+Open data
-Basic information
Entry | Database: PDB / ID: 1ytw | ||||||
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Title | YERSINIA PTPASE COMPLEXED WITH TUNGSTATE | ||||||
Components | YERSINIA PROTEIN TYROSINE PHOSPHATASE | ||||||
Keywords | HYDROLASE / PROTEIN TYROSINE PHOSPHATASE | ||||||
Function / homology | Function and homology information dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / extracellular region Similarity search - Function | ||||||
Biological species | Yersinia enterocolitica (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MIR / Resolution: 2.4 Å | ||||||
Authors | Fauman, E.B. / Schubert, H.L. / Saper, M.A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1996 Title: The X-ray crystal structures of Yersinia tyrosine phosphatase with bound tungstate and nitrate. Mechanistic implications. Authors: Fauman, E.B. / Yuvaniyama, C. / Schubert, H.L. / Stuckey, J.A. / Saper, M.A. #1: 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. #2: Journal: Nature / Year: 1994 Title: Crystal Structure of Yersinia Protein Tyrosine Phosphatase at 2.5 A 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. / 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 | 1ytw.cif.gz | 70.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ytw.ent.gz | 51.9 KB | Display | PDB format |
PDBx/mmJSON format | 1ytw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yt/1ytw ftp://data.pdbj.org/pub/pdb/validation_reports/yt/1ytw | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 33553.883 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 163 - 468 Source method: isolated from a genetically manipulated source Details: TUNGSTATE AND SULFATE LIGANDS / Source: (gene. exp.) Yersinia enterocolitica (bacteria) / Strain: W22703 / Cell line: BL21 / Gene: YOP51 / Plasmid: PT7-7 / Species (production host): Escherichia coli / Gene (production host): YOP51 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P15273, protein-tyrosine-phosphatase |
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#2: Chemical | ChemComp-WO4 / |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 4 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 52 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: THE CATALYTIC DOMAIN (RESIDUES 163 - 468) OF YOP51 WAS CRYSTALLIZED AT 20 MG/ML WITH 1 MM SODIUM TUNGSTATE AT 23 DEGREES CELSIUS, BY HANGING DROP VAPOR DIFFUSION AGAINST A WELL SOLUTION OF ...Details: THE CATALYTIC DOMAIN (RESIDUES 163 - 468) OF YOP51 WAS CRYSTALLIZED AT 20 MG/ML WITH 1 MM SODIUM TUNGSTATE AT 23 DEGREES CELSIUS, BY HANGING DROP VAPOR DIFFUSION AGAINST A WELL SOLUTION OF 22% POLYETHYLENE GLYCOL (MW 4000), 200 MM LITHIUM SULFATE, 10% ISOPROPANOL, 100 MM TRIS HCL (PH 8.5) AND 0.1% BETA-MERCAPTOETHANOL., vapor diffusion - hanging drop, temperature 296K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.5418 |
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Detector | Type: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Num. obs: 9875 / % possible obs: 89 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.107 |
Reflection | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 9999 Å |
Reflection shell | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 2.5 Å / Rmerge(I) obs: 0.274 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.4→7 Å / σ(F): 0
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Displacement parameters | Biso mean: 16 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.5 Å /
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Xplor file |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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