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- PDB-5byj: Schistosoma mansoni (Blood Fluke) Sulfotransferase/R-oxamniquine ... -

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Basic information

Entry
Database: PDB / ID: 5byj
TitleSchistosoma mansoni (Blood Fluke) Sulfotransferase/R-oxamniquine Complex
ComponentsSulfotransferase
KeywordsTRANSFERASE / sulfotransferase / parasite / oxamniquine / 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-OQR / Sulfotransferase oxamniquine resistance protein
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsTaylor, A.B. / Cao, X. / Holloway, S.P. / Hart, P.J.
Funding support United States, 1items
OrganizationGrant numberCountry
Welch FoundationAQ-1399 United States
CitationJournal: Plos Negl Trop Dis / Year: 2015
Title: Structural and Functional Characterization of the Enantiomers of the Antischistosomal Drug Oxamniquine.
Authors: Taylor, A.B. / Pica-Mattoccia, L. / Polcaro, C.M. / Donati, E. / Cao, X. / Basso, A. / Guidi, A. / Rugel, A.R. / Holloway, S.P. / Anderson, T.J. / Hart, P.J. / Cioli, D. / LoVerde, P.T.
History
DepositionJun 10, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2015Group: Database references / Structure summary
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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)30,6833
Polymers29,9771
Non-polymers7072
Water3,909217
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area770 Å2
ΔGint-6 kcal/mol
Surface area12790 Å2
2
A: Sulfotransferase
hetero molecules

A: Sulfotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,3666
Polymers59,9532
Non-polymers1,4134
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
Buried area3900 Å2
ΔGint-22 kcal/mol
Surface area23220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.542, 39.237, 54.009
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-611-

HOH

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Components

#1: Protein Sulfotransferase


Mass: 29976.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Gene: Smp_089320 / Plasmid: PAG8H / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 pLysS / References: UniProt: G4VLE5
#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-OQR / {(2R)-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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 2.48 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: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.8→42.82 Å / Num. obs: 28003 / % possible obs: 98.7 % / Redundancy: 4.2 % / Biso Wilson estimate: 29.1 Å2 / Rsym value: 0.054 / Net I/σ(I): 15.3
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 4 % / Rmerge(I) obs: 0.652 / Mean I/σ(I) obs: 2.1 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MUA

4mua


Resolution: 1.8→42.82 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2041 2000 7.15 %Random selection
Rwork0.1734 ---
obs0.1756 27971 98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.3 Å2
Refinement stepCycle: LAST / Resolution: 1.8→42.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2087 0 47 217 2351
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072204
X-RAY DIFFRACTIONf_angle_d1.0542997
X-RAY DIFFRACTIONf_dihedral_angle_d13.581828
X-RAY DIFFRACTIONf_chiral_restr0.048339
X-RAY DIFFRACTIONf_plane_restr0.005370
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8001-1.84510.38191390.31511809X-RAY DIFFRACTION99
1.8451-1.8950.32631390.28561798X-RAY DIFFRACTION97
1.895-1.95070.29211430.21561851X-RAY DIFFRACTION98
1.9507-2.01370.22251410.19451838X-RAY DIFFRACTION99
2.0137-2.08570.22731430.1871858X-RAY DIFFRACTION99
2.0857-2.16920.21171420.1791854X-RAY DIFFRACTION99
2.1692-2.26790.24541430.17511849X-RAY DIFFRACTION99
2.2679-2.38750.24961420.17751835X-RAY DIFFRACTION98
2.3875-2.5370.24741420.1851861X-RAY DIFFRACTION99
2.537-2.73290.22071440.17491868X-RAY DIFFRACTION99
2.7329-3.00780.22711460.18191886X-RAY DIFFRACTION98
3.0078-3.44290.17761430.16681849X-RAY DIFFRACTION97
3.4429-4.3370.16131450.14461886X-RAY DIFFRACTION96
4.337-42.83440.17191480.16221929X-RAY DIFFRACTION94

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