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- PDB-5wrj: Crystal structure of human tyrosylprotein sulfotransferase-1 comp... -

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Basic information

Entry
Database: PDB / ID: 5wrj
TitleCrystal structure of human tyrosylprotein sulfotransferase-1 complexed with PAP and gastrin peptide
Components
  • Protein-tyrosine sulfotransferase 1
  • gastrin peptide
KeywordsTRANSFERASE
Function / homology
Function and homology information


protein-tyrosine sulfotransferase / protein-tyrosine sulfotransferase activity / Defective F8 sulfation at Y1699 / Cytosolic sulfonation of small molecules / Gamma carboxylation, hypusinylation, hydroxylation, and arylsulfatase activation / 3'-phosphoadenosine 5'-phosphosulfate metabolic process / Gastrin-CREB signalling pathway via PKC and MAPK / response to food / post-translational protein modification / trans-Golgi network ...protein-tyrosine sulfotransferase / protein-tyrosine sulfotransferase activity / Defective F8 sulfation at Y1699 / Cytosolic sulfonation of small molecules / Gamma carboxylation, hypusinylation, hydroxylation, and arylsulfatase activation / 3'-phosphoadenosine 5'-phosphosulfate metabolic process / Gastrin-CREB signalling pathway via PKC and MAPK / response to food / post-translational protein modification / trans-Golgi network / hormone activity / Golgi lumen / G alpha (q) signalling events / G protein-coupled receptor signaling pathway / Golgi membrane / Golgi apparatus / signal transduction / protein homodimerization activity / extracellular space / extracellular region / membrane
Similarity search - Function
Gastrin / Protein-tyrosine sulfotransferase / Gastrin/cholecystokinin peptide hormone / Gastrin/cholecystokinin, conserved site / Gastrin/cholecystokinin family / Gastrin / cholecystokinin family signature. / gastrin / cholecystokinin / caerulein family / Sulfotransferase family / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold ...Gastrin / Protein-tyrosine sulfotransferase / Gastrin/cholecystokinin peptide hormone / Gastrin/cholecystokinin, conserved site / Gastrin/cholecystokinin family / Gastrin / cholecystokinin family signature. / gastrin / cholecystokinin / caerulein family / Sulfotransferase family / 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 / Protein-tyrosine sulfotransferase 1 / Gastrin
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsTanaka, S. / Nishiyori, T. / Kojo, H. / Otsubo, R. / Kakuta, Y.
CitationJournal: Sci Rep / Year: 2017
Title: Structural basis for the broad substrate specificity of the human tyrosylprotein sulfotransferase-1.
Authors: Tanaka, S. / Nishiyori, T. / Kojo, H. / Otsubo, R. / Tsuruta, M. / Kurogi, K. / Liu, M.C. / Suiko, M. / Sakakibara, Y. / Kakuta, Y.
History
DepositionDec 2, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 6, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 15, 2021Group: Database references / Category: database_2 / struct_ref
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref.entity_id
Revision 1.2Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein-tyrosine sulfotransferase 1
B: Protein-tyrosine sulfotransferase 1
C: Protein-tyrosine sulfotransferase 1
D: Protein-tyrosine sulfotransferase 1
F: gastrin peptide
H: gastrin peptide
J: gastrin peptide
L: gastrin peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,43716
Polymers143,6318
Non-polymers1,8068
Water2,594144
1
A: Protein-tyrosine sulfotransferase 1
B: Protein-tyrosine sulfotransferase 1
F: gastrin peptide
H: gastrin peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,7198
Polymers71,8164
Non-polymers9034
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6740 Å2
ΔGint-48 kcal/mol
Surface area22360 Å2
MethodPISA
2
C: Protein-tyrosine sulfotransferase 1
D: Protein-tyrosine sulfotransferase 1
J: gastrin peptide
L: gastrin peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,7198
Polymers71,8164
Non-polymers9034
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6740 Å2
ΔGint-46 kcal/mol
Surface area22150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.668, 93.263, 93.012
Angle α, β, γ (deg.)90.60, 93.39, 103.39
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 34373.262 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 43-341
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TPST1 / Production host: Escherichia coli (E. coli)
References: UniProt: O60507, protein-tyrosine sulfotransferase
#2: Protein/peptide
gastrin peptide


Mass: 1534.555 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-A3P / ADENOSINE-3'-5'-DIPHOSPHATE


Type: RNA linking / Mass: 427.201 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C10H15N5O10P2 / References: UniProt: P01350*PLUS
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O
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: 2.99 Å3/Da / Density % sol: 58.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M potassium sodium tartrate trihydrate, 19.5% w/v polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Oct 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.33→50 Å / Num. obs: 71093 / % possible obs: 97.5 % / Redundancy: 1.9 % / Rsym value: 0.155 / Net I/σ(I): 8.33

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WRI

5wri


Resolution: 2.31→48.99 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.899 / Cross valid method: THROUGHOUT / ESU R: 0.32 / ESU R Free: 0.239 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26943 3560 5 %RANDOM
Rwork0.24096 ---
obs0.2424 67464 95.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 46.267 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20.01 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.31→48.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8872 108 40 144 9164
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0199426
X-RAY DIFFRACTIONr_bond_other_d00.029141
X-RAY DIFFRACTIONr_angle_refined_deg1.1751.98612784
X-RAY DIFFRACTIONr_angle_other_deg3.563321096
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.05551136
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.40623.392395
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.746151690
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.8961564
X-RAY DIFFRACTIONr_chiral_restr0.0620.21395
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02110288
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022074
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1624.5834544
X-RAY DIFFRACTIONr_mcbond_other1.1624.5834543
X-RAY DIFFRACTIONr_mcangle_it1.9556.8675671
X-RAY DIFFRACTIONr_mcangle_other1.9556.8685672
X-RAY DIFFRACTIONr_scbond_it1.1944.6994882
X-RAY DIFFRACTIONr_scbond_other1.1944.6994883
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.056.9817111
X-RAY DIFFRACTIONr_long_range_B_refined3.61235.45210396
X-RAY DIFFRACTIONr_long_range_B_other3.59435.46810364
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.309→2.369 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 200 -
Rwork0.385 3735 -
obs--71.94 %

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