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- PDB-1j99: CRYSTAL STRUCTURE OF HUMAN DEHYDROEPIANDROSTERONE SULFOTRANSFERAS... -

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Basic information

Entry
Database: PDB / ID: 1j99
TitleCRYSTAL STRUCTURE OF HUMAN DEHYDROEPIANDROSTERONE SULFOTRANSFERASE IN COMPLEX WITH SUBSTRATE
ComponentsALCOHOL SULFOTRANSFERASE
KeywordsTRANSFERASE / Dehydroepiandosterone / Sulfotransferase / DHEA
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
3-BETA-HYDROXY-5-ANDROSTEN-17-ONE / MERCURY (II) IODIDE / IODIDE ION / Sulfotransferase 2A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsRehse, P.H. / Zhou, M. / Lin, S.-X.
CitationJournal: Biochem.J. / Year: 2002
Title: Crystal structure of human dehydroepiandrosterone sulphotransferase in complex with substrate.
Authors: Rehse, P.H. / Zhou, M. / Lin, S.X.
History
DepositionMay 24, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_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
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). ALTHOUGH SOLUTION STUDIES INDICATE THAT DHEA-ST IS A DIMER IN SOLUTION, IT IS NOT CLEAR AS TO WHAT THE DIMER IS. THE AUTHOR DOES NOT WISH TO DEFINE THE DIMER.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ALCOHOL SULFOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4956
Polymers34,7171
Non-polymers1,7795
Water3,891216
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.931, 137.976, 45.864
Angle α, β, γ (deg.)90, 90, 90
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein ALCOHOL SULFOTRANSFERASE / DEHYDROEPIANDROSTERONE SULFOTRANSFERASE / DHEA-ST / HYDROXYSTEROID SULFOTRANSFERASE / HST


Mass: 34716.707 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q06520, alcohol sulfotransferase
#2: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-HGI / MERCURY (II) IODIDE / MERCURY DIIODIDE


Mass: 454.399 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: HgI2
#4: Chemical ChemComp-AND / 3-BETA-HYDROXY-5-ANDROSTEN-17-ONE


Mass: 288.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H28O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 3.55 Å3/Da / Density % sol: 65.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Tris, cobalt chloride, amonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
1100 mMTris1reservoirpH7.5
21.2 mM1reservoirCoCl2
3170 mMammonium sulfate1reservoir
412 mg/mlDHEA-ST1drop0.35mM
50.5 mMDHEA1drop
610 mMTris1droppH7.5
70.5 mMEDTA1drop
80.1 %n-octyl-beta-D-glucopyranoside1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.04 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 4, 1999
RadiationMonochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 1.99→40 Å / Num. all: 32427 / Num. obs: 32427 / % possible obs: 93.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 27.1 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 17.6
Reflection shellResolution: 1.99→2.06 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.546 / Mean I/σ(I) obs: 2.1 / Num. unique all: 3189 / % possible all: 93.5
Reflection
*PLUS
Lowest resolution: 40 Å / Num. obs: 32429 / Num. measured all: 116140 / Rmerge(I) obs: 0.056
Reflection shell
*PLUS
% possible obs: 93.5 % / Rmerge(I) obs: 0.555 / Mean I/σ(I) obs: 3.1

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AQU

1aqu


Resolution: 1.99→38 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.262 3112 -random
Rwork0.231 ---
all-31210 --
obs-34833 89.6 %-
Displacement parametersBiso mean: 42.3 Å2
Baniso -1Baniso -2Baniso -3
1-2.29 Å2-4.58 Å22.29 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 1.99→38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2377 0 52 216 2645
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.023
X-RAY DIFFRACTIONc_angle_deg2.1
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_improper_angle_d1.13
LS refinement shellResolution: 1.99→2.11 Å / Rfactor Rfree error: 0.016
RfactorNum. reflection% reflection
Rfree0.329 450 -
Rwork0.312 --
obs-5689 84.3 %
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor obs: 0.231 / Rfactor Rfree: 0.262 / Rfactor Rwork: 0.231
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.13
LS refinement shell
*PLUS
Rfactor Rfree: 0.329 / Rfactor Rwork: 0.312 / Rfactor obs: 0.312

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