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- PDB-4mua: Schistosoma mansoni (Blood Fluke) Sulfotransferase -

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Basic information

Entry
Database: PDB / ID: 4mua
TitleSchistosoma mansoni (Blood Fluke) Sulfotransferase
ComponentsSulfotransferase
KeywordsTRANSFERASE / PAP / parasite / helminth / 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 / SIRAS / Resolution: 1.95 Å
AuthorsValentim, C.L.L. / Cioli, D. / Chevalier, F.D. / Cao, X. / Taylor, A.B. / Holloway, S.P. / Pica-Mattoccia, L. / Guidi, A. / Basso, A. / Tsai, I.J. ...Valentim, C.L.L. / Cioli, D. / Chevalier, F.D. / Cao, X. / Taylor, A.B. / Holloway, S.P. / Pica-Mattoccia, L. / Guidi, A. / Basso, A. / Tsai, I.J. / Berriman, M. / Carvalho-Queiroz, C. / Almeida, M. / Aguilar, H. / Frantz, D.E. / Hart, P.J. / Anderson, T.J.C. / LoVerde, P.T.
CitationJournal: Science / Year: 2013
Title: Genetic and molecular basis of drug resistance and species-specific drug action in schistosome parasites.
Authors: Valentim, C.L. / Cioli, D. / Chevalier, F.D. / Cao, X. / Taylor, A.B. / Holloway, S.P. / Pica-Mattoccia, L. / Guidi, A. / Basso, A. / Tsai, I.J. / Berriman, M. / Carvalho-Queiroz, C. / ...Authors: Valentim, C.L. / Cioli, D. / Chevalier, F.D. / Cao, X. / Taylor, A.B. / Holloway, S.P. / Pica-Mattoccia, L. / Guidi, A. / Basso, A. / Tsai, I.J. / Berriman, M. / Carvalho-Queiroz, C. / Almeida, M. / Aguilar, H. / Frantz, D.E. / Hart, P.J. / LoVerde, P.T. / Anderson, T.J.
History
DepositionSep 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sulfotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4273
Polymers29,9771
Non-polymers4502
Water5,801322
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Sulfotransferase
hetero molecules

A: Sulfotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8546
Polymers59,9532
Non-polymers9004
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
Buried area4030 Å2
ΔGint-27 kcal/mol
Surface area23440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.580, 39.581, 53.643
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-447-

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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 322 / 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: 2.47 Å3/Da / Density % sol: 50.23 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.0 M sodium citrate, 0.1 M sodium cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Jan 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.95→28.97 Å / Num. obs: 21569 / % possible obs: 96.3 % / Redundancy: 2.7 % / Biso Wilson estimate: 19.8 Å2 / Rsym value: 0.085 / Net I/σ(I): 9.4
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 2727 / Rsym value: 0.474 / % possible all: 85.4

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Processing

Software
NameVersionClassification
CrystalCleardata collection
SHARPphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: SIRAS / Resolution: 1.95→28.97 Å / SU ML: 0.26 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2331 2000 9.29 %random
Rwork0.1772 ---
obs0.1824 21534 95.86 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.3 Å2
Refinement stepCycle: LAST / Resolution: 1.95→28.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2065 0 28 322 2415
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072140
X-RAY DIFFRACTIONf_angle_d1.042906
X-RAY DIFFRACTIONf_dihedral_angle_d12.719792
X-RAY DIFFRACTIONf_chiral_restr0.073329
X-RAY DIFFRACTIONf_plane_restr0.004360
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.99890.37421070.32541043X-RAY DIFFRACTION73
1.9989-2.0530.2871400.26021367X-RAY DIFFRACTION96
2.053-2.11330.29061410.22691378X-RAY DIFFRACTION97
2.1133-2.18150.25991430.19851390X-RAY DIFFRACTION98
2.1815-2.25950.24151410.2031395X-RAY DIFFRACTION97
2.2595-2.34990.25231450.18881412X-RAY DIFFRACTION98
2.3499-2.45680.26791470.19411426X-RAY DIFFRACTION99
2.4568-2.58620.28881420.18951395X-RAY DIFFRACTION98
2.5862-2.74820.23181450.1821412X-RAY DIFFRACTION98
2.7482-2.96020.24661480.18231439X-RAY DIFFRACTION98
2.9602-3.25770.2541470.16141443X-RAY DIFFRACTION99
3.2577-3.72830.18551480.15311448X-RAY DIFFRACTION98
3.7283-4.6940.19031510.1291472X-RAY DIFFRACTION98
4.694-28.970.1871550.16261514X-RAY DIFFRACTION95

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