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Open data
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Basic information
Entry | Database: PDB / ID: 2hc2 | ||||||
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Title | Engineered protein tyrosine phosphatase beta catalytic domain | ||||||
![]() | Receptor-type tyrosine-protein phosphatase beta | ||||||
![]() | ![]() ![]() ![]() ![]() ![]() ![]() | ||||||
Function / homology | ![]() glial cell migration / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() 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 | ![]() | 149.1 KB | Display | ![]() |
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PDB format | ![]() | 116.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2hc1SC ![]() 2i3rC ![]() 2i3uC ![]() 2i4eC ![]() 2i4gC ![]() 2i4hC ![]() 2i5xC 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-MG / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.44 % |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.85 Details: 21% PEG 8000, 200 mM MgCl2, 1% BME, 0.1% BOG, 1mM DTT, 80 mM Na Citrate, pH 7.85, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction source | Source: ![]() ![]() ![]() |
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Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 2, 2006 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.4→33.67 Å / Num. all: 48397 / Num. obs: 48397 / % possible obs: 92.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Rmerge(I) obs: 0.028 / Net I/σ(I): 20.2 |
Reflection shell | Resolution: 1.4→1.5 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 4.87 / % possible all: 69.4 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 2HC1 Resolution: 1.4→33.67 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.945 / SU ML: 0.035 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / ESU R: 0.077 / ESU R Free: 0.065 / 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: 19.055 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→33.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.436 Å / Total num. of bins used: 20
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