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- PDB-6b52: Schistosoma haematobium (Blood Fluke) Sulfotransferase/Oxamniquin... -

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Basic information

Entry
Database: PDB / ID: 6b52
TitleSchistosoma haematobium (Blood Fluke) Sulfotransferase/Oxamniquine Complex, Y54F Mutant
ComponentsSulfotransferase
KeywordsTRANSFERASE / sulfotransferase / parasite / helminth
Function / homology
Function and homology information


Sulfotransferase, S. mansonii-type / Sulfotransferase domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9533
Polymers29,2471
Non-polymers7072
Water2,882160
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area760 Å2
ΔGint-7 kcal/mol
Surface area11620 Å2
Unit cell
Length a, b, c (Å)52.429, 72.551, 140.307
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-404-

HOH

21A-470-

HOH

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Components

#1: Protein Sulfotransferase


Mass: 29246.564 Da / Num. of mol.: 1 / Mutation: Y54F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma haematobium (invertebrata) / Gene: MS3_07706 / Plasmid: pAG8H / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: A0A094ZWQ2, 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.: 160 / 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: 2.28 Å3/Da / Density % sol: 46.08 %
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, PEG1000, PEG3350)

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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: 1.8→70.15 Å / Num. obs: 25230 / % possible obs: 99.9 % / Redundancy: 7 % / Biso Wilson estimate: 31.7 Å2 / Rpim(I) all: 0.021 / Rsym value: 0.049 / Net I/σ(I): 20
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 4.5 / Num. unique obs: 3611 / Rpim(I) all: 0.166 / Rsym value: 0.374 / % 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 5TIV

5tiv


Resolution: 1.8→70.154 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.41 / Phase error: 29.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.233 1999 7.95 %
Rwork0.186 --
obs0.1896 25149 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→70.154 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2010 0 47 160 2217
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082152
X-RAY DIFFRACTIONf_angle_d1.2212928
X-RAY DIFFRACTIONf_dihedral_angle_d14.197828
X-RAY DIFFRACTIONf_chiral_restr0.049322
X-RAY DIFFRACTIONf_plane_restr0.005367
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.84510.38531390.31961612X-RAY DIFFRACTION99
1.8451-1.89490.39011400.28321621X-RAY DIFFRACTION99
1.8949-1.95070.31481430.23951642X-RAY DIFFRACTION100
1.9507-2.01370.29921420.22661640X-RAY DIFFRACTION99
2.0137-2.08560.30591380.21761605X-RAY DIFFRACTION99
2.0856-2.16920.28911420.21081644X-RAY DIFFRACTION100
2.1692-2.26790.26311420.20631647X-RAY DIFFRACTION100
2.2679-2.38750.26661420.20391640X-RAY DIFFRACTION100
2.3875-2.5370.24021420.20311641X-RAY DIFFRACTION100
2.537-2.73290.25961430.20271661X-RAY DIFFRACTION100
2.7329-3.0080.23171440.2081674X-RAY DIFFRACTION100
3.008-3.44320.26791440.19541670X-RAY DIFFRACTION99
3.4432-4.3380.17741450.15751686X-RAY DIFFRACTION100
4.338-70.20680.19051530.15151767X-RAY DIFFRACTION100

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