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- PDB-2hc1: Engineered catalytic domain of protein tyrosine phosphatase HPTPbeta. -
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Open data
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Basic information
Entry | Database: PDB / ID: 2hc1 | ||||||
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Title | Engineered catalytic domain of protein tyrosine phosphatase HPTPbeta. | ||||||
![]() | 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. / Walter, R. / 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 | ![]() | 156.4 KB | Display | ![]() |
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PDB format | ![]() | 122.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 439.1 KB | Display | ![]() |
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Full document | ![]() | 446.1 KB | Display | |
Data in XML | ![]() | 17.3 KB | Display | |
Data in CIF | ![]() | 26.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2hc2C ![]() 2i3rC ![]() 2i3uC ![]() 2i4eC ![]() 2i4gC ![]() 2i4hC ![]() 2i5xC ![]() 2h02S 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: 33780.340 Da / Num. of mol.: 1 / Fragment: catalytic domain / Mutation: yes Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
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#2: Chemical | ChemComp-ACT / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.18 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.2 Details: 20% PEG 8000, 220 mM MgCl2, 1% BME, 0.1% BOG, 5mM DTT, 180 mM Nh4OAc, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction source | Source: ![]() ![]() ![]() |
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Detector | Type: MARRESEARCH / Detector: CCD / Date: Jan 1, 2005 |
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: 1.3→33.88 Å / Num. all: 59896 / Num. obs: 59896 / % possible obs: 72.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.2 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 15.32 |
Reflection shell | Resolution: 1.3→1.4 Å / Redundancy: 0.8 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.85 / % possible all: 69.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2H02 Resolution: 1.3→33.88 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.4 / SU ML: 0.027 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.06 / 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: 11.488 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→33.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.295→1.329 Å / Total num. of bins used: 20
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