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- PDB-2a3r: Crystal Structure of Human Sulfotransferase SULT1A3 in Complex wi... -

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Basic information

Entry
Database: PDB / ID: 2a3r
TitleCrystal Structure of Human Sulfotransferase SULT1A3 in Complex with Dopamine and 3-Phosphoadenosine 5-Phosphate
ComponentsMonoamine-sulfating phenol sulfotransferase
KeywordsTRANSFERASE / SULT1A3 / dopamine / complex / sulfotransferase
Function / homology
Function and homology information


amine sulfotransferase activity / aryl sulfotransferase / : / aryl sulfotransferase activity / Cytosolic sulfonation of small molecules / flavonoid metabolic process / 3'-phosphoadenosine 5'-phosphosulfate metabolic process / sulfation / calcineurin-mediated signaling / ethanol catabolic process ...amine sulfotransferase activity / aryl sulfotransferase / : / aryl sulfotransferase activity / Cytosolic sulfonation of small molecules / flavonoid metabolic process / 3'-phosphoadenosine 5'-phosphosulfate metabolic process / sulfation / calcineurin-mediated signaling / ethanol catabolic process / sulfotransferase activity / NMDA selective glutamate receptor signaling pathway / XBP1(S) activates chaperone genes / sulfate binding / dopamine catabolic process / Paracetamol ADME / cellular response to dopamine / dopamine receptor signaling pathway / dopamine metabolic process / steroid metabolic process / ERK1 and ERK2 cascade / xenobiotic metabolic process / 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 / L-DOPAMINE / Sulfotransferase 1A3 / Sulfotransferase 1A3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLu, J.H. / Li, H.T. / Liu, M.C. / Zhang, J.P. / Li, M. / An, X.M. / Chang, W.R.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2005
Title: Crystal structure of human sulfotransferase SULT1A3 in complex with dopamine and 3'-phosphoadenosine 5'-phosphate
Authors: Lu, J.H. / Li, H.T. / Liu, M.C. / Zhang, J.P. / Li, M. / An, X.M. / Chang, W.R.
History
DepositionJun 26, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 30, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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 / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_sheet.number_strands / _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: Monoamine-sulfating phenol sulfotransferase
B: Monoamine-sulfating phenol sulfotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,6356
Polymers68,4742
Non-polymers1,1614
Water1,62190
1
A: Monoamine-sulfating phenol sulfotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8183
Polymers34,2371
Non-polymers5802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Monoamine-sulfating phenol sulfotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8183
Polymers34,2371
Non-polymers5802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.263, 123.610, 73.116
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Monoamine-sulfating phenol sulfotransferase / SULT1A3 / Aryl sulfotransferase 1A3 / Sulfotransferase / monoamine-preferring / M-PST / ...SULT1A3 / Aryl sulfotransferase 1A3 / Sulfotransferase / monoamine-preferring / M-PST / Thermolabile phenol sulfotransferase / TL-PST / Placental estrogen sulfotransferase / Catecholamine-sulfating phenol sulfotransferase / HAST3


Mass: 34237.125 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX-2TK / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P50224, UniProt: P0DMM9*PLUS, aryl 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: Chemical ChemComp-LDP / L-DOPAMINE / DOPAMINE / Dopamine (medication)


Mass: 153.178 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H11NO2 / Comment: medication*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.63 Å3/Da / Density % sol: 52.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: PEG 4000, MES, Calcium Acetate, PAP, Dopamine, BAM, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL12B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 18, 2003
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→25 Å / Num. all: 21854 / Num. obs: 21767 / % possible obs: 99.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.99 % / Biso Wilson estimate: 37 Å2 / Rmerge(I) obs: 0.115
Reflection shellResolution: 2.6→2.69 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
MOLREPphasing
CNS1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1LS6

1ls6


Resolution: 2.6→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.243 1669 Random
Rwork0.206 --
all0.238 22710 -
obs0.238 20986 -
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.46 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4698 0 76 90 4864
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.57
X-RAY DIFFRACTIONc_dihedral_angle_d22.77
X-RAY DIFFRACTIONc_improper_angle_d0.89
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection obs% reflection obs (%)
2.6-2.690.3361100.284125756.2
2.69-2.80.3121570.268204692.5
2.8-2.930.3031720.252210492.8
2.93-3.080.3411620.262212195.4
3.08-3.270.3241920.253213795.2
3.27-3.520.2521800.218219197.8

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