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- PDB-4j9c: Crystal structure of the Abl-SH3 domain H59Q-N96T mutant complexe... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4j9c | ||||||
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Title | Crystal structure of the Abl-SH3 domain H59Q-N96T mutant complexed with the designed high-affinity peptide ligand P17 | ||||||
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![]() | Transferase/unknown function / beta shandwich / ![]() ![]() | ||||||
Function / homology | ![]() : / positive regulation of actin filament binding / positive regulation of oxidoreductase activity / protein localization to cytoplasmic microtubule plus-end / DNA conformation change / podocyte apoptotic process / DN4 thymocyte differentiation / Role of ABL in ROBO-SLIT signaling / response to epinephrine / transitional one stage B cell differentiation ...: / positive regulation of actin filament binding / positive regulation of oxidoreductase activity / protein localization to cytoplasmic microtubule plus-end / DNA conformation change / podocyte apoptotic process / DN4 thymocyte differentiation / Role of ABL in ROBO-SLIT signaling / response to epinephrine / transitional one stage B cell differentiation / activation of protein kinase C activity / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Camara-Artigas, A. | ||||||
![]() | ![]() Title: Crystal structure of the Abl-SH3 domain H59Q-N96T mutant complexed with the designed high-affinity peptide ligand P17 Authors: Camara-Artigas, A. #1: ![]() Title: Crystallization by capillary counter-diffusion and structure determination of the N114A mutant of the SH3 domain of Abl tyrosine kinase complexed with a high-affinity peptide ligand. Authors: Camara-Artigas, A. / Palencia, A. / Martinez, J.C. / Luque, I. / Gavira, J.A. / Garcia-Ruiz, J.M. #2: ![]() Title: Role of interfacial water molecules in proline-rich ligand recognition by the Src homology 3 domain of Abl. Authors: Palencia, A. / Camara-Artigas, A. / Pisabarro, M.T. / Martinez, J.C. / Luque, I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 56.1 KB | Display | ![]() |
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PDB format | ![]() | 40.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2o88S S: Starting model for refinement |
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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 on special symmetry positions |
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Components
#1: Protein | Mass: 6986.677 Da / Num. of mol.: 1 / Fragment: SH3 domain (unp residues 60-121) / Mutation: H59Q, N96T Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: P00519, ![]() |
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#2: Protein/peptide | Mass: 1065.218 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Chemical | ChemComp-PGE / ![]() |
#4: Chemical | ChemComp-PEG / ![]() |
#5: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.69 % |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 1.5 M AMS, 5% PEG 200, 20 mM LiCl, 0.1 M AcONa , pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Detector: CCD / Date: Apr 8, 2011 |
Radiation | Monochromator: Channel cut ESRF monochromator and torodial focusing mirror Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.051→42.995 Å / Num. all: 29920 / Num. obs: 29561 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.3 % / Biso Wilson estimate: 8.3 Å2 / Rmerge(I) obs: 0.04 / Rsym value: 0.04 / Net I/σ(I): 28.7 |
Reflection shell | Resolution: 1.05→1.11 Å / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 4.61 / Num. unique all: 4721 / % possible all: 99.1 |
-Phasing
Phasing![]() | Method: ![]() |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 2O88 Resolution: 1.051→16.754 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.08 / σ(F): 0 / σ(I): 0 / Phase error: 13.52 / 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: 40.03 Å2 / Biso mean: 14.95 Å2 / Biso min: 6.31 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.051→16.754 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: 21
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