+Open data
-Basic information
Entry | Database: PDB / ID: 1ytn | ||||||
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Title | HYDROLASE | ||||||
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 / DIFFERENCE FOURIER / Resolution: 2.4 Å | ||||||
Authors | Yuvaniyama, C. / Fauman, E.B. / 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 | 1ytn.cif.gz | 69.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ytn.ent.gz | 51.1 KB | Display | PDB format |
PDBx/mmJSON format | 1ytn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ytn_validation.pdf.gz | 379 KB | Display | wwPDB validaton report |
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Full document | 1ytn_full_validation.pdf.gz | 384.1 KB | Display | |
Data in XML | 1ytn_validation.xml.gz | 7.7 KB | Display | |
Data in CIF | 1ytn_validation.cif.gz | 11.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yt/1ytn ftp://data.pdbj.org/pub/pdb/validation_reports/yt/1ytn | HTTPS FTP |
-Related structure data
Related structure data | 1ytwSC 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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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: COMPLEXED WITH NITRATE / 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-NO3 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 52 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: THE CATALYTIC DOMAIN (RESIDUES 163 - 468) OF YOP51 WAS CRYSTALLIZED AT 23 DEGREES CELSIUS BY THE HANGING DROP VAPOR DIFFUSION METHOD. DROP WAS COMPOSED OF EQUAL VOLUMES OF PROTEIN (23 MG/ML) ...Details: THE CATALYTIC DOMAIN (RESIDUES 163 - 468) OF YOP51 WAS CRYSTALLIZED AT 23 DEGREES CELSIUS BY THE HANGING DROP VAPOR DIFFUSION METHOD. DROP WAS COMPOSED OF EQUAL VOLUMES OF PROTEIN (23 MG/ML) AND RESERVOIR SOLUTION. RESERVOIR SOLUTION WAS 27% POLYETHYLENE GLYCOL (MW 1500), 10% 2-METHYL-2,4-PENTANEDIOL, 220 MM SODIUM NITRATE, 0.1% BETA-MERCAPTOETHANOL, AND 10 MM IMIDAZOLE, PH 7.2., 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 / Date: Nov 17, 1994 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Num. obs: 9205 / % possible obs: 84 % / Observed criterion σ(I): 0 / Redundancy: 2.49 % / Rmerge(I) obs: 0.115 |
Reflection | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 9999 Å |
Reflection shell | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 2.5 Å / % possible obs: 66 % / Rmerge(I) obs: 0.226 |
-Processing
Software |
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Refinement | Method to determine structure: DIFFERENCE FOURIER Starting model: 1YTW Resolution: 2.4→7 Å / σ(F): 0
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Displacement parameters | Biso mean: 19 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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