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- PDB-2i5x: Engineering the PTPbeta catalytic domain with improved crystalliz... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2i5x | ||||||
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Title | Engineering the PTPbeta catalytic domain with improved crystallization properties | ||||||
![]() | Receptor-type tyrosine-protein phosphatase beta | ||||||
![]() | HYDROLASE / protein tyrosine phosphatase / WPD-loop / drug design / protein engineering | ||||||
Function / homology | ![]() glial cell migration / transmembrane receptor protein tyrosine phosphatase activity / phosphate-containing compound metabolic process / tertiary granule membrane / specific granule membrane / dephosphorylation / protein dephosphorylation / protein-tyrosine-phosphatase / angiogenesis / receptor complex ...glial cell migration / transmembrane receptor protein tyrosine phosphatase activity / phosphate-containing compound metabolic process / tertiary granule membrane / specific granule membrane / dephosphorylation / protein dephosphorylation / protein-tyrosine-phosphatase / angiogenesis / receptor complex / cadherin binding / Neutrophil degranulation / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Evdokimov, A.G. / Pokross, M.E. / Walter, R.L. / Mekel, M. / Klopfenstein, S. | ||||||
![]() | ![]() Title: Engineering the catalytic domain of human protein tyrosine phosphatase beta for structure-based drug discovery. Authors: Evdokimov, A.G. / Pokross, M. / Walter, R. / Mekel, M. / Cox, B. / Li, C. / Bechard, R. / Genbauffe, F. / Andrews, R. / Diven, C. / Howard, B. / Rastogi, V. / Gray, J. / Maier, M. / Peters, K.G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 137.1 KB | Display | ![]() |
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PDB format | ![]() | 105.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 457.7 KB | Display | ![]() |
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Full document | ![]() | 470.9 KB | Display | |
Data in XML | ![]() | 26.8 KB | Display | |
Data in CIF | ![]() | 37.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2hc1C ![]() 2hc2C ![]() 2i3rC ![]() 2i3uC ![]() 2i4eC ![]() 2i4gC ![]() 2i4hSC 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 36288.035 Da / Num. of mol.: 2 / Fragment: catalytic domain, residues 1662-1973 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-MG / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.9 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 21% PEG 8000, 220 mM MgCl2, 1% BME, 0.1% BOG, 5mM DTT, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jan 1, 2004 / Details: Si monochromator |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→39.6 Å / Num. all: 66068 / Num. obs: 66068 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 20.73 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 16.98 |
Reflection shell | Resolution: 1.7→1.8 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 3.64 / Num. unique all: 9811 / % possible all: 97.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2I4h Resolution: 1.7→39.6 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.633 / SU ML: 0.062 / TLS residual ADP flag: LIKELY RESIDUAL Isotropic thermal model: TLS-one group per polypeptide chain Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.107 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.261 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→39.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.703→1.748 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Selection: ALL
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