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- PDB-6bds: Schistosoma mansoni (Blood Fluke) Sulfotransferase/CIDD-0000204 (... -

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Basic information

Entry
Database: PDB / ID: 6bds
TitleSchistosoma mansoni (Blood Fluke) Sulfotransferase/CIDD-0000204 (Compound 11f) Complex
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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-3'-5'-DIPHOSPHATE / Chem-DJ4 / Sulfotransferase oxamniquine resistance protein
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsTaylor, A.B.
CitationJournal: ACS Med Chem Lett / Year: 2018
Title: Design, Synthesis, and Characterization of Novel Small Molecules as Broad Range Antischistosomal Agents.
Authors: Rugel, A. / Tarpley, R.S. / Lopez, A. / Menard, T. / Guzman, M.A. / Taylor, A.B. / Cao, X. / Kovalskyy, D. / Chevalier, F.D. / Anderson, T.J.C. / Hart, P.J. / LoVerde, P.T. / McHardy, S.F.
History
DepositionOct 24, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2018Group: Data collection / Database references / Source and taxonomy
Category: citation / citation_author / entity_src_gen
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id
Revision 1.2Oct 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 2.0May 1, 2024Group: Data collection / Derived calculations ...Data collection / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / entity / pdbx_entity_nonpoly
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.name / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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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)31,1954
Polymers29,9771
Non-polymers1,2183
Water6,305350
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area770 Å2
ΔGint-5 kcal/mol
Surface area12940 Å2
2
A: Sulfotransferase oxamniquine resistance protein
hetero molecules

A: Sulfotransferase oxamniquine resistance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,3898
Polymers59,9532
Non-polymers2,4366
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
Buried area4050 Å2
ΔGint-20 kcal/mol
Surface area23360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.780, 39.541, 53.561
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-726-

HOH

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Components

#1: Protein Sulfotransferase oxamniquine resistance protein


Mass: 29976.562 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 (E. coli) / Strain (production host): BL21 PLYSS / References: UniProt: G4VLE5
#2: Chemical ChemComp-A3P / ADENOSINE-3'-5'-DIPHOSPHATE / Adenosine 3',5'-bisphosphate


Type: RNA linking / Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2
#3: Chemical ChemComp-DJ4 / (2-nitro-4-{[(3S)-1-{[4-(trifluoromethyl)phenyl]methyl}pyrrolidin-3-yl]amino}phenyl)methanol


Mass: 395.376 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H20F3N3O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 350 / 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: 2.49 Å3/Da / Density % sol: 50.53 %
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-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.53→38.068 Å / Num. obs: 45843 / % possible obs: 99.5 % / Redundancy: 5.8 % / Biso Wilson estimate: 16.6 Å2 / Rpim(I) all: 0.033 / Rsym value: 0.074 / Net I/σ(I): 16.4
Reflection shellResolution: 1.53→1.61 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 2 / Num. unique obs: 6611 / Rpim(I) all: 0.432 / Rsym value: 0.958 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXdev_2919refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MUA

4mua


Resolution: 1.53→38.068 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 18.92
RfactorNum. reflection% reflection
Rfree0.2024 2000 4.37 %
Rwork0.1513 --
obs0.1535 45784 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 24 Å2
Refinement stepCycle: LAST / Resolution: 1.53→38.068 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2099 0 72 350 2521
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012226
X-RAY DIFFRACTIONf_angle_d1.2323030
X-RAY DIFFRACTIONf_dihedral_angle_d15.698837
X-RAY DIFFRACTIONf_chiral_restr0.06340
X-RAY DIFFRACTIONf_plane_restr0.007373
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.53-1.56830.26991420.21173094X-RAY DIFFRACTION100
1.5683-1.61070.2661400.19863084X-RAY DIFFRACTION100
1.6107-1.65810.22681430.19053115X-RAY DIFFRACTION100
1.6581-1.71160.24161420.17593119X-RAY DIFFRACTION100
1.7116-1.77280.22951410.16453084X-RAY DIFFRACTION100
1.7728-1.84370.26131430.16183118X-RAY DIFFRACTION100
1.8437-1.92760.22411410.15843115X-RAY DIFFRACTION100
1.9276-2.02930.22771430.14813112X-RAY DIFFRACTION100
2.0293-2.15640.19221440.143159X-RAY DIFFRACTION100
2.1564-2.32290.20711430.14153135X-RAY DIFFRACTION99
2.3229-2.55660.20921430.14773125X-RAY DIFFRACTION99
2.5566-2.92640.19691430.15333134X-RAY DIFFRACTION99
2.9264-3.68650.20631450.13793172X-RAY DIFFRACTION98
3.6865-38.07970.15421470.14523218X-RAY DIFFRACTION95

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