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- PDB-3ove: Crystal Structure of the Grb2 SH2 Domain in Complex with a pYXN-D... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3ove | ||||||
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Title | Crystal Structure of the Grb2 SH2 Domain in Complex with a pYXN-Derived Tripeptide | ||||||
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Function / homology | ![]() guanyl-nucleotide exchange factor adaptor activity / Grb2-EGFR complex / branching involved in labyrinthine layer morphogenesis / STAT5 Activation / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Clements, J.H. / Martin, S.F. | ||||||
![]() | ![]() Title: Protein-ligand interactions: thermodynamic effects associated with increasing nonpolar surface area. Authors: Myslinski, J.M. / Delorbe, J.E. / Clements, J.H. / Martin, S.F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 40.2 KB | Display | ![]() |
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PDB format | ![]() | 26.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3ov1C ![]() 3s8lC ![]() 3s8nC ![]() 3s8oC ![]() 3c7iS C: citing same article ( 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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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | ![]() Mass: 13614.279 Da / Num. of mol.: 1 / Fragment: unp residues 53-163 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 553.502 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Chemical | ChemComp-CL / ![]() |
#4: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.82 Å3/Da / Density % sol: 30.97 % |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.2 M magnesium chloride hexahydrate, 0.1 M TRIS,30% w/v polyethylene glycol 4,000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 27, 2010 |
Radiation | Monochromator: Blue max-flux confocal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.82→50 Å / Num. obs: 8801 / % possible obs: 93.7 % / Redundancy: 11.8 % / Rsym value: 0.076 / Net I/σ(I): 22.5 |
Reflection shell | Resolution: 1.82→1.89 Å / Redundancy: 12.6 % / Mean I/σ(I) obs: 10.1 / Num. unique all: 900 / Rsym value: 0.223 / % possible all: 96.4 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB entry 3C7I Resolution: 1.82→26.05 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.909 / SU B: 3.055 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.029 Å2
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Refinement step | Cycle: LAST / Resolution: 1.82→26.05 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.821→1.868 Å / Total num. of bins used: 20
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