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Yorodumi- PDB-5wrj: Crystal structure of human tyrosylprotein sulfotransferase-1 comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5wrj | ||||||
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Title | Crystal structure of human tyrosylprotein sulfotransferase-1 complexed with PAP and gastrin peptide | ||||||
Components |
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Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information peptidyl-tyrosine sulfation / 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 / sulfotransferase activity / Gastrin-CREB signalling pathway via PKC and MAPK / response to food ...peptidyl-tyrosine sulfation / 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 / sulfotransferase activity / Gastrin-CREB signalling pathway via PKC and MAPK / response to food / hormone activity / G alpha (q) signalling events / inflammatory response / G protein-coupled receptor signaling pathway / Golgi membrane / Golgi apparatus / signal transduction / protein homodimerization activity / extracellular space / extracellular region / membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å | ||||||
Authors | Tanaka, S. / Nishiyori, T. / Kojo, H. / Otsubo, R. / Kakuta, Y. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5wrj.cif.gz | 240 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wrj.ent.gz | 190.7 KB | Display | PDB format |
PDBx/mmJSON format | 5wrj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5wrj_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 5wrj_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 5wrj_validation.xml.gz | 40.8 KB | Display | |
Data in CIF | 5wrj_validation.cif.gz | 55.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wr/5wrj ftp://data.pdbj.org/pub/pdb/validation_reports/wr/5wrj | HTTPS FTP |
-Related structure data
Related structure data | 5wriSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | 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 | Mass: 1534.555 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: Chemical | ChemComp-A3P / #4: Chemical | ChemComp-MG / #5: Water | ChemComp-HOH / | |
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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: 2.99 Å3/Da / Density % sol: 58.91 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M potassium sodium tartrate trihydrate, 19.5% w/v polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Oct 14, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.33→50 Å / Num. obs: 71093 / % possible obs: 97.5 % / Redundancy: 1.9 % / Rsym value: 0.155 / Net I/σ(I): 8.33 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 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
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.267 Å2
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Refinement step | Cycle: 1 / Resolution: 2.31→48.99 Å
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Refine LS restraints |
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