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- PDB-8k9y: Crystal structure of Arabidopsis thaliana sulfotransferase SOT16 ... -

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Basic information

Entry
Database: PDB / ID: 8k9y
TitleCrystal structure of Arabidopsis thaliana sulfotransferase SOT16 involved in glucosinolate biosynthesis
ComponentsCytosolic sulfotransferase 16
KeywordsTRANSFERASE / sulfotransferase / sulfation
Function / homology
Function and homology information


aromatic desulfoglucosinolate sulfotransferase / response to jasmonic acid stimulus involved in jasmonic acid and ethylene-dependent systemic resistance / glucosinolate biosynthetic process / aromatic desulfoglucosinolate sulfotransferase activity / mitochondrion
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 / CITRATE ANION / ISOPROPYL ALCOHOL / Cytosolic sulfotransferase 16
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsIwamoto, Y. / Saito, S. / Teramoto, T. / Kakuta, Y.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP21K05384 Japan
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2023
Title: Crystal structure of Arabidopsis thaliana sulfotransferase SOT16 involved in glucosinolate biosynthesis.
Authors: Iwamoto, Y. / Saito, S. / Teramoto, T. / Maruyama-Nakashita, A. / Kakuta, Y.
History
DepositionAug 2, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 13, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytosolic sulfotransferase 16
B: Cytosolic sulfotransferase 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,83810
Polymers75,2692
Non-polymers1,5698
Water13,475748
1
A: Cytosolic sulfotransferase 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3434
Polymers37,6351
Non-polymers7083
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytosolic sulfotransferase 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4956
Polymers37,6351
Non-polymers8615
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.430, 138.240, 63.130
Angle α, β, γ (deg.)90.00, 104.88, 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 Cytosolic sulfotransferase 16


Mass: 37634.531 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SOT16 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9C9D0

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Non-polymers , 5 types, 756 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C3H8O3
#4: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#5: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 748 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.95 Å3/Da / Density % sol: 58.34 %
Crystal growTemperature: 293.4 K / Method: vapor diffusion, sitting drop / Details: PEG

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 3, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.82→47.58 Å / Num. obs: 73012 / % possible obs: 95 % / Redundancy: 3.32 % / CC1/2: 0.99 / Net I/σ(I): 8.28
Reflection shellResolution: 1.82→1.95 Å / Num. unique obs: 7301 / CC1/2: 0.746

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.82→47.58 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2044 3651 5 %
Rwork0.1625 --
obs0.1646 73012 94.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.82→47.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5288 0 102 748 6138
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0185591
X-RAY DIFFRACTIONf_angle_d1.477589
X-RAY DIFFRACTIONf_dihedral_angle_d8.087734
X-RAY DIFFRACTIONf_chiral_restr0.087771
X-RAY DIFFRACTIONf_plane_restr0.013974
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.82-1.840.34381210.3152122X-RAY DIFFRACTION76
1.84-1.870.32811330.30422313X-RAY DIFFRACTION81
1.87-1.90.33961170.28792359X-RAY DIFFRACTION84
1.9-1.920.30661400.26212565X-RAY DIFFRACTION90
1.92-1.950.29851200.23382699X-RAY DIFFRACTION95
1.95-1.990.26971410.21462696X-RAY DIFFRACTION96
1.99-2.020.28381290.19522809X-RAY DIFFRACTION97
2.02-2.060.21461500.18672705X-RAY DIFFRACTION97
2.06-2.10.22581500.18092779X-RAY DIFFRACTION97
2.1-2.140.2411600.17792681X-RAY DIFFRACTION97
2.14-2.190.2191670.17412777X-RAY DIFFRACTION97
2.19-2.240.25271410.17342714X-RAY DIFFRACTION97
2.24-2.290.21151430.16752731X-RAY DIFFRACTION96
2.29-2.350.20491330.16842759X-RAY DIFFRACTION97
2.35-2.420.23411300.16692773X-RAY DIFFRACTION97
2.42-2.50.21691370.16092768X-RAY DIFFRACTION97
2.5-2.590.20811610.16652695X-RAY DIFFRACTION97
2.59-2.70.23211430.16512743X-RAY DIFFRACTION97
2.7-2.820.19841400.16382722X-RAY DIFFRACTION96
2.82-2.970.2221470.17062723X-RAY DIFFRACTION96
2.97-3.150.19721550.16052727X-RAY DIFFRACTION96
3.15-3.40.181120.15142766X-RAY DIFFRACTION97
3.4-3.740.17121530.13652721X-RAY DIFFRACTION95
3.74-4.280.15381500.12962686X-RAY DIFFRACTION96
4.28-5.390.1761340.12512687X-RAY DIFFRACTION94
5.39-47.580.18081440.15462641X-RAY DIFFRACTION91
Refinement TLS params.Method: refined / Origin x: -19.4485 Å / Origin y: 19.8376 Å / Origin z: 16.2756 Å
111213212223313233
T0.1429 Å20.0129 Å2-0.0027 Å2-0.2252 Å20.0262 Å2--0.1412 Å2
L0.0215 °20.2829 °20.0368 °2-2.2495 °20.3935 °2--0.1858 °2
S0.026 Å °-0.0325 Å °-0.0033 Å °0.1149 Å °-0.0395 Å °-0.1015 Å °0.0354 Å °0.0017 Å °0.0079 Å °
Refinement TLS groupSelection details: all

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