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- PDB-7pvt: Crystal structure of the v-Src SH3 domain Q128R mutant in complex... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7pvt | ||||||
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Title | Crystal structure of the v-Src SH3 domain Q128R mutant in complex with the synthetic peptide VSL12 | ||||||
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![]() | PROTEIN BINDING / beta barrel / SH3 domain | ||||||
Function / homology | ![]() non-membrane spanning protein tyrosine kinase activity / non-specific protein-tyrosine kinase / ATP binding Similarity search - Function | ||||||
Biological species | ![]() unidentified (others) | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
Model details | Intertwined dimer | ||||||
![]() | Camara-Artigas, A. / Salinas-Garcia, M.C. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of the v-Src SH3 domain Q128R mutant in complex with the synthetic peptide VSL12 Authors: Camara-Artigas, A. / Salinas Garcia, M.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 87.7 KB | Display | ![]() |
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PDB format | ![]() | 67.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 458.6 KB | Display | ![]() |
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Full document | ![]() | 459.2 KB | Display | |
Data in XML | ![]() | 7.6 KB | Display | |
Data in CIF | ![]() | 9.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7nerS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 6861.487 Da / Num. of mol.: 2 / Mutation: Q128R Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: Schmidt-Ruppin E / Gene: V-SRC / Plasmid: pHTP1 / Production host: ![]() ![]() References: UniProt: P63185, non-specific protein-tyrosine kinase #2: Protein/peptide | Mass: 1317.622 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) unidentified (others) #3: Chemical | ChemComp-PEG / | #4: Chemical | ChemComp-GOL / | #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: 2.15 Å3/Da / Density % sol: 42.68 % / Mosaicity: 0 ° |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 2.4 M ammonium sulfate, 10% glicerol, 5% PEG300, 40 mM LiCl, 0.1M MES |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 16, 2021 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.6→17.18 Å / Num. obs: 17900 / % possible obs: 99.6 % / Redundancy: 6.5 % / Biso Wilson estimate: 25.13 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.026 / Rrim(I) all: 0.069 / Net I/σ(I): 14.2 / Num. measured all: 116716 / Scaling rejects: 242 | ||||||||||||||||||||||||||||||
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: ![]() Starting model: 7NER Resolution: 1.6→17.18 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 0.14 / Phase error: 28.03 / Stereochemistry target values: ML
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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: 87.97 Å2 / Biso mean: 36.7025 Å2 / Biso min: 17.55 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.6→17.18 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13
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