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- PDB-5tiy: Schistosoma haematobium (Blood Fluke) Sulfotransferase/S-oxamniqu... -

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Basic information

Entry
Database: PDB / ID: 5tiy
TitleSchistosoma haematobium (Blood Fluke) Sulfotransferase/S-oxamniquine Complex
ComponentsSulfotransferase
KeywordsTRANSFERASE / SULFOTRANSFERASE / PARASITE / HELMINTH / OXAMNIQUINE
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 / Chem-OAQ / Nad dependent epimerase/dehydratase
Similarity search - Component
Biological speciesSchistosoma haematobium (invertebrata)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.76 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)29,9693
Polymers29,2631
Non-polymers7072
Water3,315184
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.535, 73.394, 139.018
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-417-

HOH

21A-582-

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-OAQ / {(2S)-7-nitro-2-[(propan-2-ylamino)methyl]-1,2,3,4-tetrahydroquinolin-6-yl}methanol / Oxamniquine


Mass: 279.335 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H21N3O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 2.29 Å3/Da / Density % sol: 46.28 %
Crystal growTemperature: 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)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Sep 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 1.76→1.86 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.714 / 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: 5TIV

5tiv


Resolution: 1.76→40.835 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.04
RfactorNum. reflection% reflection
Rfree0.2136 2000 7.45 %
Rwork0.1665 --
obs0.17 26838 99.06 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 32.9 Å2
Refinement stepCycle: LAST / Resolution: 1.76→40.835 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2011 0 47 184 2242
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042137
X-RAY DIFFRACTIONf_angle_d0.692908
X-RAY DIFFRACTIONf_dihedral_angle_d15.564813
X-RAY DIFFRACTIONf_chiral_restr0.052320
X-RAY DIFFRACTIONf_plane_restr0.004364
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.8040.26561450.21351794X-RAY DIFFRACTION100
1.804-1.85280.26341390.21441741X-RAY DIFFRACTION100
1.8528-1.90730.38161390.27081721X-RAY DIFFRACTION99
1.9073-1.96890.30421440.24681785X-RAY DIFFRACTION99
1.9689-2.03920.25281420.19391762X-RAY DIFFRACTION100
2.0392-2.12090.22271410.17581751X-RAY DIFFRACTION100
2.1209-2.21740.22281410.16241756X-RAY DIFFRACTION99
2.2174-2.33430.25071400.19151741X-RAY DIFFRACTION98
2.3343-2.48050.20791460.15411806X-RAY DIFFRACTION100
2.4805-2.6720.22261430.16981778X-RAY DIFFRACTION100
2.672-2.94080.20461430.17011781X-RAY DIFFRACTION99
2.9408-3.36620.20391440.17041786X-RAY DIFFRACTION99
3.3662-4.24040.17181450.14051800X-RAY DIFFRACTION99
4.2404-40.84550.20181480.14721836X-RAY DIFFRACTION96

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