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- PDB-2i3u: Structural studies of protein tyrosine phosphatase beta catalytic... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2i3u | ||||||
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Title | Structural studies of protein tyrosine phosphatase beta catalytic domain in complex with inhibitors | ||||||
![]() | Receptor-type tyrosine-protein phosphatase beta | ||||||
![]() | HYDROLASE / protein tyrosine phosphatase / WPD-loop / sulfamic acid / phosphatase / inhibitor / drug design | ||||||
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. | ||||||
![]() | ![]() 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 | ![]() | 76.8 KB | Display | ![]() |
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PDB format | ![]() | 56.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 428.6 KB | Display | ![]() |
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Full document | ![]() | 434.1 KB | Display | |
Data in XML | ![]() | 15.1 KB | Display | |
Data in CIF | ![]() | 21.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2hc1C ![]() 2hc2C ![]() 2i3rSC ![]() 2i4eC ![]() 2i4gC ![]() 2i4hC ![]() 2i5xC C: citing same article ( 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: 36288.035 Da / Num. of mol.: 1 / Fragment: catalytic domain, residues 1662-1973 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: 2.21 Å3/Da / Density % sol: 44.32 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 21% PEG 8000, 220 mM MgCl2, 1% BME, 0.1% BOG, 5mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 278K |
-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: 1.85→22.31 Å / Num. all: 27971 / Num. obs: 27971 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 26.4 Å2 / Rmerge(I) obs: 0.028 / Net I/σ(I): 21.75 |
Reflection shell | Resolution: 1.85→1.95 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 5.11 / Num. unique all: 3939 / % possible all: 93.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2I3R Resolution: 1.85→22.31 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.939 / SU B: 5.312 / SU ML: 0.083 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.139 / ESU R Free: 0.132 / 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: 30.832 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→22.31 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.895 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Details: Chain A / Origin x: 1.907 Å / Origin y: 21.749 Å / Origin z: 14.919 Å
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Refinement TLS group | Selection: ALL |