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Yorodumi- PDB-8w5z: Crystal structure of tick tyrosylprotein sulfotransferase reveals... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8w5z | ||||||
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Title | Crystal structure of tick tyrosylprotein sulfotransferase reveals the activation mechanism of tick anticoagulant protein madanin | ||||||
Components |
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Keywords | TRANSFERASE / sulfotransferase / sulfation | ||||||
Function / homology | protein-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 species | Ixodes (arthropod) longicornis species complex (fry) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Yoshimura, M. / Teramoto, T. / Nishimoto, E. / Kakuta, Y. | ||||||
Funding support | Japan, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8w5z.cif.gz | 174.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8w5z.ent.gz | 136.6 KB | Display | PDB format |
PDBx/mmJSON format | 8w5z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8w5z_validation.pdf.gz | 3.5 MB | Display | wwPDB validaton report |
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Full document | 8w5z_full_validation.pdf.gz | 3.5 MB | Display | |
Data in XML | 8w5z_validation.xml.gz | 33.8 KB | Display | |
Data in CIF | 8w5z_validation.cif.gz | 49.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w5/8w5z ftp://data.pdbj.org/pub/pdb/validation_reports/w5/8w5z | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein / Protein/peptide , 2 types, 4 molecules ACBD
#1: Protein | 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 | 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 | #4: Chemical | ChemComp-1PS / #5: Chemical | ChemComp-TRS / #6: Chemical | ChemComp-MG / #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.28 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 12, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 1.55→1.65 Å / Redundancy: 8.6 % / Num. unique obs: 15003 / CC1/2: 0.529 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method 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
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→47.68 Å
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Refine LS restraints |
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LS refinement shell |
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