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- PDB-8w5z: Crystal structure of tick tyrosylprotein sulfotransferase reveals... -

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Basic information

Entry
Database: PDB / ID: 8w5z
TitleCrystal structure of tick tyrosylprotein sulfotransferase reveals the activation mechanism of tick anticoagulant protein madanin
Components
  • Madanin Y54-peptide
  • Protein-tyrosine sulfotransferase (Fragment)
KeywordsTRANSFERASE / sulfotransferase / sulfation
Function / homologyprotein-tyrosine sulfotransferase / protein-tyrosine sulfotransferase activity / Protein-tyrosine sulfotransferase / Sulfotransferase family / P-loop containing nucleoside triphosphate hydrolase / 3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE / ADENOSINE-3'-5'-DIPHOSPHATE / Protein-tyrosine sulfotransferase
Function and homology information
Biological speciesIxodes (arthropod)
longicornis species complex (fry)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsYoshimura, M. / Teramoto, T. / Nishimoto, E. / Kakuta, Y.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP21K05384 Japan
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Crystal structure of tick tyrosylprotein sulfotransferase reveals the activation mechanism of the tick anticoagulant protein madanin.
Authors: Yoshimura, M. / Teramoto, T. / Asano, H. / Iwamoto, Y. / Kondo, M. / Nishimoto, E. / Kakuta, Y.
History
DepositionAug 28, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 10, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein-tyrosine sulfotransferase (Fragment)
B: Madanin Y54-peptide
C: Protein-tyrosine sulfotransferase (Fragment)
D: Madanin Y54-peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,48818
Polymers92,2434
Non-polymers2,24514
Water8,719484
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11540 Å2
ΔGint-25 kcal/mol
Surface area28730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.130, 151.190, 93.330
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-410-

MG

21A-411-

MG

31C-717-

HOH

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Components

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

#1: Protein Protein-tyrosine sulfotransferase (Fragment)


Mass: 44801.168 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ixodes (arthropod) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A147BHN3
#2: Protein/peptide Madanin Y54-peptide


Mass: 1320.227 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) longicornis species complex (fry)

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Non-polymers , 5 types, 498 molecules

#3: 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
#4: Chemical
ChemComp-1PS / 3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE / 1-(3-SULFOPROPYL) PYRIDINIUM / PPS


Mass: 201.243 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C8H11NO3S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H12NO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 484 / 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: 2.81 Å3/Da / Density % sol: 56.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M Tris HCl [pH 8.0, 0.1 M magnesium chloride, 15% v/v PEG 400, 16% w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→105.5 Å / Num. obs: 150031 / % possible obs: 100 % / Redundancy: 8.8 % / CC1/2: 0.993 / Net I/σ(I): 6.43
Reflection shellResolution: 1.55→1.65 Å / Redundancy: 8.6 % / Num. unique obs: 15003 / CC1/2: 0.529 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→47.68 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1954 1988 1.33 %
Rwork0.1731 --
obs0.1734 149908 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.55→47.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5490 0 142 484 6116
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0166155
X-RAY DIFFRACTIONf_angle_d1.4368422
X-RAY DIFFRACTIONf_dihedral_angle_d7.957885
X-RAY DIFFRACTIONf_chiral_restr0.092904
X-RAY DIFFRACTIONf_plane_restr0.0131095
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.590.29481370.310363X-RAY DIFFRACTION99
1.59-1.630.30191420.268910473X-RAY DIFFRACTION100
1.63-1.680.28331390.250910493X-RAY DIFFRACTION100
1.68-1.730.25121400.248110508X-RAY DIFFRACTION100
1.73-1.80.26031470.230510492X-RAY DIFFRACTION100
1.8-1.870.221370.201610519X-RAY DIFFRACTION100
1.87-1.950.20071460.184310543X-RAY DIFFRACTION100
1.95-2.060.19361340.177610492X-RAY DIFFRACTION100
2.06-2.180.19981470.174610576X-RAY DIFFRACTION100
2.18-2.350.19121420.160810573X-RAY DIFFRACTION100
2.35-2.590.17751460.165410591X-RAY DIFFRACTION100
2.59-2.960.2041440.168910609X-RAY DIFFRACTION100
2.96-3.740.17481430.166910705X-RAY DIFFRACTION100
3.74-47.680.18031440.150310983X-RAY DIFFRACTION100

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