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- PDB-2bij: Crystal structure of the human protein tyrosine phosphatase PTPN5... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2bij | ||||||
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Title | Crystal structure of the human protein tyrosine phosphatase PTPN5 (STEP, striatum enriched enriched Phosphatase) | ||||||
![]() | TYROSINE-PROTEIN PHOSPHATASE, NON-RECEPTOR TYPE 5 | ||||||
![]() | HYDROLASE / PTPN5 / STEP / PHOSPHATASE | ||||||
Function / homology | ![]() Interleukin-37 signaling / phosphotyrosine residue binding / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / cell junction / endoplasmic reticulum membrane / protein kinase binding / signal transduction / nucleoplasm ...Interleukin-37 signaling / phosphotyrosine residue binding / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / cell junction / endoplasmic reticulum membrane / protein kinase binding / signal transduction / nucleoplasm / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Barr, A.J. / Debreczeni, J.E. / Eswaran, J. / Smee, C. / Burgess, N. / Gileadi, O. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. / Knapp, S. / von Delft, F. | ||||||
![]() | ![]() Title: Crystal structures and inhibitor identification for PTPN5, PTPRR and PTPN7: a family of human MAPK-specific protein tyrosine phosphatases. Authors: Eswaran, J. / von Kries, J.P. / Marsden, B. / Longman, E. / Debreczeni, J.E. / Ugochukwu, E. / Turnbull, A. / Lee, W.H. / Knapp, S. / Barr, 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 | ![]() | 73.3 KB | Display | ![]() |
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PDB format | ![]() | 52.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 438.5 KB | Display | ![]() |
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Full document | ![]() | 439.1 KB | Display | |
Data in XML | ![]() | 12.9 KB | Display | |
Data in CIF | ![]() | 17.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2a8bC ![]() 2bv5C ![]() 1jlnS S: Starting model for refinement C: citing same article ( |
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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: 35204.844 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 258-539 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-SO4 / |
#3: Water | ChemComp-HOH / |
Sequence details | RESIDUES ASP 289, LEU 298, VAL 299 AND THR 517 ARE GIVEN AS VARIANTS IN THE SWISS-PROT ENTRY FOR ...RESIDUES ASP 289, LEU 298, VAL 299 AND THR 517 ARE GIVEN AS VARIANTS IN THE SWISS-PROT ENTRY FOR P54829. RESIDUES -23 TO -1 FORM PART OF A N-TERMINAL HIS-TAG USED FOR EXPRESSION |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48 % |
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Crystal grow | Details: PROTEIN SOLUTION: 10 MG/ML PTPN5, 50 MM HEPES PH 7.5, 200 MM NACL, 10 MM DTT PRECIPITANT: 25% PEG3350, 0.2 M LI2SO4, 100 MM BIS-TR-S PH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Dec 2, 2004 / Details: MULTILAYER MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→39.74 Å / Num. obs: 20825 / % possible obs: 95 % / Observed criterion σ(I): 3 / Redundancy: 4.7 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.14 |
Reflection shell | Resolution: 2.05→2.15 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 3.05 / % possible all: 97 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1JLN Resolution: 2.05→54.23 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.895 / SU B: 9.811 / SU ML: 0.197 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.22 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 380-382 ARE DISORDERED AND NOT VISIBLE IN THE ELECTRON DENSITY.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.21 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→54.23 Å
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Refine LS restraints |
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