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

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Basic information

Entry
Database: PDB / ID: 4jvl
TitleCrystal structure of human estrogen sulfotransferase (SULT1E1) in complex with inactive cofactor PAP and estradiol (E2)
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 / 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
ADENOSINE-3'-5'-DIPHOSPHATE / ESTRADIOL / Sulfotransferase 1E1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.943 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

Downloads & links

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Assembly

Deposited unit
A: Estrogen sulfotransferase
B: Estrogen sulfotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,12913
Polymers70,4132
Non-polymers1,71611
Water10,521584
1
A: Estrogen sulfotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1157
Polymers35,2061
Non-polymers9096
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Estrogen sulfotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0146
Polymers35,2061
Non-polymers8085
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.762, 96.902, 61.987
Angle α, β, γ (deg.)90.00, 92.06, 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, 595 molecules

#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-EST / ESTRADIOL


Mass: 272.382 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H24O2
#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.: 584 / 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: 54.02 %
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 11, 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: 1.943→50 Å / Num. all: 54299 / Num. obs: 54299 / % possible obs: 99.8 % / Redundancy: 3.7 % / Rsym value: 0.084 / Net I/σ(I): 14.3
Reflection shellResolution: 1.943→2.02 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 5404 / Rsym value: 0.345 / % possible all: 99.9

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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: 1.943→27.248 Å / SU ML: 0.18 / σ(F): 1.34 / Phase error: 21.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2157 2567 4.74 %PDB ENTRIES 4JVL, 4JVM, AND 4JVN USE SAME TEST SET
Rwork0.1733 ---
obs0.1753 54134 99.22 %-
all-54299 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.943→27.248 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4867 0 113 584 5564
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075214
X-RAY DIFFRACTIONf_angle_d1.1367073
X-RAY DIFFRACTIONf_dihedral_angle_d12.0881959
X-RAY DIFFRACTIONf_chiral_restr0.077723
X-RAY DIFFRACTIONf_plane_restr0.005892
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.943-1.98030.30611320.24182649X-RAY DIFFRACTION93
1.9803-2.02070.27821380.2212887X-RAY DIFFRACTION100
2.0207-2.06460.24891500.20532889X-RAY DIFFRACTION100
2.0646-2.11260.25411350.19312834X-RAY DIFFRACTION100
2.1126-2.16540.2221580.18892899X-RAY DIFFRACTION100
2.1654-2.2240.2421280.18542861X-RAY DIFFRACTION100
2.224-2.28940.24981410.19052875X-RAY DIFFRACTION100
2.2894-2.36320.23691460.18172889X-RAY DIFFRACTION100
2.3632-2.44760.24641510.1792853X-RAY DIFFRACTION100
2.4476-2.54560.21661410.18962884X-RAY DIFFRACTION100
2.5456-2.66130.23591440.18312856X-RAY DIFFRACTION100
2.6613-2.80150.25921360.18642897X-RAY DIFFRACTION99
2.8015-2.97680.23591500.19572820X-RAY DIFFRACTION98
2.9768-3.20630.18631370.18892891X-RAY DIFFRACTION99
3.2063-3.52840.22531570.16682865X-RAY DIFFRACTION100
3.5284-4.03750.18031410.14722879X-RAY DIFFRACTION99
4.0375-5.08150.15771460.13412883X-RAY DIFFRACTION99
5.0815-27.25110.2191360.16482956X-RAY DIFFRACTION100

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