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

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Entry
Database: PDB / ID: 9wwf
TitleCrystal structure of human tyrosylprotein sulfotransferase 2 (TPST2) in Mn2+-bound state
ComponentsProtein-tyrosine sulfotransferase 2
KeywordsMETAL BINDING PROTEIN / TPST2 / Sulfotransferase / Mn
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 / : / Protein-tyrosine sulfotransferase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 Mn2+-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)36,7347
Polymers35,9581
Non-polymers7766
Water5,134285
1
A: Protein-tyrosine sulfotransferase 2
hetero molecules

A: Protein-tyrosine sulfotransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,46814
Polymers71,9152
Non-polymers1,55212
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_455-x-1,y,-z1
Buried area5870 Å2
ΔGint-67 kcal/mol
Surface area24600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.817, 102.817, 103.115
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322
Space group name HallP4cw2c
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: x,-y,-z+1/2
#5: -x,y,-z
#6: -x,-y,z+1/2
#7: y,x,-z+1/4
#8: -y,-x,-z+3/4
Components on special symmetry positions
IDModelComponents
11A-783-

HOH

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Components

#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
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-A3P / ADENOSINE-3'-5'-DIPHOSPHATE


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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.79 Å3/Da / Density % sol: 67.54 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion
Details: 0.1M HEPES-NaOH (pH7.0), 14.2% (w/v) PEG 6000, 0.1M Potassium sodium tartrate, 1mM ZnCl2, 20mM MnCl2

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 29, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2→46.09 Å / Num. obs: 38050 / % possible obs: 100 % / Redundancy: 25 % / Biso Wilson estimate: 14.73 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.176 / Χ2: 1.06 / Net I/σ(I): 24.4
Reflection shellResolution: 2→2.05 Å / Redundancy: 25.1 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 10.8 / Num. unique obs: 2761 / CC1/2: 0.873 / Χ2: 1.05 / % possible all: 99.3

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
PHENIXphasing
PHENIX1.21_5207refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→46.09 Å / SU ML: 0.223 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.7252
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2255 1885 4.98 %
Rwork0.1832 35962 -
obs0.1853 37847 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.89 Å2
Refinement stepCycle: LAST / Resolution: 2→46.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2334 0 42 285 2661
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00652453
X-RAY DIFFRACTIONf_angle_d0.90163338
X-RAY DIFFRACTIONf_chiral_restr0.051376
X-RAY DIFFRACTIONf_plane_restr0.0088424
X-RAY DIFFRACTIONf_dihedral_angle_d14.0582934
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.35731450.29672715X-RAY DIFFRACTION99.06
2.05-2.110.30811450.26972716X-RAY DIFFRACTION99.72
2.11-2.180.29861390.25422708X-RAY DIFFRACTION99.65
2.18-2.260.2831460.22232727X-RAY DIFFRACTION99.69
2.26-2.350.22131450.19582757X-RAY DIFFRACTION99.97
2.35-2.460.23591420.18382735X-RAY DIFFRACTION100
2.46-2.590.22731450.16972759X-RAY DIFFRACTION99.97
2.59-2.750.20811460.17322760X-RAY DIFFRACTION100
2.75-2.960.17211430.15042763X-RAY DIFFRACTION100
2.96-3.260.20931470.16162790X-RAY DIFFRACTION99.9
3.26-3.730.20491470.14562803X-RAY DIFFRACTION99.8
3.73-4.70.16871480.13882841X-RAY DIFFRACTION99.37
4.7-46.090.21251470.1792888X-RAY DIFFRACTION96.38

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