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Yorodumi- PDB-5s9j: PanDDA analysis group deposition -- Crystal Structure of PHIP in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5s9j | ||||||
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Title | PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with starting material | ||||||
Components | PH-interacting protein | ||||||
Keywords | SIGNALING PROTEIN / SGC - Diamond I04-1 fragment screening / PanDDA / XChemExplorer / Robotic chemistry / Crystal soaking / Reaction crudes | ||||||
Function / homology | Function and homology information 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 / regulation of protein phosphorylation / lysine-acetylated histone binding / insulin receptor binding / insulin receptor signaling pathway ...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 / regulation of protein phosphorylation / lysine-acetylated histone binding / insulin receptor binding / insulin receptor signaling pathway / regulation of cell shape / positive regulation of cell population proliferation / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.15 Å | ||||||
Authors | Grosjean, H. / Aimon, A. / Hassel-Hart , S. / Krojer, T. / Talon, R. / Douangamath, A. / Koekemoer, L. / Biggin, P.C. / Spencer, J. / von Delft, F. | ||||||
Citation | Journal: To Be Published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5s9j.cif.gz | 68.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5s9j.ent.gz | 49.3 KB | Display | PDB format |
PDBx/mmJSON format | 5s9j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s9/5s9j ftp://data.pdbj.org/pub/pdb/validation_reports/s9/5s9j | 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 |
-Links
-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.) Homo sapiens (human) / Gene: PHIP, DCAF14, WDR11 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8WWQ0 |
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#2: Chemical | ChemComp-3M0 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.7 Å3/Da / Density % sol: 27.51 % / 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: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9127 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 8, 2020 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9127 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.15→54.91 Å / Num. obs: 35016 / % possible obs: 82.7 % / Redundancy: 2.7 % / Biso Wilson estimate: 13.91 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.036 / Rrim(I) all: 0.065 / Net I/σ(I): 8.2 / Num. measured all: 94019 / Scaling rejects: 28 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 5RJI Resolution: 1.15→54.9 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.948 / SU R Cruickshank DPI: 0.051 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.056 / SU Rfree Blow DPI: 0.056 / SU Rfree Cruickshank DPI: 0.052
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Displacement parameters | Biso max: 108.98 Å2 / Biso mean: 18.6 Å2 / Biso min: 10.25 Å2
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Refine analyze | Luzzati coordinate error obs: 0.18 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.15→54.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.15→1.17 Å / Total num. of bins used: 51
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Refinement TLS params. | Method: refined / Origin x: -14.2209 Å / Origin y: 12.3551 Å / Origin z: 12.6226 Å
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Refinement TLS group | Selection details: { A|* } |