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- PDB-1jln: Crystal structure of the catalytic domain of protein tyrosine pho... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1jln | ||||||
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Title | Crystal structure of the catalytic domain of protein tyrosine phosphatase PTP-SL/BR7 | ||||||
![]() | Protein Tyrosine Phosphatase, receptor type, R | ||||||
![]() | HYDROLASE / protein tyrosine phosphatase / PTP-SL / PTPBR7 / ERK2-MAP kinase regulation | ||||||
Function / homology | ![]() negative regulation of epithelial cell migration / ERBB2 signaling pathway / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / negative regulation of ERK1 and ERK2 cascade / cell junction / in utero embryonic development / membrane => GO:0016020 / protein kinase binding ...negative regulation of epithelial cell migration / ERBB2 signaling pathway / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / negative regulation of ERK1 and ERK2 cascade / cell junction / in utero embryonic development / membrane => GO:0016020 / protein kinase binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Szedlacsek, S.E. / Aricescu, A.R. / Fulga, T.A. / Renault, L. / Scheidig, A.J. | ||||||
![]() | ![]() Title: Crystal structure of PTP-SL/PTPBR7 catalytic domain: implications for MAP kinase regulation. Authors: Szedlacsek, S.E. / Aricescu, A.R. / Fulga, T.A. / Renault, L. / Scheidig, A.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 76.1 KB | Display | ![]() |
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PDB format | ![]() | 56.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 425.2 KB | Display | ![]() |
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Full document | ![]() | 431.8 KB | Display | |
Data in XML | ![]() | 15.4 KB | Display | |
Data in CIF | ![]() | 22.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1yfoS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 33745.637 Da / Num. of mol.: 1 / Fragment: catalytic domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.84 % | |||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP at 293K | |||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Jan 26, 1999 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.81→19.69 Å / Num. all: 26218 / Num. obs: 24970 / % possible obs: 83.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 28.4 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 5.7 / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 1.81→1.9 Å / Mean I/σ(I) obs: 2.62 / % possible all: 40.3 |
Reflection | *PLUS Num. measured all: 118144 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1YFO Resolution: 1.81→19.69 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 197719.79 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 43.4434 Å2 / ksol: 0.32837 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.81→19.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 28.3 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.296 / % reflection Rfree: 5 % / Rfactor Rwork: 0.24 |