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- PDB-22ga: Crystal structure of sorghum sulfotransferase LGS1 reveals sulfat... -

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Basic information

Entry
Database: PDB / ID: 22ga
TitleCrystal structure of sorghum sulfotransferase LGS1 reveals sulfation-assisted BC-ring formation in strigolactone biosynthesis
ComponentsSulfotransferase
KeywordsTRANSFERASE / Sulfotransferase / LGS1 / strigolactone
Function / homologyTransferases; Transferring sulfur-containing groups; Sulfotransferases / sulfation / sulfotransferase activity / Sulfotransferase domain / Sulfotransferase domain / P-loop containing nucleoside triphosphate hydrolase / cytoplasm / ADENOSINE-3'-5'-DIPHOSPHATE / Sulfotransferase
Function and homology information
Biological speciesSorghum bicolor (sorghum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsAsano, H. / Teramoto, T. / Kakuta, Y.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)24K09353 Japan
Japan Society for the Promotion of Science (JSPS)25H01276 Japan
CitationJournal: To Be Published
Title: Crystal structure of sorghum sulfotransferase LGS1 reveals sulfation-assisted BC-ring formation in strigolactone biosynthesis
Authors: Asano, H. / Teramoto, T. / Kakuta, Y.
History
DepositionJan 9, 2026Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 4, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sulfotransferase
B: Sulfotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,72811
Polymers81,2292
Non-polymers1,4999
Water5,603311
1
A: Sulfotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3185
Polymers40,6151
Non-polymers7034
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area780 Å2
ΔGint-4 kcal/mol
Surface area15450 Å2
MethodPISA
2
B: Sulfotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4106
Polymers40,6151
Non-polymers7965
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area780 Å2
ΔGint-4 kcal/mol
Surface area15880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.920, 96.500, 179.930
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Sulfotransferase


Mass: 40614.512 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sorghum bicolor (sorghum) / Gene: LGS1, SORBI_3005G213600 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A1B6PTZ0, Transferases; Transferring sulfur-containing groups; Sulfotransferases
#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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 311 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.19 Å3/Da / Density % sol: 43.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 11, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.94→48.25 Å / Num. obs: 53943 / % possible obs: 100 % / Redundancy: 10.73 % / CC1/2: 0.999 / Net I/σ(I): 11.84
Reflection shellResolution: 1.94→2.06 Å / Num. unique obs: 8746 / CC1/2: 0.669

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Processing

Software
NameVersionClassification
PHENIX(1.21.1_5286: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.94→48.25 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2664 1994 3.71 %
Rwork0.2259 --
obs0.2274 53745 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.94→48.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5139 0 96 311 5546
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035571
X-RAY DIFFRACTIONf_angle_d0.5567582
X-RAY DIFFRACTIONf_dihedral_angle_d14.4932075
X-RAY DIFFRACTIONf_chiral_restr0.039805
X-RAY DIFFRACTIONf_plane_restr0.005980
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-1.990.38551370.42683581X-RAY DIFFRACTION100
1.99-2.040.39821430.38273679X-RAY DIFFRACTION100
2.04-2.10.37381390.35743605X-RAY DIFFRACTION100
2.1-2.170.37041390.3373672X-RAY DIFFRACTION100
2.17-2.250.41021410.31643633X-RAY DIFFRACTION100
2.25-2.340.30711420.29983656X-RAY DIFFRACTION100
2.34-2.440.29351400.27163667X-RAY DIFFRACTION100
2.44-2.570.3151420.2413672X-RAY DIFFRACTION100
2.57-2.730.24451420.24083684X-RAY DIFFRACTION100
2.73-2.950.28621410.24373698X-RAY DIFFRACTION100
2.95-3.240.30341440.22243701X-RAY DIFFRACTION100
3.24-3.710.24991450.19793765X-RAY DIFFRACTION100
3.71-4.670.20371450.17313767X-RAY DIFFRACTION100
4.68-48.250.22591540.18493971X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -15.1723 Å / Origin y: -0.0553 Å / Origin z: -62.4842 Å
111213212223313233
T0.1889 Å20.0111 Å20.0011 Å2-0.3705 Å2-0.0034 Å2--0.3283 Å2
L0.0836 °2-0.0179 °2-0.0198 °2-0.5983 °20.3544 °2--2.7718 °2
S0.013 Å °0.1187 Å °0.0692 Å °-0.0951 Å °0.0005 Å °-0.1164 Å °-0.1519 Å °0.321 Å °-0.0187 Å °
Refinement TLS groupSelection details: all

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