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- PDB-5s9d: PanDDA analysis group deposition -- Crystal Structure of PHIP in ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5s9d | ||||||
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Title | PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z198194396 synthetic derivative | ||||||
![]() | PH-interacting protein | ||||||
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Function / homology | ![]() regulation of cell morphogenesis / positive regulation of insulin-like growth factor receptor signaling pathway / RHOBTB2 GTPase cycle / cytoskeleton organization / positive regulation of mitotic nuclear division / negative regulation of extrinsic apoptotic signaling pathway / ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Grosjean, H. / Aimon, A. / Hassel-Hart , S. / Krojer, T. / Talon, R. / Douangamath, A. / Koekemoer, L. / Biggin, P.C. / Spencer, J. / von Delft, F. | ||||||
![]() | ![]() Title: Crystal Structures of the second bromodomain of Pleckstrin homology domain interacting protein (PHIP) in space group C2 soaked with crude reaction mixtures Authors: Grosjean, H. / Aimon, A. / Hart , S. / Krojer, T. / Talon, R. / Douangamath, A. / Koekemoer, L. / Biggin, P.C. / Spencer, J. / von Delft, 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 | ![]() | 44.8 KB | Display | ![]() |
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PDB format | ![]() | 30.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Group deposition
ID | G_1002190 (26 entries) |
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Title | PanDDA analysis group deposition |
Type | changed state |
Description | XDomainX of XOrganismX PHIP screened against crude reaction mixtures by X-ray Crystallography at the XChem facility of Diamond Light Source beamline I04-1 |
-Related structure data
Related structure data | ![]() 5rjiS 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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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 17627.859 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-Y44 / |
#3: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.71 Å3/Da / Density % sol: 28.17 % / Mosaicity: 0 ° |
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Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: 20% PEG 8000, 0.04M POTASSIUM PHOSPHATE |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 16, 2020 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.19→54.76 Å / Num. obs: 34986 / % possible obs: 90.6 % / Redundancy: 2.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.033 / Rrim(I) all: 0.057 / Net I/σ(I): 8.3 / Num. measured all: 90606 / Scaling rejects: 51 | ||||||||||||||||||||||||||||||
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: 5RJI Resolution: 1.19→54.77 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.331 / SU ML: 0.055 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.059 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 62.8 Å2 / Biso mean: 18.626 Å2 / Biso min: 10.73 Å2
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Refinement step | Cycle: final / Resolution: 1.19→54.77 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.19→1.221 Å / Total num. of bins used: 20
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