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- PDB-1efh: CRYSTAL STRUCTURE OF THE HUMAN HYDROXYSTEROID SULFOTRANSFERASE IN... -

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Basic information

Entry
Database: PDB / ID: 1efh
TitleCRYSTAL STRUCTURE OF THE HUMAN HYDROXYSTEROID SULFOTRANSFERASE IN THE PRESENCE OF PAP
ComponentsHYDROXYSTEROID SULFOTRANSFERASE
KeywordsTRANSFERASE / hydroxysteroid / sulfotransferase / DHEA / A3P / PAPS / SULT2A3
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 / thyroid hormone metabolic process / 3'-phosphoadenosine 5'-phosphosulfate binding / Cytosolic sulfonation of small molecules / 3'-phosphoadenosine 5'-phosphosulfate metabolic process ...bile-salt sulfotransferase / alcohol sulfotransferase activity / bile-salt sulfotransferase activity / alcohol sulfotransferase / steroid sulfotransferase activity / bile acid catabolic process / thyroid hormone metabolic process / 3'-phosphoadenosine 5'-phosphosulfate binding / Cytosolic sulfonation of small molecules / 3'-phosphoadenosine 5'-phosphosulfate metabolic process / sulfation / ethanol catabolic process / sulfotransferase activity / Paracetamol ADME / steroid metabolic process / lipid catabolic process / cholesterol metabolic process / xenobiotic metabolic process / PPARA activates gene expression / cytosol / cytoplasm
Similarity search - Function
Sulfotransferase domain / Sulfotransferase domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-3'-5'-DIPHOSPHATE / Sulfotransferase 2A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsPedersen, L.C. / Petrotchenko, E.V. / Negishi, M.
CitationJournal: FEBS Lett. / Year: 2000
Title: Crystal structure of SULT2A3, human hydroxysteroid sulfotransferase.
Authors: Pedersen, L.C. / Petrotchenko, E.V. / Negishi, M.
History
DepositionFeb 8, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 6, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 6, 2018Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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
Remark 300 BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ... BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). Despite the large surface interaction between the two molecules in the chosen asymmetric unit, the authors believe that the biological dimer is represented by the symmetry operators below. This data will be reported in the near future and referenced here at that time.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HYDROXYSTEROID SULFOTRANSFERASE
B: HYDROXYSTEROID SULFOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,9464
Polymers69,0912
Non-polymers8542
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-21 kcal/mol
Surface area24410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.190, 96.820, 127.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein HYDROXYSTEROID SULFOTRANSFERASE


Mass: 34545.613 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDNA LIBRARY / Organ: LIVER / Plasmid: PET21A / Production host: Escherichia coli (E. coli) / References: UniProt: Q06520, alcohol sulfotransferase
#2: Chemical ChemComp-A3P / ADENOSINE-3'-5'-DIPHOSPHATE / Adenosine 3',5'-bisphosphate


Type: RNA linking / Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 3.26 Å3/Da / Density % sol: 62.33 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 5.75
Details: 0.8 M citrate, 80 mM cacodylate, 4 mM PAP, pH 5.75, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal grow
*PLUS
pH: 7.5 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
125 mg/mlprotein11
225 mMHEPES12
34 mMPAP12
40.8 Mcitrate12
580 mMcacodylate12

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.9786
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 27, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.4→25 Å / Num. obs: 113997 / % possible obs: 94.4 % / Observed criterion σ(I): -3 / Redundancy: 3.34 % / Biso Wilson estimate: 29.6 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.3
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.146 / Num. unique all: 3087 / % possible all: 86.9
Reflection
*PLUS
Num. obs: 34110 / Num. measured all: 113997 / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
% possible obs: 86.9 % / Mean I/σ(I) obs: 6.7

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.5refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.4→20 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 585066.79 / Data cutoff high rms absF: 585066.79 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.239 1653 4.9 %RANDOM
Rwork0.202 ---
obs0.204 33481 92.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 29.18 Å2 / ksol: 0.316 e/Å3
Displacement parametersBiso mean: 36.9 Å2
Baniso -1Baniso -2Baniso -3
1--12.08 Å20 Å20 Å2
2--13.29 Å20 Å2
3----1.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4603 0 54 185 4842
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.7
X-RAY DIFFRACTIONc_improper_angle_d0.77
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.303 247 4.9 %
Rwork0.248 4786 -
obs--84.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2PAP.PARWATER_REP.TOP
X-RAY DIFFRACTION3WATER_REP.PARAPAP.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 4.9 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 36.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.77
LS refinement shell
*PLUS
Rfactor Rfree: 0.303 / % reflection Rfree: 4.9 % / Rfactor Rwork: 0.248

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