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- PDB-6uux: Schistosoma mansoni (Blood Fluke) Sulfotransferase/Hycanthone Complex -

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Basic information

Entry
Database: PDB / ID: 6uux
TitleSchistosoma mansoni (Blood Fluke) Sulfotransferase/Hycanthone Complex
ComponentsSulfotransferase
KeywordsTRANSFERASE / sulfotransferase / parasite / hycanthone / drug resistance / schistosome
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 / hycanthone / Sulfotransferase oxamniquine resistance protein
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsTaylor, A.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI115691 United States
CitationJournal: Mol.Biochem.Parasitol. / Year: 2020
Title: Molecular basis for hycanthone drug action in schistosome parasites.
Authors: Guzman, M. / Rugel, A. / Tarpley, R.S. / Cao, X. / McHardy, S.F. / LoVerde, P.T. / Taylor, A.B.
History
DepositionNov 1, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Oct 11, 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 1.3Oct 23, 2024Group: Structure summary / Category: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8643
Polymers30,0811
Non-polymers7842
Water5,909328
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area770 Å2
ΔGint-7 kcal/mol
Surface area12700 Å2
Unit cell
Length a, b, c (Å)139.620, 39.300, 54.120
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-699-

HOH

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Components

#1: Protein Sulfotransferase / 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, 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-QHM / hycanthone / 1-{[2-(diethylamino)ethyl]amino}-4-(hydroxymethyl)-9H-thioxanthen-9-one


Mass: 356.482 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H24N2O2S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 328 / 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: 2.48 Å3/Da / Density % sol: 50.34 %
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 / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Aug 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.5→39.3 Å / Num. obs: 48756 / % possible obs: 100 % / Redundancy: 17.7 % / Biso Wilson estimate: 18.58 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.028 / Rrim(I) all: 0.119 / Net I/σ(I): 15.1
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 10.7 % / Rmerge(I) obs: 1.429 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 7017 / CC1/2: 0.382 / Rpim(I) all: 0.447 / Rrim(I) all: 1.499 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5BYK

5byk


Resolution: 1.5→35.29 Å / SU ML: 0.1682 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.2533
RfactorNum. reflection% reflection
Rfree0.2086 2000 4.11 %
Rwork0.1692 --
obs0.1708 48695 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 25.87 Å2
Refinement stepCycle: LAST / Resolution: 1.5→35.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2097 0 52 328 2477
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00712224
X-RAY DIFFRACTIONf_angle_d1.00783024
X-RAY DIFFRACTIONf_chiral_restr0.0754339
X-RAY DIFFRACTIONf_plane_restr0.005373
X-RAY DIFFRACTIONf_dihedral_angle_d18.1409832
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.540.35791400.31713281X-RAY DIFFRACTION99.91
1.54-1.580.34281410.27723283X-RAY DIFFRACTION100
1.58-1.630.27231410.23893278X-RAY DIFFRACTION99.94
1.63-1.680.26331400.22083282X-RAY DIFFRACTION100
1.68-1.740.30141410.21133299X-RAY DIFFRACTION100
1.74-1.810.23151420.19653320X-RAY DIFFRACTION100
1.81-1.890.22671400.17993276X-RAY DIFFRACTION100
1.89-1.990.2551440.17533327X-RAY DIFFRACTION100
1.99-2.110.20281410.16623306X-RAY DIFFRACTION100
2.11-2.280.20361430.15633333X-RAY DIFFRACTION100
2.28-2.510.20331430.15943351X-RAY DIFFRACTION99.97
2.51-2.870.22571440.17113373X-RAY DIFFRACTION100
2.87-3.610.18461470.15293411X-RAY DIFFRACTION100
3.61-35.290.16441530.14523575X-RAY DIFFRACTION99.89

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