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- PDB-6b4z: Schistosoma mansoni (Blood Fluke) Sulfotransferase, T157S Mutant -

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Basic information

Entry
Database: PDB / ID: 6b4z
TitleSchistosoma mansoni (Blood Fluke) Sulfotransferase, T157S 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 / Sulfotransferase oxamniquine resistance protein
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.74 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
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)30,6163
Polymers30,0671
Non-polymers5492
Water7,746430
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-3 kcal/mol
Surface area12830 Å2
2
A: Sulfotransferase oxamniquine resistance protein
hetero molecules

A: Sulfotransferase oxamniquine resistance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2326
Polymers60,1332
Non-polymers1,0994
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
Buried area4600 Å2
ΔGint-16 kcal/mol
Surface area23300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.005, 39.316, 54.079
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-771-

HOH

21A-797-

HOH

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Components

#1: Protein Sulfotransferase oxamniquine resistance protein / Sulfotransferase


Mass: 30066.520 Da / Num. of mol.: 1 / Mutation: T157S
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-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 430 / Source method: isolated from a natural source / Formula: H2O
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: 2.48 Å3/Da / Density % sol: 50.48 %
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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: May 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.74→46.67 Å / Num. obs: 31578 / % possible obs: 100 % / Redundancy: 6.8 % / Biso Wilson estimate: 17.2 Å2 / Rpim(I) all: 0.05 / Rsym value: 0.113 / Net I/σ(I): 14
Reflection shellResolution: 1.74→1.83 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 2 / Num. unique obs: 4517 / Rpim(I) all: 0.426 / Rsym value: 0.949 / % possible all: 100

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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: 1.74→42.796 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 18.95
RfactorNum. reflection% reflection
Rfree0.2077 2000 6.34 %
Rwork0.1735 --
obs0.1757 31526 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 21 Å2
Refinement stepCycle: LAST / Resolution: 1.74→42.796 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2089 0 35 430 2554
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062209
X-RAY DIFFRACTIONf_angle_d1.1153006
X-RAY DIFFRACTIONf_dihedral_angle_d13.983829
X-RAY DIFFRACTIONf_chiral_restr0.042338
X-RAY DIFFRACTIONf_plane_restr0.003374
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.74-1.78350.29721410.26132088X-RAY DIFFRACTION100
1.7835-1.83180.28521400.24292050X-RAY DIFFRACTION100
1.8318-1.88570.30981400.24052077X-RAY DIFFRACTION100
1.8857-1.94650.26291410.2112090X-RAY DIFFRACTION100
1.9465-2.01610.19941400.18962066X-RAY DIFFRACTION100
2.0161-2.09680.21631420.17632085X-RAY DIFFRACTION100
2.0968-2.19220.18811410.16882091X-RAY DIFFRACTION100
2.1922-2.30780.23291430.1842097X-RAY DIFFRACTION100
2.3078-2.45240.22661420.17032103X-RAY DIFFRACTION100
2.4524-2.64170.19391420.1692094X-RAY DIFFRACTION100
2.6417-2.90750.21471420.1682112X-RAY DIFFRACTION100
2.9075-3.32810.18621460.15742140X-RAY DIFFRACTION100
3.3281-4.19250.1741460.14582161X-RAY DIFFRACTION100
4.1925-42.80890.18461540.16152272X-RAY DIFFRACTION99

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