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Yorodumi- PDB-1yts: A LIGAND-INDUCED CONFORMATIONAL CHANGE IN THE YERSINIA PROTEIN TY... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1yts | ||||||
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Title | A LIGAND-INDUCED CONFORMATIONAL CHANGE IN THE YERSINIA PROTEIN TYROSINE PHOSPHATASE | ||||||
Components | YERSINIA PROTEIN TYROSINE PHOSPHATASE | ||||||
Keywords | HYDROLASE / PROTEIN TYROSINE PHOSPHATASE | ||||||
Function / homology | Function and homology information protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / extracellular region Similarity search - Function | ||||||
Biological species | Yersinia enterocolitica (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.5 Å | ||||||
Authors | Schubert, H.L. / Stuckey, J.A. / Fauman, E.B. / Dixon, J.E. / Saper, M.A. | ||||||
Citation | Journal: Protein Sci. / Year: 1995 Title: A ligand-induced conformational change in the Yersinia protein tyrosine phosphatase. Authors: Schubert, H.L. / Fauman, E.B. / Stuckey, J.A. / Dixon, J.E. / Saper, M.A. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1994 Title: Dissecting the Catalytic Mechanism of Protein-Tyrosine Phosphatases Authors: Zhang, Z.-Y. / Wang, Y. / Dixon, J.E. #2: Journal: Nature / Year: 1994 Title: Crystal Structure of Yersinia Protein Tyrosine Phosphatase at 2.5 Angstroms and the Complex with Tungstate Authors: Stuckey, J.A. / Schubert, H.L. / Fauman, E.B. / Zhang, Z.-Y. / Dixon, J.E. / Saper, M.A. #3: Journal: J.Biol.Chem. / Year: 1992 Title: Expression, Purification, and Physicochemical Characterization of a Recombinant Yersinia Protein Tyrosine Phosphatase Authors: Zhang, Z.-Y. / Clemens, J.C. / Schubert, H.L. / Stuckey, J.A. / Fischer, M.W.F. / Hume, D.M. / Saper, M.A. / Dixon, J.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yts.cif.gz | 67.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yts.ent.gz | 49.9 KB | Display | PDB format |
PDBx/mmJSON format | 1yts.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1yts_validation.pdf.gz | 380 KB | Display | wwPDB validaton report |
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Full document | 1yts_full_validation.pdf.gz | 387.2 KB | Display | |
Data in XML | 1yts_validation.xml.gz | 7.9 KB | Display | |
Data in CIF | 1yts_validation.cif.gz | 11.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yt/1yts ftp://data.pdbj.org/pub/pdb/validation_reports/yt/1yts | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 30631.664 Da / Num. of mol.: 1 Mutation: CYS 235 REPLACED BY ARG, CYS 403 REPLACED BY SER, C235R, C403S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yersinia enterocolitica (bacteria) / Strain: W22703 / Gene: YOP51 / Plasmid: PT7-7 / Gene (production host): YOP51 / Production host: Escherichia coli (E. coli) / References: UniProt: P15273, protein-tyrosine-phosphatase | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | YERSINIA PROTEIN TYROSINE PHOSPHATASE. ONLY THE CATALYTIC DOMAIN (RESIDUES 163 - 468) WAS ...YERSINIA PROTEIN TYROSINE PHOSPHATAS | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.54 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 296 K / pH: 8.5 Details: MOLECULE: YERSINIA PROTEIN TYROSINE PHOSPHATASE CYS(403)SER COMPLEXED WITH SULFATE. THE CATALYTIC DOMAIN (RESIDUES 163 - 468) OF YOP51 WAS CRYSTALLIZED AT 23 DEGREES CELSIUS, IN A SOLUTION ...Details: MOLECULE: YERSINIA PROTEIN TYROSINE PHOSPHATASE CYS(403)SER COMPLEXED WITH SULFATE. THE CATALYTIC DOMAIN (RESIDUES 163 - 468) OF YOP51 WAS CRYSTALLIZED AT 23 DEGREES CELSIUS, IN A SOLUTION OF 18 - 24% POLYETHYLENE GLYCOL (MW 4000), 5% 2-METHYL-2,4-PENTANEDIOL, 0.1% BETA-MERCAPTOETHANOL, 200MM LI2SO4, 0.1M TRIS-HCL, pH 8.5, temperature 296K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 52 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 5.7 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.5418 Å |
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Detector | Date: Jul 30, 1992 |
Radiation | Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Num. obs: 9156 / % possible obs: 92 % / Redundancy: 2.49 % / Rmerge(I) obs: 0.052 |
Reflection | *PLUS Highest resolution: 2.5 Å / Rmerge(I) obs: 0.082 |
-Processing
Software |
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Refinement | Resolution: 2.5→10 Å /
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Displacement parameters | Biso mean: 18.43 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→10 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |