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- PDB-3qcn: Human receptor protein tyrosine phosphatase gamma, domain 1, trig... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3qcn | ||||||
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Title | Human receptor protein tyrosine phosphatase gamma, domain 1, trigonal crystal form | ||||||
![]() | Receptor-type tyrosine-protein phosphatase gamma | ||||||
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Function / homology | ![]() negative regulation of epithelial cell migration / ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Sheriff, S. | ||||||
![]() | ![]() Title: Small molecule receptor protein tyrosine phosphatase [gamma](RPTP[gamma]) ligands that inhibit phosphatase activity via perturbation of the tryptophan-proline-aspartate (WPD) loop Authors: Sheriff, S. / Beno, B.R. / Zhai, W. / Kostich, W.A. / McDonnell, P.A. / Kish, K. / Goldfarb, V. / Gao, M. / Kiefer, S.E. / Yanchunas, J. / Huang, Y. / Shi, S. / Zhu, S. / Dzierba, C. / ...Authors: Sheriff, S. / Beno, B.R. / Zhai, W. / Kostich, W.A. / McDonnell, P.A. / Kish, K. / Goldfarb, V. / Gao, M. / Kiefer, S.E. / Yanchunas, J. / Huang, Y. / Shi, S. / Zhu, S. / Dzierba, C. / Bronson, J. / Macor, J.E. / Appiah, K.K. / Westphal, R.S. / O'Connell, J. / Gerritz, S.W. #1: ![]() Title: Cloning, purification, crystallization and preliminary X-ray analysis of the catalytic domain of human receptor-like protein Tyrosine Phosphatase g in three different crystal forms Authors: Kish, K. / McDonnell, P.A. / Goldfarb, V. / Gao, M. / Metzler, W.J. / Langley, D.R. / Bryson, J.W. / Kiefer, S.E. / Kostich, W.A. / Carpenter, B. / Westphal, R.S. / Sheriff, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 73.6 KB | Display | ![]() |
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PDB format | ![]() | 53.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3qcbC ![]() 3qccC ![]() 3qcdSC ![]() 3qceC ![]() 3qcfC ![]() 3qcgC ![]() 3qchC ![]() 3qciC ![]() 3qcjC ![]() 3qckC ![]() 3qclC ![]() 3qcmC 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: 35705.531 Da / Num. of mol.: 1 / Fragment: CYTOSOLIC MEMBRANE PROXIMAL CATALYTIC DOMAIN / Mutation: C858S, S970T 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: 3.48 Å3/Da / Density % sol: 64.67 % |
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Crystal grow![]() | pH: 7 / Details: pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 27, 2006 / Details: VARIMAX HR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.41→50 Å / Num. obs: 19097 / % possible obs: 96 % / Observed criterion σ(I): 0 / Redundancy: 8.9 % / Biso Wilson estimate: 59.85 Å2 / Rmerge(I) obs: 0.186 / Net I/σ(I): 8 |
Reflection shell | Resolution: 2.41→2.5 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.537 / Mean I/σ(I) obs: 4.3 / % possible all: 92 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 3QCD Resolution: 2.41→49.49 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.931 / SU R Cruickshank DPI: 0.24 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.25 / SU Rfree Blow DPI: 0.2 / SU Rfree Cruickshank DPI: 0.2
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Displacement parameters | Biso mean: 53.79 Å2
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Refine analyze | Luzzati coordinate error obs: 0.31 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.41→49.49 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.41→2.54 Å / Total num. of bins used: 10
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