+Open data
-Basic information
Entry | Database: PDB / ID: 8a1f | |||||||||
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Title | Human PTPRK N-terminal domains MAM-Ig-FN1 | |||||||||
Components | Receptor-type tyrosine-protein phosphatase kappa | |||||||||
Keywords | CELL ADHESION / Receptor phosphatase / homophilic complex | |||||||||
Function / homology | Function and homology information gamma-catenin binding / transmembrane receptor protein tyrosine phosphatase activity / leading edge membrane / focal adhesion assembly / protein localization to cell surface / negative regulation of cell cycle / negative regulation of keratinocyte proliferation / protein dephosphorylation / protein-tyrosine-phosphatase / transforming growth factor beta receptor signaling pathway ...gamma-catenin binding / transmembrane receptor protein tyrosine phosphatase activity / leading edge membrane / focal adhesion assembly / protein localization to cell surface / negative regulation of cell cycle / negative regulation of keratinocyte proliferation / protein dephosphorylation / protein-tyrosine-phosphatase / transforming growth factor beta receptor signaling pathway / EGFR downregulation / negative regulation of cell migration / protein tyrosine phosphatase activity / adherens junction / cellular response to reactive oxygen species / beta-catenin binding / cell junction / cellular response to UV / cell-cell junction / cell migration / cell adhesion / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / protein kinase binding / cell surface / signal transduction / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | |||||||||
Authors | Hay, I.M. / Graham, S.C. / Sharpe, H.J. / Deane, J.E. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: J.Biol.Chem. / Year: 2023 Title: Determinants of receptor tyrosine phosphatase homophilic adhesion: Structural comparison of PTPRK and PTPRM extracellular domains. Authors: Hay, I.M. / Shamin, M. / Caroe, E.R. / Mohammed, A.S.A. / Svergun, D.I. / Jeffries, C.M. / Graham, S.C. / Sharpe, H.J. / Deane, J.E. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8a1f.cif.gz | 359.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8a1f.ent.gz | 248.6 KB | Display | PDB format |
PDBx/mmJSON format | 8a1f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a1/8a1f ftp://data.pdbj.org/pub/pdb/validation_reports/a1/8a1f | HTTPS FTP |
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-Related structure data
Related structure data | 8a16C 8a17C 2v5yS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
Other databases |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: givenMatrix: (-0.0685288151742, -0.9899693746, -0.123549337693), (-0.991234028204, 0.0535426248905, 0.120781988106), (-0.112955313385, 0.130743354222, -0.984960543628)Vector: 69. ...NCS oper: (Code: given Matrix: (-0.0685288151742, -0.9899693746, -0.123549337693), Vector: |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 41397.191 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PTPRK, PTPK / Cell line (production host): HEK293-F / Production host: Homo sapiens (human) / References: UniProt: Q15262, protein-tyrosine-phosphatase |
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-Sugars , 5 types, 6 molecules
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#3: Polysaccharide | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#5: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#6: Sugar |
-Non-polymers , 2 types, 4 molecules
#7: Chemical | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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: 4.52 Å3/Da / Density % sol: 72.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 100 mM HEPES, pH 7, 10% (w/v) polyethylene glycol (PEG) 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97951 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 29, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97951 Å / Relative weight: 1 |
Reflection | Resolution: 3→79.05 Å / Num. obs: 30882 / % possible obs: 100 % / Redundancy: 13.3 % / Biso Wilson estimate: 111.24 Å2 / CC1/2: 1 / Net I/σ(I): 18.7 |
Reflection shell | Resolution: 3→3.05 Å / Num. unique obs: 1502 / CC1/2: 0.561 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2V5Y Resolution: 3→60.46 Å / SU ML: 0.4045 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.3765 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 116.93 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→60.46 Å
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Refine LS restraints |
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Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 2.9815483003 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
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