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- PDB-8e5r: Schistosoma mansoni (Blood Fluke) Sulfotransferase/CIDD-0150610 C... -

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Basic information

Entry
Database: PDB / ID: 8e5r
TitleSchistosoma mansoni (Blood Fluke) Sulfotransferase/CIDD-0150610 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-ULX / Sulfotransferase oxamniquine resistance protein
Function and homology information
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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 1.1Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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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)31,0483
Polymers30,0811
Non-polymers9682
Water3,999222
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)140.889, 39.668, 53.839
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-713-

HOH

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Components

#1: Protein Sulfotransferase oxamniquine resistance protein


Mass: 30080.547 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-ULX / [4-({[(3R)-1-[(1H-indol-3-yl)methyl]-3-{[4-(trifluoromethyl)phenyl]methyl}pyrrolidin-3-yl]methyl}amino)-3-nitrophenyl]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.: 222 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.51 Å3/Da / Density % sol: 50.98 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: MCSG-3 condition A1: 20% PEG 8000, 0.1 M HEPES:NaOH pH 7.5

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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: Sep 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.4→140.89 Å / Num. obs: 59038 / % possible obs: 97.6 % / Redundancy: 6 % / Biso Wilson estimate: 23.74 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.022 / Net I/σ(I): 13.3
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 1 / Num. unique obs: 8718 / CC1/2: 0.515 / Rpim(I) all: 0.817 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BDR

6bdr


Resolution: 1.4→53.84 Å / SU ML: 0.1726 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.9043
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1991 2000 3.39 %
Rwork0.169 56966 -
obs0.17 58966 97.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.47 Å2
Refinement stepCycle: LAST / Resolution: 1.4→53.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2129 0 39 222 2390
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01292257
X-RAY DIFFRACTIONf_angle_d1.24693081
X-RAY DIFFRACTIONf_chiral_restr0.0836344
X-RAY DIFFRACTIONf_plane_restr0.0064380
X-RAY DIFFRACTIONf_dihedral_angle_d15.0539846
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.440.35981440.31994101X-RAY DIFFRACTION99.79
1.44-1.470.34631450.28984127X-RAY DIFFRACTION99.86
1.47-1.520.32641430.26524094X-RAY DIFFRACTION99.93
1.52-1.570.26971450.22484112X-RAY DIFFRACTION99.88
1.57-1.620.20561450.19234127X-RAY DIFFRACTION99.84
1.62-1.690.21821440.18294118X-RAY DIFFRACTION99.79
1.69-1.760.23861450.16964135X-RAY DIFFRACTION99.88
1.76-1.860.20351470.16174153X-RAY DIFFRACTION99.91
1.86-1.970.20781440.16144136X-RAY DIFFRACTION99.91
1.97-2.130.2141240.15763518X-RAY DIFFRACTION84.64
2.13-2.340.20111310.1553747X-RAY DIFFRACTION89.05
2.34-2.680.16451480.16794191X-RAY DIFFRACTION99.93
2.68-3.370.18561500.18084254X-RAY DIFFRACTION99.82
3.37-53.840.19091450.15234153X-RAY DIFFRACTION93.19

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