+Open data
-Basic information
Entry | Database: PDB / ID: 5lm2 | ||||||
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Title | Crystal Structure of HD-PTP phosphatase | ||||||
Components | Tyrosine-protein phosphatase non-receptor type 23 | ||||||
Keywords | HYDROLASE / coiled coil | ||||||
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 / SAD / Resolution: 2.54 Å | ||||||
Authors | Levy, C. | ||||||
Citation | Journal: Structure / Year: 2016 Title: Structural Basis for Selective Interaction between the ESCRT Regulator HD-PTP and UBAP1. Authors: Gahloth, D. / Levy, C. / Heaven, G. / Stefani, F. / Wunderley, L. / Mould, P. / Cliff, M.J. / Bella, J. / Fielding, A.J. / 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 | 5lm2.cif.gz | 138.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lm2.ent.gz | 115.8 KB | Display | PDB format |
PDBx/mmJSON format | 5lm2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lm/5lm2 ftp://data.pdbj.org/pub/pdb/validation_reports/lm/5lm2 | HTTPS FTP |
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-Related 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: 40725.312 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN23, KIAA1471 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / 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: 2.73 Å3/Da / Density % sol: 54.86 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop Details: 0.1 M Bis-Tris pH 6.0, 0.1-0.2 M Na-Formate and 13-15% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 12, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.54→43.24 Å / Num. obs: 28609 / % possible obs: 98 % / Redundancy: 13.5 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 19.3 |
Reflection shell | Resolution: 2.54→2.63 Å / Redundancy: 13.8 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 3.84 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.54→43.242 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 30.25 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.54→43.242 Å
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Refine LS restraints |
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LS refinement shell |
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