structure data | 6b4xC 6b4yC 6b4zC 6b51C 6b52C 6b53C 6b54C 5bykS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 29962.539 Da / Num. of mol.: 1 / Mutation: T157S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Gene: SULT-OR, Smp_089320 / Plasmid: pAG8H / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 pLysS References: UniProt: G4VLE5, 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: 2.48 Å3/Da / Density % sol: 50.41 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 1.0 M sodium citrate, 0.1 M sodium cacodylate, pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 6, 2014 |
Radiation | Monochromator: single crystal Si(220) side bounce / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→140.19 Å / Num. obs: 25205 / % possible obs: 99 % / Redundancy: 7 % / Biso Wilson estimate: 25.2 Å2 / Rpim(I) all: 0.046 / Rsym value: 0.103 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 1.87→1.97 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 2 / Num. unique obs: 3574 / Rpim(I) all: 0.442 / Rsym value: 1.042 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 5BYK Resolution: 1.87→53.816 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.5 / Phase error: 23.7
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.87→53.816 Å
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Refine LS restraints |
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LS refinement shell |
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