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- PDB-3nfk: Crystal structure of the PTPN4 PDZ domain complexed with the C-te... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3nfk | ||||||
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Title | Crystal structure of the PTPN4 PDZ domain complexed with the C-terminus of a rabies virus G protein | ||||||
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Function / homology | ![]() Toll Like Receptor 4 (TLR4) Cascade / Interleukin-37 signaling / non-membrane spanning protein tyrosine phosphatase activity / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Babault, N. / Cordier, F. / Lafage, M. / Cockburn, J. / Haouz, A. / Rey, F.A. / Delepierre, M. / Buc, H. / Lafon, M. / Wolff, N. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 95.7 KB | Display | ![]() |
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PDB format | ![]() | 72.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3nflC ![]() 2vphS 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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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 11694.363 Da / Num. of mol.: 2 / Fragment: PDZ domain (UNP residues 499-604) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #2: Protein/peptide | Mass: 1476.572 Da / Num. of mol.: 2 / Fragment: UNP residues 512-524 / Source method: obtained synthetically Details: Cyto13-att peptide has been chemically synthetized. The sequence occurs naturally in rabies virus G protein Source: (synth.) ![]() ![]() #3: Chemical | ![]() #4: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.78 % |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 24% PEG 1500, 20% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 29, 2009 / Details: BI-MORPH MIRRORS |
Radiation | Monochromator: CRYOGENICALLY COOLED MONOCHROMATOR CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.43→34.37 Å / Num. all: 44164 / Num. obs: 42795 / % possible obs: 96.9 % / Redundancy: 3.5 % / Biso Wilson estimate: 16.28 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 11 |
Reflection shell | Resolution: 1.43→1.51 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.301 / Mean I/σ(I) obs: 4.3 / Num. unique all: 6255 / % possible all: 98.5 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 2VPH Resolution: 1.43→14.41 Å / Cor.coef. Fo:Fc: 0.9495 / Cor.coef. Fo:Fc free: 0.9447 / SU R Cruickshank DPI: 0.062 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 20.78 Å2
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Refine analyze | Luzzati coordinate error obs: 0.175 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.43→14.41 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.43→1.47 Å / Total num. of bins used: 20
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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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