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Open data
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Basic information
Entry | Database: PDB / ID: 7nym | |||||||||
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Title | Mutant V517A - SH3 domain of JNK-interacting Protein 1 (JIP1) | |||||||||
![]() | SH3 domain of JNK-interacting Protein 1 (JIP1) | |||||||||
![]() | SIGNALING PROTEIN / SH3 domain of JNK-interacting protein 1 (JIP1) | |||||||||
Function / homology | ![]() dentate gyrus mossy fiber / regulation of CD8-positive, alpha-beta T cell proliferation / negative regulation of JUN kinase activity / MAP-kinase scaffold activity / JUN kinase binding / protein kinase inhibitor activity / kinesin binding / regulation of JNK cascade / negative regulation of intrinsic apoptotic signaling pathway / vesicle-mediated transport ...dentate gyrus mossy fiber / regulation of CD8-positive, alpha-beta T cell proliferation / negative regulation of JUN kinase activity / MAP-kinase scaffold activity / JUN kinase binding / protein kinase inhibitor activity / kinesin binding / regulation of JNK cascade / negative regulation of intrinsic apoptotic signaling pathway / vesicle-mediated transport / JNK cascade / mitochondrial membrane / positive regulation of JNK cascade / neuronal cell body / synapse / dendrite / regulation of DNA-templated transcription / endoplasmic reticulum membrane / perinuclear region of cytoplasm / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Perez, L.M. / Ielasi, F.S. / Palencia, A. / Jensen, M.R. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Visualizing protein breathing motions associated with aromatic ring flipping. Authors: Marino Perez, L. / Ielasi, F.S. / Bessa, L.M. / Maurin, D. / Kragelj, J. / Blackledge, M. / Salvi, N. / Bouvignies, G. / Palencia, A. / Jensen, M.R. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 121.9 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 13.9 KB | Display | |
Data in CIF | ![]() | 20.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7nykSC ![]() 7nylC ![]() 7nynC ![]() 7nyoC ![]() 7nzbC ![]() 7nzcC ![]() 7nzdC 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 7498.314 Da / Num. of mol.: 4 / Mutation: V517A Source method: isolated from a genetically manipulated source Details: GHME belongs to expression vector pET28a / Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-PO4 / | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 47 % / Description: Needles |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7.5 Details: 0.1 M HEPES pH 7.5, 1-5 % PEG 400, 2-2.5 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 30, 2020 |
Radiation | Monochromator: SILICON CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8731 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→63.976 Å / Num. obs: 45428 / % possible obs: 94 % / Redundancy: 12.5 % / CC1/2: 0.99 / Net I/σ(I): 7 |
Reflection shell | Resolution: 1.454→1.518 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2272 / CC1/2: 0.46 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7NYK Resolution: 1.614→63.976 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.629 / SU ML: 0.055 / Cross valid method: FREE R-VALUE / ESU R: 0.09 / ESU R Free: 0.085 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.598 Å2
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Refinement step | Cycle: LAST / Resolution: 1.614→63.976 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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