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- PDB-2qp3: Identification and Characterization of Two Amino Acids Critical f... -

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Basic information

Entry
Database: PDB / ID: 2qp3
TitleIdentification and Characterization of Two Amino Acids Critical for the Substrate Inhibition of SULT2A1
ComponentsBile salt sulfotransferase
KeywordsTRANSFERASE / Dehydroepiandrosterone(DHEA) / androsterone(ADT) / substrate inhibition / sulfotransferase / substrate binding orientation / Bile acid catabolism / Lipid metabolism / Steroid metabolism
Function / homology
Function and homology information


bile-salt sulfotransferase / alcohol sulfotransferase activity / bile-salt sulfotransferase activity / alcohol sulfotransferase / steroid sulfotransferase activity / bile acid catabolic process / 3'-phosphoadenosine 5'-phosphosulfate binding / Cytosolic sulfonation of small molecules / 3'-phosphoadenosine 5'-phosphosulfate metabolic process / thyroid hormone metabolic process ...bile-salt sulfotransferase / alcohol sulfotransferase activity / bile-salt sulfotransferase activity / alcohol sulfotransferase / steroid sulfotransferase activity / bile acid catabolic process / 3'-phosphoadenosine 5'-phosphosulfate binding / Cytosolic sulfonation of small molecules / 3'-phosphoadenosine 5'-phosphosulfate metabolic process / thyroid hormone metabolic process / ethanol catabolic process / sulfation / sulfotransferase activity / Paracetamol ADME / steroid metabolic process / lipid catabolic process / cholesterol metabolic process / xenobiotic metabolic process / PPARA activates gene expression / cytoplasm / cytosol
Similarity search - Function
Sulfotransferase domain / 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
(3Beta,5alpha)-3-Hydroxyandrostan-17-one / Sulfotransferase 2A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsHsieh, Y.C.
CitationJournal: Mol.Pharmacol. / Year: 2008
Title: Identification and characterization of two amino acids critical for the substrate inhibition of human dehydroepiandrosterone sulfotransferase (SULT2A1)
Authors: Lu, L.Y. / Hsieh, Y.C. / Liu, M.Y. / Lin, Y.H. / Chen, C.J. / Yang, Y.S.
History
DepositionJul 23, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 3, 2013Group: Database references / Non-polymer description
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software
Revision 1.4Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bile salt sulfotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9922
Polymers33,7021
Non-polymers2901
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.285, 131.720, 44.552
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Bile salt sulfotransferase / Hydroxysteroid Sulfotransferase / HST / Dehydroepiandrosterone sulfotransferase / DHEA-ST / ST2 / ST2A3


Mass: 33701.574 Da / Num. of mol.: 1 / Mutation: M137I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX-2TK / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q06520, bile-salt sulfotransferase
#2: Chemical ChemComp-AOX / (3Beta,5alpha)-3-Hydroxyandrostan-17-one / Epiandrosterone


Mass: 290.440 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H30O2 / Comment: hormone*YM

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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: 3.32 Å3/Da / Density % sol: 62.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.5
Details: (NH4)2SO4, NaCl, pH 7.5, vapor diffusion, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 11, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 16159 / Redundancy: 14.1 %

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3data extraction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→20 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.264 1412 9.8 %
Rwork0.226 --
obs-14138 98.3 %
Solvent computationBsol: 27.302 Å2
Displacement parametersBiso mean: 46.438 Å2
Baniso -1Baniso -2Baniso -3
1-2.522 Å20 Å20 Å2
2---2.403 Å20 Å2
3----0.12 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2248 0 21 0 2269
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.219
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2ADT1.param

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