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- PDB-7v1o: Crystal structure of mouse cytosolic sulfotransferase mSULT3A1 -

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Basic information

Entry
Database: PDB / ID: 7v1o
TitleCrystal structure of mouse cytosolic sulfotransferase mSULT3A1
ComponentsAmine sulfotransferase
KeywordsTRANSFERASE / Sulfotransferase Cytosolic sulfotransferase SULT
Function / homology
Function and homology information


amine sulfotransferase / amine sulfotransferase activity / sulfation / sulfotransferase activity / cytoplasm
Similarity search - Function
Sulfotransferase domain / Sulfotransferase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
naphthalen-1-amine / ADENOSINE-3'-5'-DIPHOSPHATE / Amine sulfotransferase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsTeramoto, T. / Inada, K. / Kakuta, Y.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)21K05384 Japan
CitationJournal: To Be Published
Title: Crystal structure of SULT3A1, mouse amine N-sulfotransferase
Authors: Teramoto, T. / Inada, K. / Kurogi, K. / Sakakibara, Y. / Kakuta, Y.
History
DepositionAug 5, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)71,4996
Polymers70,3582
Non-polymers1,1414
Water1,26170
1
A: Amine sulfotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7503
Polymers35,1791
Non-polymers5702
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint-5 kcal/mol
Surface area12940 Å2
MethodPISA
2
B: Amine sulfotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7503
Polymers35,1791
Non-polymers5702
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint-5 kcal/mol
Surface area12810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.440, 116.440, 203.310
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-551-

HOH

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Components

#1: Protein Amine sulfotransferase / SULT-X2 / Sulfotransferase 3A1 / ST3A1


Mass: 35179.215 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sult3a1, St3a1 / Production host: Escherichia coli (E. coli) / References: UniProt: O35403, amine sulfotransferase
#2: Chemical ChemComp-5I2 / naphthalen-1-amine


Mass: 143.185 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C10H9N / Feature type: SUBJECT OF INVESTIGATION
#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 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O
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: 2.89 Å3/Da / Density % sol: 57.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 26% PEG 3,350 200 mM LiSO4 20 mM DTT 100 mM Tris, pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 29326 / % possible obs: 89.9 % / Redundancy: 9.6 % / Rsym value: 0.056 / Net I/σ(I): 22.3
Reflection shellResolution: 2.4→2.48 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1732 / Rsym value: 0.426 / % possible all: 60.2

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→30.11 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.267 1496 5.1 %
Rwork0.231 --
obs0.2328 29324 90 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→30.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4857 0 76 70 5003
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045098
X-RAY DIFFRACTIONf_angle_d0.6436890
X-RAY DIFFRACTIONf_dihedral_angle_d23.8731886
X-RAY DIFFRACTIONf_chiral_restr0.045711
X-RAY DIFFRACTIONf_plane_restr0.003867
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.480.3542950.3561637X-RAY DIFFRACTION60
2.48-2.570.3551020.33732008X-RAY DIFFRACTION73
2.57-2.670.41141110.3562395X-RAY DIFFRACTION86
2.67-2.790.45721540.34582646X-RAY DIFFRACTION96
2.79-2.940.36561250.32462713X-RAY DIFFRACTION98
2.94-3.120.31891590.30642692X-RAY DIFFRACTION97
3.12-3.360.31651430.28552716X-RAY DIFFRACTION97
3.36-3.70.29951670.24112677X-RAY DIFFRACTION97
3.7-4.230.25641380.19972744X-RAY DIFFRACTION96
4.23-5.330.20381440.17792758X-RAY DIFFRACTION96
5.33-30.110.20681580.19032842X-RAY DIFFRACTION93

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