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Open data
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Basic information
Entry | Database: PDB / ID: 1jyu | ||||||
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Title | Xray Structure of Grb2 SH2 Domain | ||||||
![]() | GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2![]() | ||||||
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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 | ![]() ![]() ![]() | ||||||
![]() | Nioche, P. / Liu, W.-Q. / Broutin, I. / Charbonnier, F. / Latreille, M.-T. / Vidal, M. / Roques, B. / Garbay, C. / Ducruix, A. | ||||||
![]() | ![]() Title: Crystal structures of the SH2 domain of Grb2: highlight on the binding of a new high-affinity inhibitor. Authors: Nioche, P. / Liu, W.Q. / Broutin, I. / Charbonnier, F. / Latreille, M.T. / Vidal, M. / Roques, B. / Garbay, C. / Ducruix, 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 | ![]() | 29.8 KB | Display | ![]() |
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PDB format | ![]() | 19.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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2 | ![]()
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Unit cell |
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Components
#1: Protein | ![]() Mass: 11071.563 Da / Num. of mol.: 1 / Fragment: SH2 Domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.01 Å3/Da / Density % sol: 59.17 % | ||||||||||||||||||||||||
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG4000, glycerol, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6 / Method: unknown | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 290 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Highest resolution: 2.75 Å / Num. all: 3698 / Num. obs: 3408 / % possible obs: 98.5 % / Biso Wilson estimate: 37.7 Å2 / Rsym value: 0.071 |
Reflection | *PLUS Num. obs: 3698 / Num. measured all: 62581 / Rmerge(I) obs: 0.071 |
Reflection shell | *PLUS % possible obs: 97.4 % / Rmerge(I) obs: 0.38 |
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Processing
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Refinement | Method to determine structure![]() ![]()
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Displacement parameters | Biso mean: 37.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.75→7.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.75→2.91 Å / Rfactor Rfree error: 0.066 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 9.9 % / Rfactor obs: 0.231 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 37.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.463 / % reflection Rfree: 9.8 % / Rfactor Rwork: 0.363 |