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- PDB-6bdp: Schistosoma mansoni (Blood Fluke) Sulfotransferase/CIDD-0000071 (... -

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Basic information

Entry
Database: PDB / ID: 6bdp
TitleSchistosoma mansoni (Blood Fluke) Sulfotransferase/CIDD-0000071 (Compound 9c) 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-3'-5'-DIPHOSPHATE / Chem-DE4 / Sulfotransferase oxamniquine resistance protein
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.43 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
Revision 2.1Oct 16, 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)30,8353
Polymers30,0811
Non-polymers7552
Water6,143341
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area770 Å2
ΔGint-6 kcal/mol
Surface area12650 Å2
2
A: Sulfotransferase oxamniquine resistance protein
hetero molecules

A: Sulfotransferase oxamniquine resistance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,6706
Polymers60,1612
Non-polymers1,5094
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
Buried area3950 Å2
ΔGint-21 kcal/mol
Surface area22890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.859, 39.456, 53.763
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-712-

HOH

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Components

#1: Protein 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 (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-DE4 / (4-{[(3R)-1-benzylpyrrolidin-3-yl]amino}-2-nitrophenyl)methanol


Mass: 327.378 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H21N3O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 341 / 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: 2.49 Å3/Da / Density % sol: 50.64 %
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: Dec 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.43→26.405 Å / Num. obs: 56095 / % possible obs: 99.5 % / Redundancy: 4.5 % / Biso Wilson estimate: 13.5 Å2 / Rpim(I) all: 0.03 / Rsym value: 0.066 / Net I/σ(I): 16.7
Reflection shellResolution: 1.43→1.51 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 8033 / Rpim(I) all: 0.368 / Rsym value: 0.784 / % possible all: 99.3

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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: 1.43→26.405 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.42
RfactorNum. reflection% reflection
Rfree0.2073 2000 3.57 %
Rwork0.1704 --
obs0.1718 56031 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 20.5 Å2
Refinement stepCycle: LAST / Resolution: 1.43→26.405 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2060 0 51 342 2453
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082161
X-RAY DIFFRACTIONf_angle_d1.1282934
X-RAY DIFFRACTIONf_dihedral_angle_d14.57810
X-RAY DIFFRACTIONf_chiral_restr0.076329
X-RAY DIFFRACTIONf_plane_restr0.006362
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.43-1.46580.29141390.25283752X-RAY DIFFRACTION98
1.4658-1.50540.25291410.22223810X-RAY DIFFRACTION100
1.5054-1.54970.25051400.19333806X-RAY DIFFRACTION99
1.5497-1.59970.23691410.18373794X-RAY DIFFRACTION100
1.5997-1.65690.24721420.17013831X-RAY DIFFRACTION100
1.6569-1.72320.22081430.17963846X-RAY DIFFRACTION100
1.7232-1.80160.23081420.17223859X-RAY DIFFRACTION100
1.8016-1.89660.19331420.16423832X-RAY DIFFRACTION100
1.8966-2.01540.19611430.16593857X-RAY DIFFRACTION100
2.0154-2.17090.20131430.15813871X-RAY DIFFRACTION100
2.1709-2.38920.19711430.15953877X-RAY DIFFRACTION99
2.3892-2.73470.20561440.17043889X-RAY DIFFRACTION99
2.7347-3.44420.2011460.17183932X-RAY DIFFRACTION99
3.4442-26.40950.19041510.16084075X-RAY DIFFRACTION98

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