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- PDB-7pvw: Crystal structure of the intertwined dimer of the c-Src SH3 domai... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7pvw | ||||||
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Title | Crystal structure of the intertwined dimer of the c-Src SH3 domain E93V-S94A-R95S-T96G-N112G-N113Y-T114N-E115H mutant | ||||||
![]() | Isoform 1 of Proto-oncogene tyrosine-protein kinase Src | ||||||
![]() | PROTEIN BINDING / beta barrel / SH3 domain | ||||||
Function / homology | non-specific protein-tyrosine kinase / ACETATE ION / Isoform 1 of Proto-oncogene tyrosine-protein kinase Src![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
Model details | Chimera construction c-Src-Abl SH3 domain | ||||||
![]() | Camara-Artigas, A. / Salinas Garcia, M.C. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The effect of the hinge loops composition in the domain swapping of the SH3 domain 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 | ![]() | 82.6 KB | Display | ![]() |
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PDB format | ![]() | 62.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 425.1 KB | Display | ![]() |
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Full document | ![]() | 425.1 KB | Display | |
Data in XML | ![]() | 7.4 KB | Display | |
Data in CIF | ![]() | 9.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7pvqC ![]() 7pvrC ![]() 7pvsC ![]() 7pvvC ![]() 7pvyC ![]() 7pvzC ![]() 7pw0C ![]() 7pw2C ![]() 4le9S S: Starting model for refinement C: citing same article ( |
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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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Unit cell |
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Components
#1: Protein | Mass: 6603.213 Da / Num. of mol.: 2 / Mutation: E93V, S94A, R95S,T96G, N112G, N113Y, T114N, E115H Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P00523-1, non-specific protein-tyrosine kinase #2: Chemical | ChemComp-PG4 / | #3: Chemical | ChemComp-ACT / | #4: 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: 2.34 Å3/Da / Density % sol: 47.36 % / Mosaicity: 0.14 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 0.9 M ammonium sulfate, 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: Mar 16, 2018 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97926 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.5→19.64 Å / Num. obs: 19622 / % possible obs: 99.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 22.7 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.018 / Rrim(I) all: 0.046 / Net I/σ(I): 17.9 / Num. measured all: 126662 | ||||||||||||||||||||||||||||||
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: 4LE9 Resolution: 1.5→19.64 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 0.15 / Phase error: 28.82 / 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: 73.14 Å2 / Biso mean: 32.9015 Å2 / Biso min: 18.25 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.5→19.64 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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