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- PDB-6b4y: Schistosoma mansoni (Blood Fluke) Sulfotransferase/Oxamniquine Co... -

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Basic information

Entry
Database: PDB / ID: 6b4y
TitleSchistosoma mansoni (Blood Fluke) Sulfotransferase/Oxamniquine Complex, F39Y Mutant
ComponentsSulfotransferase oxamniquine resistance protein
KeywordsTRANSFERASE / sulfotransferase / parasite / drug resistance
Function / homology
Function and homology information


transferase activity
Similarity search - Function
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 / Sulfotransferase oxamniquine resistance protein
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsTaylor, A.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI115691 United States
CitationJournal: Int.J.Parasitol. / Year: 2020
Title: Why does oxamniquine kill Schistosoma mansoni and not S. haematobium and S. japonicum?
Authors: Rugel, A.R. / Guzman, M.A. / Taylor, A.B. / Chevalier, F.D. / Tarpley, R.S. / McHardy, S.F. / Cao, X. / Holloway, S.P. / Anderson, T.J.C. / Hart, P.J. / LoVerde, P.T.
History
DepositionSep 27, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Author supporting evidence / Structure summary / Category: entity / pdbx_audit_support
Item: _entity.formula_weight / _pdbx_audit_support.funding_organization
Revision 1.2Apr 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year
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 oxamniquine resistance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6993
Polymers29,9931
Non-polymers7072
Water1,964109
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area760 Å2
ΔGint-5 kcal/mol
Surface area12790 Å2
Unit cell
Length a, b, c (Å)140.217, 39.410, 53.504
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-507-

HOH

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Components

#1: Protein Sulfotransferase oxamniquine resistance protein / Sulfotransferase


Mass: 29992.562 Da / Num. of mol.: 1 / Mutation: F39Y
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 (bacteria) / Strain (production host): BL21 pLysS
References: UniProt: G4VLE5, Transferases; Transferring sulfur-containing groups; Sulfotransferases
#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 / Comment: medication*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.46 Å3/Da / Density % sol: 50.09 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 1.0 M sodium citrate, 0.1 M sodium cacodylate, pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 5, 2014
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.95→140.22 Å / Num. obs: 22010 / % possible obs: 98.5 % / Redundancy: 3.6 % / Biso Wilson estimate: 37.7 Å2 / Rpim(I) all: 0.038 / Rsym value: 0.051 / Net I/σ(I): 12
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3204 / Rpim(I) all: 0.402 / Rsym value: 0.557 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5BYK

5byk


Resolution: 1.95→70.108 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2168 1998 9.1 %
Rwork0.1856 --
obs0.1885 21951 97.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→70.108 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 47 109 2205
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092163
X-RAY DIFFRACTIONf_angle_d1.1892940
X-RAY DIFFRACTIONf_dihedral_angle_d16.562845
X-RAY DIFFRACTIONf_chiral_restr0.318331
X-RAY DIFFRACTIONf_plane_restr0.004363
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.99880.34761420.32761414X-RAY DIFFRACTION100
1.9988-2.05280.28211410.2821421X-RAY DIFFRACTION100
2.0528-2.11330.32131410.24441411X-RAY DIFFRACTION99
2.1133-2.18150.28191430.23811426X-RAY DIFFRACTION100
2.1815-2.25940.2781410.22571400X-RAY DIFFRACTION98
2.2594-2.34990.25081420.19771422X-RAY DIFFRACTION98
2.3499-2.45690.25041410.20331403X-RAY DIFFRACTION97
2.4569-2.58640.23121420.1941418X-RAY DIFFRACTION99
2.5864-2.74850.2631440.20321432X-RAY DIFFRACTION99
2.7485-2.96070.25371440.20631440X-RAY DIFFRACTION99
2.9607-3.25860.25861420.20181424X-RAY DIFFRACTION97
3.2586-3.73010.2211400.17171389X-RAY DIFFRACTION95
3.7301-4.69940.17161470.14661464X-RAY DIFFRACTION97
4.6994-70.15380.15921480.16581489X-RAY DIFFRACTION93

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