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Open data
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Basic information
Entry | Database: PDB / ID: 7nes | ||||||
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Title | Crystal structure of the v-Src SH3 domain N117D-V124L mutant | ||||||
![]() | v-Src SH3 domain | ||||||
![]() | PROTEIN BINDING / beta barrel / SH3 domain | ||||||
Function / homology | GLYCINE![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
Model details | Intertwined dimer | ||||||
![]() | Camara-Artigas, A. / Salinas-Garcia, M.C. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The impact of oncogenic mutations of the viral Src kinase on the structure and stability of the SH3 domain. Authors: Salinas-Garcia, M.C. / Plaza-Garrido, M. / Camara-Artigas, A. #1: ![]() Title: The impact of oncogenic mutations of the viral Src kinase on the structure and stability of the SH3 domain Authors: Salinas-Garcia, M.C. / Plaza-Garrido, M. / Camara-Artigas, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 47.5 KB | Display | ![]() |
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PDB format | ![]() | 33.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 423 KB | Display | ![]() |
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Full document | ![]() | 423 KB | Display | |
Data in XML | ![]() | 5 KB | Display | |
Data in CIF | ![]() | 6.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 6847.434 Da / Num. of mol.: 1 / Mutation: N117D, V124L Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-GLY / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.92 Å3/Da / Density % sol: 35.84 % / Mosaicity: 0.12 ° |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.8M ammonium sulfate, 0.5M glycine and 0.1M HEPES |
-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: Feb 11, 2018 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.976251 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.35→18.59 Å / Num. obs: 12108 / % possible obs: 100 % / Redundancy: 7.6 % / CC1/2: 1 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.018 / Rrim(I) all: 0.049 / Net I/σ(I): 18.1 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 71.89 Å2 / Biso mean: 21.8414 Å2 / Biso min: 12.98 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.35→18.59 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8
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