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- PDB-2h04: Structural studies of protein tyrosine phosphatase beta catalytic... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2h04 | ||||||
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Title | Structural studies of protein tyrosine phosphatase beta catalytic domain in complex with inhibitors | ||||||
![]() | Protein tyrosine phosphatase, receptor type, B,![]() | ||||||
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Function / homology | ![]() glial cell migration / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Evdokimov, A.G. / Pokross, M.E. / Walter, R.L. / Mekel, M. / Gray, J.L. / Peters, K.G. / Maier, M.B. / Amarasinghe, K.D. / Clark, C.M. / Nichols, R. | ||||||
![]() | ![]() Title: Design and synthesis of potent, non-peptidic inhibitors of HPTPbeta. Authors: Amarasinghe, K.K. / Evdokimov, A.G. / Xu, K. / Clark, C.M. / Maier, M.B. / Srivastava, A. / Colson, A.O. / Gerwe, G.S. / Stake, G.E. / Howard, B.W. / Pokross, M.E. / Gray, J.L. / 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 | ![]() | 76.1 KB | Display | ![]() |
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PDB format | ![]() | 55.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2h02C ![]() 2h03C ![]() 1rpmS 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: 36288.035 Da / Num. of mol.: 1 / Fragment: catalytic domain, residues 1662-1973 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: Q3MIV7, UniProt: P23467*PLUS, ![]() |
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#2: Chemical | ChemComp-4UN / { |
#3: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37.28 % |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion / pH: 8 Details: 21% PEG 8000, 220 mM MgCl2, 1% BME, 0.1% BOG, 5mM DTT, pH 8.0, vapor diffusion, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 3, 2005 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.3→34.86 Å / Num. all: 13248 / Num. obs: 13248 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 22 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 8.88 |
Reflection shell | Resolution: 2.3→2.4 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.83 / Num. unique all: 1529 / % possible all: 98.3 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1RPM (WITH MODIFICATIONS) Resolution: 2.3→34.86 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.906 / SU B: 11.831 / SU ML: 0.157 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.381 / ESU R Free: 0.248 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 16.455 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→34.86 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
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