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- PDB-7eov: Crystal structure of mouse cytosolic sulfotransferase mSULT2A8 in... -

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Basic information

Entry
Database: PDB / ID: 7eov
TitleCrystal structure of mouse cytosolic sulfotransferase mSULT2A8 in complex with PAP and cholic acid
Componentscytosolic sulfotransferase SULT2A8
KeywordsTRANSFERASE / Sulfotransferase Sulfation Bile acid metabolism
Function / homology
Function and homology information


glycochenodeoxycholate sulfotransferase / alcohol sulfotransferase activity / bile-salt sulfotransferase activity / steroid sulfotransferase activity / bile acid catabolic process / 3'-phosphoadenosine 5'-phosphosulfate binding / thyroid hormone metabolic process / 3'-phosphoadenosine 5'-phosphosulfate metabolic process / sulfation / ethanol catabolic process ...glycochenodeoxycholate sulfotransferase / alcohol sulfotransferase activity / bile-salt sulfotransferase activity / steroid sulfotransferase activity / bile acid catabolic process / 3'-phosphoadenosine 5'-phosphosulfate binding / thyroid hormone metabolic process / 3'-phosphoadenosine 5'-phosphosulfate metabolic process / sulfation / ethanol catabolic process / sulfotransferase activity / steroid metabolic process / lipid catabolic process / xenobiotic metabolic process / cholesterol metabolic process / cytosol / cytoplasm
Similarity search - Function
Sulfotransferase domain / Sulfotransferase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-3'-5'-DIPHOSPHATE / CHOLIC ACID / Sulfotransferase 2A8
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsTeramoto, T. / Nishio, T. / Kakuta, Y.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2021
Title: The crystal structure of mouse SULT2A8 reveals the mechanism of 7 alpha-hydroxyl, bile acid sulfation.
Authors: Teramoto, T. / Nishio, T. / Kurogi, K. / Sakakibara, Y. / Kakuta, Y.
History
DepositionApr 22, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 9, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: cytosolic sulfotransferase SULT2A8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7524
Polymers35,5081
Non-polymers1,2443
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1060 Å2
ΔGint-3 kcal/mol
Surface area13300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.564, 94.564, 244.555
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein cytosolic sulfotransferase SULT2A8


Mass: 35507.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sult2a8, 2810007J24Rik / Production host: Escherichia coli (E. coli)
References: UniProt: Q8BGL3, Transferases; Transferring sulfur-containing groups; Sulfotransferases
#2: Chemical ChemComp-A3P / ADENOSINE-3'-5'-DIPHOSPHATE / Adenosine 3',5'-bisphosphate


Type: RNA linking / Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CHD / CHOLIC ACID / Cholic acid


Mass: 408.571 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H40O5 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 4.22 Å3/Da / Density % sol: 70.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.5M ammonium sulfate, 0.1M tri-sodium citrate dihydrate pH 5.6, 0.7M lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 23, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→47.3 Å / Num. obs: 17560 / % possible obs: 99.6 % / Redundancy: 14.3 % / CC1/2: 1 / Rpim(I) all: 0.022 / Net I/σ(I): 24.4
Reflection shellResolution: 2.6→2.73 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2425 / CC1/2: 0.741 / Rpim(I) all: 0.549

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1q22

1q22


Resolution: 2.6→37.4 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2652 935 5.32 %
Rwork0.2344 --
obs0.2359 17560 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→37.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2289 0 85 0 2374
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112442
X-RAY DIFFRACTIONf_angle_d1.0363319
X-RAY DIFFRACTIONf_dihedral_angle_d26.953883
X-RAY DIFFRACTIONf_chiral_restr0.072362
X-RAY DIFFRACTIONf_plane_restr0.007404
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.730.37051140.33512311X-RAY DIFFRACTION98
2.73-2.90.34511280.30992341X-RAY DIFFRACTION100
2.9-3.130.34971370.30632323X-RAY DIFFRACTION100
3.13-3.440.29271490.2692343X-RAY DIFFRACTION100
3.44-3.940.27751480.23712370X-RAY DIFFRACTION100
3.94-4.960.21221230.20532399X-RAY DIFFRACTION100
4.97-37.40.24981360.21312538X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 38.526 Å / Origin y: 25.1805 Å / Origin z: -15.5555 Å
111213212223313233
T0.7781 Å20.1047 Å2-0.041 Å2-0.4714 Å20.024 Å2--0.4653 Å2
L4.4491 °2-0.4123 °2-0.4409 °2-5.2694 °20.967 °2--2.1944 °2
S0.2145 Å °0.0863 Å °-0.008 Å °-0.5348 Å °-0.182 Å °-0.362 Å °-0.1222 Å °-0.1632 Å °-0.0519 Å °
Refinement TLS groupSelection details: all

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