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- PDB-5mk1: Crystal structure of the His Domain Protein Tyrosine Phosphatase ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5mk1 | ||||||||||||
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Title | Crystal structure of the His Domain Protein Tyrosine Phosphatase (HD-PTP/PTPN23) Bro1 domain (CHMP4A peptide complex structure) | ||||||||||||
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Function / homology | ![]() positive regulation of adherens junction organization / positive regulation of homophilic cell adhesion / membrane invagination / plasma membrane tubulation / positive regulation of Wnt protein secretion / positive regulation of early endosome to late endosome transport / amphisome membrane / multivesicular body-lysosome fusion / vesicle fusion with vacuole / late endosome to lysosome transport ...positive regulation of adherens junction organization / positive regulation of homophilic cell adhesion / membrane invagination / plasma membrane tubulation / positive regulation of Wnt protein secretion / positive regulation of early endosome to late endosome transport / amphisome membrane / multivesicular body-lysosome fusion / vesicle fusion with vacuole / late endosome to lysosome transport / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Levy, C. / Gahloth, D. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Basis for Specific Interaction of TGF beta Signaling Regulators SARA/Endofin with HD-PTP. Authors: Gahloth, D. / Levy, C. / Walker, L. / Wunderley, L. / Mould, A.P. / Taylor, S. / Woodman, P. / Tabernero, L. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 582.5 KB | Display | ![]() |
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PDB format | ![]() | 482.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5mjyC ![]() 5mjzC ![]() 5mk0C ![]() 5mk2C ![]() 5mk3C ![]() 3rauS 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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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 40719.941 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #2: Protein/peptide | Mass: 2088.270 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() #3: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.48 % |
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Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 0.1 M Tris pH 7.8, 5% (poly-glutamic acid low molecular weight polymer) 20% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 23, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.5→28.41 Å / Num. obs: 47548 / % possible obs: 93.05 % / Redundancy: 3.5 % / CC1/2: 0.989 / Rmerge(I) obs: 0.1342 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 2.5→2.589 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.799 / Mean I/σ(I) obs: 1.94 / CC1/2: 0.442 / % possible all: 84.76 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 3RAU Resolution: 2.5→28.41 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 0.02 / Phase error: 24.67
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→28.41 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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