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- PDB-1hy3: CRYSTAL STRUCTURE OF HUMAN ESTROGEN SULFOTRANSFERASE V269E MUTANT... -

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Basic information

Entry
Database: PDB / ID: 1hy3
TitleCRYSTAL STRUCTURE OF HUMAN ESTROGEN SULFOTRANSFERASE V269E MUTANT IN THE PRESENCE OF PAPS
ComponentsESTROGEN SULFOTRANSFERASE
KeywordsTRANSFERASE / ESTROGEN / SULFOTRANSFERASE / PAPS / HUMAN
Function / homology
Function and homology information


estrogen catabolic process / estrone sulfotransferase / estrone sulfotransferase activity / flavonol 3-sulfotransferase activity / steroid sulfotransferase activity / aryl sulfotransferase activity / Cytosolic sulfonation of small molecules / 3'-phosphoadenosine 5'-phosphosulfate metabolic process / sulfation / sulfotransferase activity ...estrogen catabolic process / estrone sulfotransferase / estrone sulfotransferase activity / flavonol 3-sulfotransferase activity / steroid sulfotransferase activity / aryl sulfotransferase activity / Cytosolic sulfonation of small molecules / 3'-phosphoadenosine 5'-phosphosulfate metabolic process / sulfation / sulfotransferase activity / ethanol catabolic process / Paracetamol ADME / estrogen metabolic process / steroid metabolic process / positive regulation of fat cell differentiation / steroid binding / nuclear membrane / cytosol / cytoplasm
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'-PHOSPHATE-ADENOSINE-5'-PHOSPHATE SULFATE / Sulfotransferase 1E1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPedersen, L.C. / Petrochenko, E.V. / Shevtsov, S. / Negishi, M.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Crystal structure of the human estrogen sulfotransferase-PAPS complex: evidence for catalytic role of Ser137 in the sulfuryl transfer reaction.
Authors: Pedersen, L.C. / Petrotchenko, E. / Shevtsov, S. / Negishi, M.
History
DepositionJan 17, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
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 1.5Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.6Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)71,4274
Polymers70,4132
Non-polymers1,0152
Water8,107450
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.925, 97.263, 62.733
Angle α, β, γ (deg.)90.00, 91.93, 90.00
Int Tables number4
Space group name H-MP1211
DetailsASYMMETRIC UNIT MOST LIKELY REPRESENTS FUNCTIONAL DIMER

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Components

#1: Protein ESTROGEN SULFOTRANSFERASE / SULFOTRANSFERASE / ESTROGEN-PREFERRING


Mass: 35206.359 Da / Num. of mol.: 2 / Mutation: V269E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STE / Plasmid: PGEX4T3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P49888, estrone sulfotransferase
#2: Chemical ChemComp-PPS / 3'-PHOSPHATE-ADENOSINE-5'-PHOSPHATE SULFATE


Mass: 507.264 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O13P2S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 450 / 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: 2.68 Å3/Da / Density % sol: 54.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: MES, PEG 8K, PAP, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.2 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
115 mg/mlprotein1drop
20.5 mM1dropNaH2PO4
3100 mM1dropNaCl
44 mMPAP1droppH7.2
50.1 MMES1reservoirpH6.0
618 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 23, 2000 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→25 Å / Num. all: 63064 / Num. obs: 62882 / % possible obs: 91.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 19.6
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.229 / Mean I/σ(I) obs: 2.22 / Num. unique all: 3569 / % possible all: 52.1
Reflection
*PLUS
Num. obs: 63064 / Num. measured all: 182966 / Rmerge(I) obs: 0.049
Reflection shell
*PLUS
% possible obs: 52.1 % / Rmerge(I) obs: 0.229 / Mean I/σ(I) obs: 2.2

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Processing

Software
NameClassification
CNSrefinement
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HUMAN EST

Resolution: 1.8→22.54 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 494998.12 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: CNS target values
RfactorNum. reflection% reflectionSelection details
Rfree0.217 3123 5 %RANDOM
Rwork0.197 ---
all0.198 61877 --
obs0.197 61877 89.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.4 Å2 / ksol: 0.346 e/Å3
Displacement parametersBiso mean: 27.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.8→22.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4788 0 62 450 5300
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21.4
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_mcbond_it1.231.5
X-RAY DIFFRACTIONc_mcangle_it1.912
X-RAY DIFFRACTIONc_scbond_it1.982
X-RAY DIFFRACTIONc_scangle_it2.832.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.291 320 5.1 %
Rwork0.296 5910 -
obs--54.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3PPS.PARPPS.TOP
Refinement
*PLUS
Highest resolution: 1.82 Å / Lowest resolution: 50 Å / % reflection Rfree: 5 % / Rfactor all: 0.198 / Rfactor obs: 0.197 / Rfactor Rfree: 0.217 / Rfactor Rwork: 0.197
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.72
LS refinement shell
*PLUS
Rfactor Rfree: 0.291 / Rfactor Rwork: 0.296 / Rfactor obs: 0.296

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