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- PDB-9wwe: Crystal structure of human tyrosylprotein sulfotransferase 2 (TPS... -

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Basic information

Entry
Database: PDB / ID: 9wwe
TitleCrystal structure of human tyrosylprotein sulfotransferase 2 (TPST2) in cation-bound state
ComponentsProtein-tyrosine sulfotransferase 2
KeywordsPEPTIDE BINDING PROTEIN / TPST2 / Sulfotransferase / Cation
Function / homology
Function and homology information


peptidyl-tyrosine sulfation / protein-tyrosine sulfotransferase / protein-tyrosine sulfotransferase activity / prevention of polyspermy / Defective F8 sulfation at Y1699 / Cytosolic sulfonation of small molecules / Gamma carboxylation, hypusinylation, hydroxylation, and arylsulfatase activation / fusion of sperm to egg plasma membrane involved in single fertilization / 3'-phosphoadenosine 5'-phosphosulfate metabolic process / trans-Golgi network ...peptidyl-tyrosine sulfation / protein-tyrosine sulfotransferase / protein-tyrosine sulfotransferase activity / prevention of polyspermy / Defective F8 sulfation at Y1699 / Cytosolic sulfonation of small molecules / Gamma carboxylation, hypusinylation, hydroxylation, and arylsulfatase activation / fusion of sperm to egg plasma membrane involved in single fertilization / 3'-phosphoadenosine 5'-phosphosulfate metabolic process / trans-Golgi network / Golgi lumen / Golgi membrane / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity
Similarity search - Function
Protein-tyrosine sulfotransferase / Sulfotransferase family / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-3'-5'-DIPHOSPHATE / L(+)-TARTARIC ACID / Protein-tyrosine sulfotransferase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsJin, M. / Yang, J. / Kim, H. / Eom, S.H.
Funding support Korea, Republic Of, 3items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2021R1A2C1006267 Korea, Republic Of
National Research Foundation (NRF, Korea)RS-2024-00344154 Korea, Republic Of
National Research Foundation (NRF, Korea)RS-2024- 00440614 Korea, Republic Of
CitationJournal: To Be Published
Title: Crystal structure of human tyrosylprotein sulfotransferase 2 (TPST2) in cation-bound state
Authors: Jin, M. / Yang, J. / Kim, H. / Eom, S.H.
History
DepositionSep 23, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 31, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein-tyrosine sulfotransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8048
Polymers35,9581
Non-polymers8467
Water4,648258
1
A: Protein-tyrosine sulfotransferase 2
hetero molecules

A: Protein-tyrosine sulfotransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,60816
Polymers71,9152
Non-polymers1,69214
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_455-x-1,y,-z1
Buried area6390 Å2
ΔGint-210 kcal/mol
Surface area24540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.254, 102.254, 103.600
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322
Space group name HallP4cw2c
Components on special symmetry positions
IDModelComponents
11A-568-

HOH

21A-746-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Protein-tyrosine sulfotransferase 2 / Tyrosylprotein sulfotransferase 2 / TPST-2


Mass: 35957.715 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TPST2 / Production host: Escherichia coli (E. coli)
References: UniProt: O60704, protein-tyrosine sulfotransferase

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Non-polymers , 6 types, 265 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-A3P / ADENOSINE-3'-5'-DIPHOSPHATE


Type: RNA linking / Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 3.77 Å3/Da / Density % sol: 67.34 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion
Details: 0.1M HEPES-NaOH (pH 7.0), 16% (w/v) PEG 6000, 0.1M Potassium sodium tartrate, 20mM ZnCl2

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Apr 2, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→46.21 Å / Num. obs: 55466 / % possible obs: 100 % / Redundancy: 26.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.144 / Χ2: 1.02 / Net I/σ(I): 18.7
Reflection shellResolution: 1.75→1.79 Å / Redundancy: 26.3 % / Rmerge(I) obs: 1.235 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 2964 / CC1/2: 0.76 / Χ2: 0.99 / % possible all: 99.2

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
PHENIX1.21_5207refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→46.21 Å / SU ML: 0.1501 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.0064
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1876 2005 3.62 %
Rwork0.1709 53396 -
obs0.1715 55401 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.29 Å2
Refinement stepCycle: LAST / Resolution: 1.75→46.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2339 0 47 258 2644
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00632476
X-RAY DIFFRACTIONf_angle_d0.90013368
X-RAY DIFFRACTIONf_chiral_restr0.0549378
X-RAY DIFFRACTIONf_plane_restr0.008429
X-RAY DIFFRACTIONf_dihedral_angle_d12.8405947
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.80.29061440.23983720X-RAY DIFFRACTION99.36
1.8-1.850.241370.22263754X-RAY DIFFRACTION100
1.85-1.90.21371480.20663746X-RAY DIFFRACTION100
1.9-1.960.21031400.1933776X-RAY DIFFRACTION100
1.96-2.030.20111390.17613762X-RAY DIFFRACTION100
2.03-2.110.17831470.16073776X-RAY DIFFRACTION100
2.11-2.210.16081380.15923780X-RAY DIFFRACTION100
2.21-2.330.2281420.16063795X-RAY DIFFRACTION100
2.33-2.470.19741410.16613800X-RAY DIFFRACTION100
2.47-2.660.17251400.16723813X-RAY DIFFRACTION99.97
2.66-2.930.1721480.17093833X-RAY DIFFRACTION100
2.93-3.360.17751430.16463861X-RAY DIFFRACTION99.98
3.36-4.230.17621430.15573899X-RAY DIFFRACTION100
4.23-46.210.18061550.17254081X-RAY DIFFRACTION99.44

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