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- PDB-2d06: Human Sult1A1 Complexed With Pap and estradiol -

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Basic information

Entry
Database: PDB / ID: 2d06
TitleHuman Sult1A1 Complexed With Pap and estradiol
ComponentsSulfotransferase 1A1
KeywordsTRANSFERASE / SULT 1A1 / PAP / estradiol / substrarte inhibition / dead end complex
Function / homology
Function and homology information


flavonol 3-sulfotransferase activity / aryl sulfotransferase / steroid sulfotransferase activity / 3'-phosphoadenosine 5'-phosphosulfate binding / aryl sulfotransferase activity / Cytosolic sulfonation of small molecules / flavonoid metabolic process / 3'-phosphoadenosine 5'-phosphosulfate metabolic process / sulfation / ethanol catabolic process ...flavonol 3-sulfotransferase activity / aryl sulfotransferase / steroid sulfotransferase activity / 3'-phosphoadenosine 5'-phosphosulfate binding / aryl sulfotransferase activity / Cytosolic sulfonation of small molecules / flavonoid metabolic process / 3'-phosphoadenosine 5'-phosphosulfate metabolic process / sulfation / ethanol catabolic process / sulfotransferase activity / catecholamine metabolic process / Paracetamol ADME / amine metabolic process / estrogen metabolic process / 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 / ESTRADIOL / Sulfotransferase 1A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGamage, N.U. / Tsvetanov, S. / Duggleby, R.G. / McManus, M.E. / Martin, J.L.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: The structure of human SULT1A1 crystallized with estradiol. An insight into active site plasticity and substrate inhibition with multi-ring substrates
Authors: Gamage, N.U. / Tsvetanov, S. / Duggleby, R.G. / McManus, M.E. / Martin, J.L.
History
DepositionJul 25, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 25, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Advisory / Category: pdbx_unobs_or_zero_occ_atoms
Revision 1.4Oct 25, 2023Group: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_atoms / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sulfotransferase 1A1
B: Sulfotransferase 1A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,8406
Polymers68,4412
Non-polymers1,3994
Water2,144119
1
A: Sulfotransferase 1A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9203
Polymers34,2201
Non-polymers7002
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sulfotransferase 1A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9203
Polymers34,2201
Non-polymers7002
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)123.640, 86.070, 72.950
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 Sulfotransferase 1A1 / SULT1A1 / Phenol Sulfotransferase 1 / Aryl sulfotransferase 1 / Phenol-sulfating phenol ...SULT1A1 / Phenol Sulfotransferase 1 / Aryl sulfotransferase 1 / Phenol-sulfating phenol sulfotransferase 1 / P- PST 1 / Thermostable phenol sulfotransferase / Ts-PST / HAST1/HAST2 / ST1A3


Mass: 34220.309 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: liver / Gene: SULT1A1 / Plasmid: PET20a+ / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P50225, 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-EST / ESTRADIOL / Estradiol


Mass: 272.382 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H24O2 / Comment: hormone*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.79 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Tris-HCl, 20% PEG 4000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 3, 2003 / Details: OSMIC MAXFLUX CONFOCAL BLUE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→29.77 Å / Num. all: 35314 / Num. obs: 35123 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.01 % / Biso Wilson estimate: 25.1 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 6.1
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2.96 % / Rmerge(I) obs: 0.442 / Mean I/σ(I) obs: 2.2 / % possible all: 99.8

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Processing

Software
NameVersionClassification
SCALEdata collection
TRUNCATEdata reduction
CNSrefinement
SCALEdata reduction
CCP4(TRUNCATE)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LS6

1ls6


Resolution: 2.3→29.77 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.283 448 -RANDOM
Rwork0.217 ---
all0.453 35207 --
obs0.463 35123 99.6 %-
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.77 Å0.68 Å
Refinement stepCycle: LAST / Resolution: 2.3→29.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4608 0 94 119 4821
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_improper_angle_d1.07
LS refinement shellResolution: 2.3→2.4 Å / Rfactor Rfree error: 0.022
RfactorNum. reflection% reflection
Rfree0.463 448 -
Rwork0.453 --
obs-4350 10.3 %

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