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- PDB-4jvm: Crystal structure of human estrogen sulfotransferase (SULT1E1) in... -

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Basic information

Entry
Database: PDB / ID: 4jvm
TitleCrystal structure of human estrogen sulfotransferase (SULT1E1) in complex with inactive cofactor PAP and brominated flame retardant TBBPA (tetrabromobisphenol A)
ComponentsEstrogen sulfotransferase
KeywordsTRANSFERASE / cytosolic sulfotransferase
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
ADENOSINE-3'-5'-DIPHOSPHATE / 4,4'-propane-2,2-diylbis(2,6-dibromophenol) / Sulfotransferase 1E1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.994 Å
AuthorsGosavi, R.A. / Knudsen, G.A. / Birnbaum, L.S. / Pedersen, L.C.
CitationJournal: Environ.Health Perspect. / Year: 2013
Title: Mimicking of Estradiol Binding by Flame Retardants and Their Metabolites: A Crystallographic Analysis.
Authors: Gosavi, R.A. / Knudsen, G.A. / Birnbaum, L.S. / Pedersen, L.C.
History
DepositionMar 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2013Group: Database references
Revision 1.2Sep 20, 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_asym_id / _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_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)72,67213
Polymers70,4132
Non-polymers2,25911
Water9,044502
1
A: Estrogen sulfotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3256
Polymers35,2061
Non-polymers1,1185
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Estrogen sulfotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3487
Polymers35,2061
Non-polymers1,1416
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.566, 97.437, 61.779
Angle α, β, γ (deg.)90.00, 91.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Estrogen sulfotransferase / EST-1 / Sulfotransferase 1E1 / ST1E1 / 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, SULT1E1 / Production host: Escherichia coli (E. coli) / References: UniProt: P49888, estrone sulfotransferase

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Non-polymers , 5 types, 513 molecules

#2: Chemical ChemComp-XDI / 4,4'-propane-2,2-diylbis(2,6-dibromophenol)


Mass: 543.871 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H12Br4O2
#3: Chemical ChemComp-A3P / ADENOSINE-3'-5'-DIPHOSPHATE


Type: RNA linking / Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 502 / 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: 2.67 Å3/Da / Density % sol: 53.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES, pH 7.5, 18-24% w/v PEG8000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: Dec 4, 2012 / Details: VARIMAX-HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.994→50 Å / Num. all: 49762 / Num. obs: 49762 / % possible obs: 99 % / Redundancy: 6.1 % / Rsym value: 0.119 / Net I/σ(I): 13.2
Reflection shellResolution: 1.994→2.07 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2 / Rsym value: 0.548 / % possible all: 93.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1G3M

1g3m


Resolution: 1.994→27.167 Å / SU ML: 0.21 / σ(F): 1.33 / Phase error: 23.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2304 2352 4.77 %
Rwork0.1828 --
obs0.1851 49280 97.68 %
all-49762 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.994→27.167 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4878 0 115 502 5495
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075186
X-RAY DIFFRACTIONf_angle_d1.0457026
X-RAY DIFFRACTIONf_dihedral_angle_d14.4691952
X-RAY DIFFRACTIONf_chiral_restr0.073708
X-RAY DIFFRACTIONf_plane_restr0.006885
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9937-2.03440.31581290.27722398X-RAY DIFFRACTION85
2.0344-2.07860.23861460.21992632X-RAY DIFFRACTION95
2.0786-2.12690.25381360.20052737X-RAY DIFFRACTION97
2.1269-2.18010.23791500.19292791X-RAY DIFFRACTION99
2.1801-2.2390.2511310.18762813X-RAY DIFFRACTION100
2.239-2.30490.25971390.19992821X-RAY DIFFRACTION100
2.3049-2.37920.24291340.18852823X-RAY DIFFRACTION100
2.3792-2.46420.25241440.20532812X-RAY DIFFRACTION100
2.4642-2.56280.26051390.21422804X-RAY DIFFRACTION99
2.5628-2.67930.30021390.21412784X-RAY DIFFRACTION99
2.6793-2.82050.31461380.22822762X-RAY DIFFRACTION98
2.8205-2.9970.24731320.23372652X-RAY DIFFRACTION94
2.997-3.2280.23371350.20522793X-RAY DIFFRACTION98
3.228-3.55220.21841510.1642794X-RAY DIFFRACTION100
3.5522-4.06480.1961350.15872828X-RAY DIFFRACTION99
4.0648-5.11560.17721400.13872785X-RAY DIFFRACTION98
5.1156-27.16910.21571340.15722899X-RAY DIFFRACTION100

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