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Yorodumi- PDB-5mjz: Crystal structure of the His Domain Protein Tyrosine Phosphatase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5mjz | ||||||||||||
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Title | Crystal structure of the His Domain Protein Tyrosine Phosphatase (HD-PTP/PTPN23) Bro1 domain (Apo structure) | ||||||||||||
Components | Tyrosine-protein phosphatase non-receptor type 23 | ||||||||||||
Keywords | HYDROLASE / ESCRT-III | ||||||||||||
Function / homology | Function and homology information positive regulation of adherens junction organization / positive regulation of homophilic cell adhesion / positive regulation of Wnt protein secretion / positive regulation of early endosome to late endosome transport / negative regulation of epithelial cell migration / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / early endosome to late endosome transport / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / endocytic recycling / Interleukin-37 signaling ...positive regulation of adherens junction organization / positive regulation of homophilic cell adhesion / positive regulation of Wnt protein secretion / positive regulation of early endosome to late endosome transport / negative regulation of epithelial cell migration / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / early endosome to late endosome transport / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / endocytic recycling / Interleukin-37 signaling / cilium assembly / dephosphorylation / protein-tyrosine-phosphatase / ciliary basal body / protein tyrosine phosphatase activity / nuclear body / early endosome / endosome / intracellular membrane-bounded organelle / protein kinase binding / extracellular exosome / nucleoplasm / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.867 Å | ||||||||||||
Authors | Levy, C. / Gahloth, D. | ||||||||||||
Funding support | United Kingdom, 3items
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Citation | Journal: Structure / Year: 2017 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mjz.cif.gz | 163.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mjz.ent.gz | 129.3 KB | Display | PDB format |
PDBx/mmJSON format | 5mjz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mj/5mjz ftp://data.pdbj.org/pub/pdb/validation_reports/mj/5mjz | HTTPS FTP |
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-Related structure data
Related structure data | 5mjyC 5mk0C 5mk1C 5mk2C 5mk3C 3rauS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 40719.941 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN23, KIAA1471 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9H3S7, protein-tyrosine-phosphatase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.57 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: Apo- HD-PTPBro1 crystals were obtained in 0.2M L-Na-Glutamate, 0.2M Alanine, 0.2M Glycine, 0.2M Lysine HCl, 0.2M Serine, 0.1 M Imidazole; MES monohydrate at pH 6.5 and 30% Ethylene glycol, PEG8K. Temp details: Cold Room |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.969 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 8, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.969 Å / Relative weight: 1 |
Reflection | Resolution: 1.867→28.49 Å / Num. obs: 60112 / % possible obs: 99.34 % / Redundancy: 4.1 % / CC1/2: 0.995 / Rmerge(I) obs: 0.1246 / Net I/σ(I): 9.24 |
Reflection shell | Resolution: 1.867→1.934 Å / Redundancy: 4 % / Rmerge(I) obs: 0.8821 / Mean I/σ(I) obs: 1.99 / CC1/2: 0.586 / % possible all: 97.25 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3RAU Resolution: 1.867→28.49 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.51
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.867→28.49 Å
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Refine LS restraints |
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LS refinement shell |
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