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

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Basic information

Entry
Database: PDB / ID: 5wri
TitleCrystal structure of human tyrosylprotein sulfotransferase-1 complexed with PAP and C4 peptide
Components
  • ASP-PHE-GLU-ASP-TYR-GLU-PHE-ASP
  • Protein-tyrosine sulfotransferase 1
KeywordsTRANSFERASE
Function / homology
Function and homology information


protein-tyrosine sulfotransferase / protein-tyrosine sulfotransferase activity / Defective F8 sulfation at Y1699 / Gamma carboxylation, hypusinylation, hydroxylation, and arylsulfatase activation / Cytosolic sulfonation of small molecules / 3'-phosphoadenosine 5'-phosphosulfate metabolic process / post-translational protein modification / trans-Golgi network / Golgi lumen / Golgi membrane ...protein-tyrosine sulfotransferase / protein-tyrosine sulfotransferase activity / Defective F8 sulfation at Y1699 / Gamma carboxylation, hypusinylation, hydroxylation, and arylsulfatase activation / Cytosolic sulfonation of small molecules / 3'-phosphoadenosine 5'-phosphosulfate metabolic process / post-translational protein modification / trans-Golgi network / Golgi lumen / Golgi membrane / Golgi apparatus / protein homodimerization activity / membrane
Similarity search - Function
Protein-tyrosine sulfotransferase / 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
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.6 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 13, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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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
D: ASP-PHE-GLU-ASP-TYR-GLU-PHE-ASP
E: ASP-PHE-GLU-ASP-TYR-GLU-PHE-ASP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,74310
Polymers74,6834
Non-polymers1,0616
Water10,287571
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8300 Å2
ΔGint-74 kcal/mol
Surface area22070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.576, 155.972, 48.892
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABDE

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


Mass: 36262.348 Da / Num. of mol.: 2 / 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 ASP-PHE-GLU-ASP-TYR-GLU-PHE-ASP


Mass: 1079.028 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 577 molecules

#3: Chemical ChemComp-A3P / ADENOSINE-3'-5'-DIPHOSPHATE


Type: RNA linking / Mass: 427.201 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C10H15N5O10P2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 571 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.01 Å3/Da / Density % sol: 38.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M trimethylamine N-oxide dihydrate, 0.1 M Tris-HCl, pH 8.5, 20% w/v polyethylene glycol monomethyl ether 2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1.3 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 78540 / % possible obs: 98 % / Redundancy: 5.8 % / Rsym value: 0.084 / Net I/σ(I): 20.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementResolution: 1.6→31.34 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.965 / SU B: 4.096 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.08 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17807 3941 5 %RANDOM
Rwork0.13327 ---
obs0.13548 74483 97.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 19.394 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.03 Å20 Å2
3----0.04 Å2
Refinement stepCycle: 1 / Resolution: 1.6→31.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4499 0 63 571 5133
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0195166
X-RAY DIFFRACTIONr_bond_other_d0.0020.025014
X-RAY DIFFRACTIONr_angle_refined_deg1.5161.9857092
X-RAY DIFFRACTIONr_angle_other_deg1.0283.00111646
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6685.015678
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.8123.256215
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.36215945
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1051535
X-RAY DIFFRACTIONr_chiral_restr0.0970.2772
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215808
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021171
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_it1.6451.6972462
X-RAY DIFFRACTIONr_mcbond_other1.6451.6982463
X-RAY DIFFRACTIONr_mcangle_it2.1012.5443127
X-RAY DIFFRACTIONr_mcangle_other2.1012.5443128
X-RAY DIFFRACTIONr_scbond_it1.791.9342704
X-RAY DIFFRACTIONr_scbond_other1.791.9342704
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0842.8073929
X-RAY DIFFRACTIONr_long_range_B_refined3.24415.0556452
X-RAY DIFFRACTIONr_long_range_B_other2.92814.5236278
X-RAY DIFFRACTIONr_rigid_bond_restr4.015310180
X-RAY DIFFRACTIONr_sphericity_free34.7345143
X-RAY DIFFRACTIONr_sphericity_bonded7.76510418
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 200 -
Rwork0.342 4189 -
obs--75 %

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