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- PDB-5tiv: Schistosoma haematobium (Blood Fluke) Sulfotransferase -

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Basic information

Entry
Database: PDB / ID: 5tiv
TitleSchistosoma haematobium (Blood Fluke) Sulfotransferase
ComponentsSulfotransferase
KeywordsTRANSFERASE / SULFOTRANSFERASE / PARASITE / HELMINTH
Function / homology
Function and homology information


Sulfotransferase, S. mansonii-type / Sulfotransferase domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-3'-5'-DIPHOSPHATE / Nad dependent epimerase/dehydratase
Similarity search - Component
Biological speciesSchistosoma haematobium (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 Å
AuthorsTaylor, A.B. / Hart, P.J.
CitationJournal: 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
DepositionOct 3, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2017Group: Database references
Revision 1.2Jul 19, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sulfotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8123
Polymers29,2631
Non-polymers5492
Water4,324240
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.595, 73.561, 139.624
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-469-

HOH

21A-638-

HOH

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Components

#1: Protein Sulfotransferase


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 / ADENOSINE-3'-5'-DIPHOSPHATE


Type: RNA linking / Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.7 %
Crystal growTemperature: 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; PEG 1000; PEG 3350)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.43→139.62 Å / Num. obs: 50294 / % possible obs: 99.7 % / Redundancy: 7 % / Biso Wilson estimate: 17.6 Å2 / Rsym value: 0.055 / Net I/σ(I): 18.3
Reflection shellResolution: 1.43→1.51 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.901 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MUA

4mua


Resolution: 1.43→36.479 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 17.41
RfactorNum. reflection% reflection
Rfree0.1906 1999 3.98 %
Rwork0.1591 --
obs0.1603 50234 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 23.5 Å2
Refinement stepCycle: LAST / Resolution: 1.43→36.479 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2011 0 35 240 2286
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082164
X-RAY DIFFRACTIONf_angle_d1.0032947
X-RAY DIFFRACTIONf_dihedral_angle_d13.255816
X-RAY DIFFRACTIONf_chiral_restr0.072324
X-RAY DIFFRACTIONf_plane_restr0.006370
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.43-1.46580.27871410.23613425X-RAY DIFFRACTION100
1.4658-1.50540.25211420.20553425X-RAY DIFFRACTION100
1.5054-1.54970.21261420.1853416X-RAY DIFFRACTION100
1.5497-1.59970.23221410.16023405X-RAY DIFFRACTION100
1.5997-1.65690.21051410.16213389X-RAY DIFFRACTION100
1.6569-1.72320.22021430.1563447X-RAY DIFFRACTION100
1.7232-1.80170.20931430.15313464X-RAY DIFFRACTION100
1.8017-1.89660.19861420.15023428X-RAY DIFFRACTION100
1.8966-2.01550.20311420.15893419X-RAY DIFFRACTION100
2.0155-2.17110.1811430.14943466X-RAY DIFFRACTION100
2.1711-2.38950.18041440.15113461X-RAY DIFFRACTION100
2.3895-2.73520.18771440.16283463X-RAY DIFFRACTION100
2.7352-3.44560.19181450.16423509X-RAY DIFFRACTION100
3.4456-36.49060.16851460.15123518X-RAY DIFFRACTION96

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