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- PDB-1g3m: CRYSTAL STRUCTURE OF HUMAN ESTROGEN SULFOTRANSFERASE IN COMPLEX W... -

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Basic information

Entry
Database: PDB / ID: 1g3m
TitleCRYSTAL STRUCTURE OF HUMAN ESTROGEN SULFOTRANSFERASE IN COMPLEX WITH IN-ACTIVE COFACTOR PAP AND 3,5,3',5'-TETRACHLORO-BIPHENYL-4,4'-DIOL
ComponentsESTROGEN SULFOTRANSFERASE
KeywordsTRANSFERASE / estrogen / sulfotransferase / PCB / 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 / ethanol catabolic process ...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 / ethanol catabolic process / sulfotransferase activity / 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
ADENOSINE-3'-5'-DIPHOSPHATE / 3,5,3',5'-TETRACHLORO-BIPHENYL-4,4'-DIOL / Sulfotransferase 1E1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsShevtsov, S. / Petrochenko, E.V. / Negishi, M. / Pedersen, L.C.
CitationJournal: Environ.Health Perspect. / Year: 2003
Title: Crystallographic analysis of a hydroxylated polychlorinated biphenyl (OH-PCB) bound to the catalytic estrogen binding site of human estrogen sulfotransferase.
Authors: Shevtsov, S. / Petrotchenko, E.V. / Pedersen, L.C. / Negishi, M.
History
DepositionOct 24, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 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)72,10310
Polymers70,3532
Non-polymers1,7518
Water10,863603
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.687, 96.894, 61.724
Angle α, β, γ (deg.)90.00, 92.58, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe asymmetric unit represents the proposed biological dimer.

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Components

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


Mass: 35176.375 Da / Num. of mol.: 2
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-A3P / ADENOSINE-3'-5'-DIPHOSPHATE


Type: RNA linking / Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2
#3: Chemical ChemComp-PCQ / 3,5,3',5'-TETRACHLORO-BIPHENYL-4,4'-DIOL


Mass: 323.987 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H6Cl4O2
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 603 / 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: 2.66 Å3/Da / Density % sol: 53.77 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M MES 22% PEG8000 , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
115 mg/mlprotein1drop
20.5 mMmonosodium phosphate1drop
3100 mM1dropNaCl
44 mMPAP1droppH7.5
50.1 MMES1reservoirpH6.0
618 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.542 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 15, 2000 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.7→25 Å / Num. obs: 81460 / % possible obs: 92.6 % / Observed criterion σ(I): -3 / Redundancy: 2 % / Biso Wilson estimate: 18.4 Å2 / Rsym value: 0.058 / Net I/σ(I): 8.39
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 1.37 % / Mean I/σ(I) obs: 1.94 / Rsym value: 0.262 / % possible all: 82.9
Reflection
*PLUS
Lowest resolution: 50 Å / Num. obs: 75359 / Num. measured all: 151066 / Rmerge(I) obs: 0.058
Reflection shell
*PLUS
% possible obs: 82.9 % / Rmerge(I) obs: 0.262 / Mean I/σ(I) obs: 1.9

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CCP4model building
CNSrefinement
Omodel building
CCP4phasing
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HUMAN EST

Resolution: 1.7→24.53 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 644110.07 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.219 3751 5.1 %RANDOM
Rwork0.193 ---
obs0.193 74034 91.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.22 Å2 / ksol: 0.369 e/Å3
Displacement parametersBiso mean: 21.4 Å2
Baniso -1Baniso -2Baniso -3
1--3.34 Å20 Å21.79 Å2
2--0.62 Å20 Å2
3---2.73 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.7→24.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4775 0 106 603 5484
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.131.5
X-RAY DIFFRACTIONc_mcangle_it1.712
X-RAY DIFFRACTIONc_scbond_it1.772
X-RAY DIFFRACTIONc_scangle_it2.572.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.282 517 4.7 %
Rwork0.274 10563 -
obs--82.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3COMBINE.PARPAP.TOP
X-RAY DIFFRACTION4TCB.TOP
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 50 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.76

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