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- PDB-8e5q: Schistosoma mansoni (Blood Fluke) Sulfotransferase/CIDD-0150303 C... -

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Basic information

Entry
Database: PDB / ID: 8e5q
TitleSchistosoma mansoni (Blood Fluke) Sulfotransferase/CIDD-0150303 Complex
ComponentsSulfotransferase oxamniquine resistance protein
KeywordsTRANSFERASE / SULFOTRANSFERASE / PARASITE / DRUG RESISTANCE
Function / homologySulfotransferase, S. mansonii-type / Sulfotransferase domain / transferase activity / P-loop containing nucleoside triphosphate hydrolase / ADENOSINE-3'-5'-DIPHOSPHATE / Chem-UMI / Sulfotransferase oxamniquine resistance protein
Function and homology information
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 Å
AuthorsTaylor, A.B. / Alwan, S.N.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI115691 United States
CitationJournal: Plos Pathog. / Year: 2023
Title: Oxamniquine derivatives overcome Praziquantel treatment limitations for Schistosomiasis.
Authors: Alwan, S.N. / Taylor, A.B. / Rhodes, J. / Tidwell, M. / McHardy, S.F. / LoVerde, P.T.
History
DepositionAug 22, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sulfotransferase oxamniquine resistance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9443
Polymers29,9771
Non-polymers9682
Water3,855214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.769, 58.486, 90.528
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Sulfotransferase oxamniquine resistance protein


Mass: 29976.562 Da / Num. of mol.: 1
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(DE3) (bacteria) / Strain (production host): pLysS / References: UniProt: G4VLE5
#2: Chemical ChemComp-UMI / [2-(dihydroxyamino)-4-({[(3R)-1-[(1H-indol-3-yl)methyl]-3-{[3-(trifluoromethyl)phenyl]methyl}pyrrolidin-3-yl]methyl}amino)phenyl]methanol


Mass: 540.577 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H31F3N4O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-A3P / ADENOSINE-3'-5'-DIPHOSPHATE


Type: RNA linking / Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.07 Å3/Da / Density % sol: 40.44 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: Molecular Dimensions Morpheus condition 1-1: 30% Precipitant Mix 1 (30% PEG 500 MME; 20% PEG 20000), 0.06 M Divalents Mix (0.3 M magnesium chloride hexahydrate, 0.3 M calcium chloride ...Details: Molecular Dimensions Morpheus condition 1-1: 30% Precipitant Mix 1 (30% PEG 500 MME; 20% PEG 20000), 0.06 M Divalents Mix (0.3 M magnesium chloride hexahydrate, 0.3 M calcium chloride dihydrate), 0.1 M Buffer System 1 pH 6.5 (1.0 M imidazole:MES)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.33→90.53 Å / Num. obs: 57572 / % possible obs: 99.6 % / Redundancy: 6.2 % / Biso Wilson estimate: 18.28 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.025 / Net I/σ(I): 13.6
Reflection shellResolution: 1.33→1.4 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 1 / Num. unique obs: 8186 / CC1/2: 0.557 / Rpim(I) all: 0.785 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BDR

6bdr


Resolution: 1.33→49.13 Å / SU ML: 0.1692 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.8009
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2172 1999 3.48 %
Rwork0.181 55488 -
obs0.1823 57487 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.36 Å2
Refinement stepCycle: LAST / Resolution: 1.33→49.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1977 0 66 214 2257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00832139
X-RAY DIFFRACTIONf_angle_d1.04882917
X-RAY DIFFRACTIONf_chiral_restr0.0789322
X-RAY DIFFRACTIONf_plane_restr0.0072361
X-RAY DIFFRACTIONf_dihedral_angle_d16.5726794
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.33-1.360.31161370.29993816X-RAY DIFFRACTION97.44
1.36-1.40.30831420.27443910X-RAY DIFFRACTION99.34
1.4-1.440.29651400.25173905X-RAY DIFFRACTION99.61
1.44-1.490.25081420.21733915X-RAY DIFFRACTION99.63
1.49-1.540.27641410.19243927X-RAY DIFFRACTION99.51
1.54-1.60.22271410.18043937X-RAY DIFFRACTION99.68
1.6-1.680.23961410.18073934X-RAY DIFFRACTION99.66
1.68-1.760.23671430.18153957X-RAY DIFFRACTION99.93
1.76-1.870.23991430.17363968X-RAY DIFFRACTION99.88
1.87-2.020.22891440.16963977X-RAY DIFFRACTION99.85
2.02-2.220.22081420.17043968X-RAY DIFFRACTION99.66
2.22-2.540.22211460.184018X-RAY DIFFRACTION99.74
2.54-3.210.19741450.18584033X-RAY DIFFRACTION99.59
3.21-49.130.1981520.16954223X-RAY DIFFRACTION99.36

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