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Yorodumi- PDB-5eyz: CRYSTAL STRUCTURE OF THE PTPN4 PDZ DOMAIN COMPLEXED WITH THE TAIL... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5eyz | ||||||
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Title | CRYSTAL STRUCTURE OF THE PTPN4 PDZ DOMAIN COMPLEXED WITH THE TAILORED PEPTIDE CYTO8-RETEV | ||||||
Components |
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Keywords | APOPTOSIS / CELL DEATH / GLIOBLASTOMA / MULTIPROTEIN COMPLEXES / PDZ DOMAINS / PEPTIDES DESIGN / PROTEIN BINDING / NON-RECEPTOR TYPE 4 / PTPN4 / RABIES VIRUS / PDZ BINDING MOTIF | ||||||
Function / homology | Function and homology information Toll Like Receptor 4 (TLR4) Cascade / Interleukin-37 signaling / non-membrane spanning protein tyrosine phosphatase activity / glutamate receptor binding / MECP2 regulates neuronal receptors and channels / cytoskeletal protein binding / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / cytoplasmic side of plasma membrane ...Toll Like Receptor 4 (TLR4) Cascade / Interleukin-37 signaling / non-membrane spanning protein tyrosine phosphatase activity / glutamate receptor binding / MECP2 regulates neuronal receptors and channels / cytoskeletal protein binding / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / cytoplasmic side of plasma membrane / cytoskeleton / nucleoplasm / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å | ||||||
Authors | Maisonneuve, P. / Vaney, M.C. / Babault, B. / Caillet-Saguy, C. / Lafon, M. / Delepierre, M. / Cordier, F. / Wolff, N. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2016 Title: Molecular Basis of the Interaction of the Human Protein Tyrosine Phosphatase Non-receptor Type 4 (PTPN4) with the Mitogen-activated Protein Kinase p38 gamma. Authors: Maisonneuve, P. / Caillet-Saguy, C. / Vaney, M.C. / Bibi-Zainab, E. / Sawyer, K. / Raynal, B. / Haouz, A. / Delepierre, M. / Lafon, M. / Cordier, F. / Wolff, N. #1: Journal: Structure / Year: 2011 Title: Peptides targeting the PDZ domain of PTPN4 are efficient inducers of glioblastoma cell death. Authors: Babault, N. / Cordier, F. / Lafage, M. / Cockburn, J. / Haouz, A. / Prehaud, C. / Rey, F.A. / Delepierre, M. / Buc, H. / Lafon, M. / Wolff, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5eyz.cif.gz | 172.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5eyz.ent.gz | 136.8 KB | Display | PDB format |
PDBx/mmJSON format | 5eyz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ey/5eyz ftp://data.pdbj.org/pub/pdb/validation_reports/ey/5eyz | HTTPS FTP |
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-Related structure data
Related structure data | 5ez0C 3nfkS 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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2 |
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3 |
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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 11694.363 Da / Num. of mol.: 4 / Fragment: PDZ DOMAIN, RESIDUES 499-604 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN4 / Plasmid: PDEST15 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): Star / References: UniProt: P29074, protein-tyrosine-phosphatase #2: Protein/peptide | Mass: 1534.607 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: Chemical | ChemComp-CL / | #4: 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: 3.37 Å3/Da / Density % sol: 63.55 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 23% PEG 8000, 0.1 M MES PH 6.0, 0.2 M CALCIUM ACETATE, 0.143 MM AMMONIUM SULFATE |
-Data collection
Diffraction | Mean temperature: 291 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.28268 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 8, 2011 |
Radiation | Monochromator: CHANNEL CUT SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.28268 Å / Relative weight: 1 |
Reflection | Resolution: 2.09→46.8 Å / Num. all: 30269 / Num. obs: 30269 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 4.7 % / Biso Wilson estimate: 54.44 Å2 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.025 / Rrim(I) all: 0.056 / Net I/av σ(I): 6.39 / Net I/σ(I): 14.2 / Num. measured all: 141532 |
Reflection shell | Resolution: 2.09→2.2 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 1.7 / Num. measured all: 4830 / Num. unique all: 1120 / Rpim(I) all: 0.022 / Net I/σ(I) obs: 31.2 / Rejects: 0 / % possible all: 63 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3NFK Resolution: 2.09→42.56 Å / Cor.coef. Fo:Fc: 0.9419 / Cor.coef. Fo:Fc free: 0.9452 / SU R Cruickshank DPI: 0.207 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.208 / SU Rfree Blow DPI: 0.164 / SU Rfree Cruickshank DPI: 0.165 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
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Displacement parameters | Biso max: 141.04 Å2 / Biso mean: 65.36 Å2 / Biso min: 37.3 Å2
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Refine analyze | Luzzati coordinate error obs: 0.419 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.09→42.56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.09→2.16 Å / Total num. of bins used: 15
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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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