[English] 日本語
Yorodumi- PDB-5tiy: Schistosoma haematobium (Blood Fluke) Sulfotransferase/S-oxamniqu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5tiy | ||||||
---|---|---|---|---|---|---|---|
Title | Schistosoma haematobium (Blood Fluke) Sulfotransferase/S-oxamniquine Complex | ||||||
Components | Sulfotransferase | ||||||
Keywords | TRANSFERASE / SULFOTRANSFERASE / PARASITE / HELMINTH / OXAMNIQUINE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Schistosoma haematobium (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.76 Å | ||||||
Authors | Taylor, A.B. / Hart, P.J. | ||||||
Citation | Journal: J. Biol. Chem. / Year: 2017 Title: Structural and enzymatic insights into species-specific resistance to schistosome parasite drug therapy. Authors: Taylor, A.B. / Roberts, K.M. / Cao, X. / Clark, N.E. / Holloway, S.P. / Donati, E. / Polcaro, C.M. / Pica-Mattoccia, L. / Tarpley, R.S. / McHardy, S.F. / Cioli, D. / LoVerde, P.T. / ...Authors: Taylor, A.B. / Roberts, K.M. / Cao, X. / Clark, N.E. / Holloway, S.P. / Donati, E. / Polcaro, C.M. / Pica-Mattoccia, L. / Tarpley, R.S. / McHardy, S.F. / Cioli, D. / LoVerde, P.T. / Fitzpatrick, P.F. / Hart, P.J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5tiy.cif.gz | 124.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5tiy.ent.gz | 93.3 KB | Display | PDB format |
PDBx/mmJSON format | 5tiy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5tiy_validation.pdf.gz | 996.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5tiy_full_validation.pdf.gz | 1003.8 KB | Display | |
Data in XML | 5tiy_validation.xml.gz | 12.9 KB | Display | |
Data in CIF | 5tiy_validation.cif.gz | 18.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ti/5tiy ftp://data.pdbj.org/pub/pdb/validation_reports/ti/5tiy | HTTPS FTP |
-Related structure data
Related structure data | 5tivSC 5tiwC 5tixC 5tizC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 29262.564 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schistosoma haematobium (invertebrata) / Gene: MS3_07706 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 pLysS / References: UniProt: A0A094ZWQ2 |
---|---|
#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 |
---|
-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.28 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.06 M (magnesium chloride; calcium chloride), 0.1 M (Tris; bicine) pH 8.5, 37.5% (MPD; PEG 1000; PEG 3350) |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Sep 15, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→46.34 Å / Num. obs: 26953 / % possible obs: 99.6 % / Redundancy: 4.6 % / Biso Wilson estimate: 27.3 Å2 / Rsym value: 0.055 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 1.76→1.86 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.714 / Mean I/σ(I) obs: 2 / % possible all: 100 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5TIV Resolution: 1.76→40.835 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.04
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.9 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.76→40.835 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|