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- PDB-1ov4: Crystal structure of human DHEA-ST complexed with androsterone -

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Basic information

Entry
Database: PDB / ID: 1ov4
TitleCrystal structure of human DHEA-ST complexed with androsterone
ComponentsAlcohol sulfotransferase
KeywordsTRANSFERASE / alpha/beta fold
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 / sulfation / sulfotransferase activity / ethanol catabolic process / Paracetamol ADME / steroid metabolic process / cholesterol metabolic process / lipid catabolic 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 / FOURIER SYNTHESIS / Resolution: 2.7 Å
AuthorsChang, H.J. / Shi, R. / Rhese, P. / Lin, S.X.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Identifying androsterone (ADT) as a cognate substrate for human dehydroepiandrosterone sulfotransferase (DHEA-ST) important for steroid homeostasis: structure of the enzyme-ADT complex.
Authors: Chang, H.J. / Shi, R. / Rehse, P. / Lin, S.X.
History
DepositionMar 25, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 3, 2013Group: Non-polymer description
Revision 1.4Oct 27, 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 1.5Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alcohol sulfotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1033
Polymers34,7171
Non-polymers3872
Water45025
1
A: Alcohol sulfotransferase
hetero molecules

A: Alcohol sulfotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,2066
Polymers69,4332
Non-polymers7734
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
Unit cell
Length a, b, c (Å)75.293, 129.818, 44.287
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 34716.707 Da / Num. of mol.: 1 / Mutation: A242T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SULT2A1 OR STD OR HST / Production host: Escherichia coli (E. coli) / References: UniProt: Q06520, alcohol sulfotransferase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-AOX / (3Beta,5alpha)-3-Hydroxyandrostan-17-one / Epiandrosterone


Mass: 290.440 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H30O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 3.12 Å3/Da / Density % sol: 60.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: ammonium sulfate, HEPES, sodium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
115 mg/mlprotein1drop
210 mMTris1droppH7.5
30.1 %n-octyl beta-D-glucopyranoside1drop
41.6 Mammonium sulfate1reservoir
50.1 MHEPES1reservoirpH7.5
60.1 M1reservoirNaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.0721 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 27, 2001
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0721 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. obs: 11911 / % possible obs: 95.2 % / Observed criterion σ(I): 1 / Redundancy: 3.05 % / Rsym value: 0.075
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 2.95 % / Rsym value: 0.424 / % possible all: 96.7
Reflection
*PLUS
Highest resolution: 2.7 Å / Redundancy: 3.1 % / Num. measured all: 36310 / Rmerge(I) obs: 0.075
Reflection shell
*PLUS
% possible obs: 96.7 % / Redundancy: 3 % / Num. unique obs: 1189 / Num. measured obs: 3571 / Rmerge(I) obs: 0.424 / Mean I/σ(I) obs: 2.1

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTYR 1J99

1j99


Resolution: 2.7→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.27 700 -RANDOM
Rwork0.23 ---
all-12482 --
obs-11485 92 %-
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2137 0 26 25 2188
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007297
X-RAY DIFFRACTIONc_angle_deg1.26605
LS refinement shellResolution: 2.7→2.77 Å /
RfactorNum. reflection
Rfree0.459 52
Rwork0.369 -
obs-714
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.271 / Rfactor Rwork: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3

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