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- PDB-5s9b: 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: 5s9b | ||||||
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Title | PanDDA analysis group deposition -- Crystal Structure of PHIP in complex withstarting material | ||||||
![]() | 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 | ![]() | 68.5 KB | Display | ![]() |
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PDB format | ![]() | 49.6 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-OVM / ![]() |
#3: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.71 Å3/Da / Density % sol: 27.95 % / 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 15, 2020 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.15→54.83 Å / Num. obs: 36049 / % possible obs: 84.2 % / Redundancy: 2.4 % / Biso Wilson estimate: 14.01 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.032 / Rrim(I) all: 0.056 / Net I/σ(I): 6.8 / Num. measured all: 87062 / Scaling rejects: 100 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing![]() | Method: ![]() |
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Processing
Software |
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Refinement | Method to determine structure![]() ![]() Starting model: 5RJI Resolution: 1.153→54.82 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.948 / SU R Cruickshank DPI: 0.048 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.053 / SU Rfree Blow DPI: 0.055 / SU Rfree Cruickshank DPI: 0.051
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Displacement parameters | Biso max: 90.24 Å2 / Biso mean: 20.46 Å2 / Biso min: 11.74 Å2
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Refine analyze | Luzzati coordinate error obs: 0.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.153→54.82 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.15→1.18 Å / Total num. of bins used: 51
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Refinement TLS params. | Method: refined / Origin x: -14.2807 Å / Origin y: 12.3501 Å / Origin z: 12.7413 Å
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Refinement TLS group | Selection details: { A|* } |