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Open data
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Basic information
Entry | Database: PDB / ID: 7ner | ||||||
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Title | Crystal structure of the v-Src SH3 domain Q128R mutant | ||||||
![]() | v-Src SH3 domain | ||||||
![]() | PROTEIN BINDING / beta barrel / SH3 domain | ||||||
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 | ![]() | 50.9 KB | Display | ![]() |
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PDB format | ![]() | 34.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7nesC ![]() 7netC ![]() 6xvnS 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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Unit cell |
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Components
#1: Protein | Mass: 6861.487 Da / Num. of mol.: 1 / Mutation: Q128R Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-PG4 / |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.79 Å3/Da / Density % sol: 31.37 % / Mosaicity: 0.09 ° |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 2.1 M ammonium sulfate, 5% PEG 200, 10% glycerol, 40 mM LiCl and 0.1M sodium acetate |
-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: Sep 30, 2020 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.55→30.95 Å / Num. obs: 6888 / % possible obs: 98 % / Redundancy: 2.7 % / Biso Wilson estimate: 14.77 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.039 / Rrim(I) all: 0.067 / Net I/σ(I): 10.4 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 2.6 %
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6XVN Resolution: 1.55→19.08 Å / SU ML: 0.0741 / Cross valid method: FREE R-VALUE / σ(F): 0.34 / Phase error: 18.649 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 18.69 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→19.08 Å
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Refine LS restraints |
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LS refinement shell |
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