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Yorodumi- PDB-5rk3: PanDDA analysis group deposition -- Crystal Structure of PHIP in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5rk3 | ||||||
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Title | PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z1501469697 | ||||||
Components | PH-interacting protein | ||||||
Keywords | PROTEIN BINDING / SGC - Diamond I04-1 fragment screening / PanDDA / XChemExplorer / Fragment-based drug design / SAMPL7 | ||||||
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: 1.31 Å | ||||||
Authors | Grosjean, H. / Aimon, A. / Krojer, T. / Talon, R. / Douangamath, A. / Koekemoer, L. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / von Delft, F. / Biggin, P.C. | ||||||
Citation | Journal: To Be Published Title: PanDDA analysis group deposition of ground-state model Authors: Grosjean, H. / Aimon, A. / Krojer, T. / Talon, R. / Douangamath, A. / Koekemoer, L. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / von Delft, F. / Biggin, P.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5rk3.cif.gz | 68.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5rk3.ent.gz | 49.3 KB | Display | PDB format |
PDBx/mmJSON format | 5rk3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rk/5rk3 ftp://data.pdbj.org/pub/pdb/validation_reports/rk/5rk3 | HTTPS FTP |
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-Group deposition
ID | G_1002162 (52 entries) |
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Title | PanDDA analysis group deposition |
Type | changed state |
Description | The second bromodomain of Pleckstrin homology domain interacting protein (PHIP) screened against the DSI and FragLite fragment libraries by X-ray Crystallography at the XChem facility of Diamond Light Source beamline I04-1 |
-Related structure data
Related structure data | 3mb3S 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-UVV / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.73 Å3/Da / Density % sol: 29.04 % |
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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: I03 / Wavelength: 0.97622 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 21, 2019 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97622 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.311→40.279 Å / Num. obs: 25326 / % possible obs: 87.3 % / Redundancy: 5.9 % / Biso Wilson estimate: 14.23 Å2 / CC1/2: 1 / Rpim(I) all: 0.014 / Rrim(I) all: 0.036 / Net I/σ(I): 23.7 / Num. measured all: 150357 | ||||||||||||||||||||||||
Reflection shell | Num. unique all: 1266 / 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: 3MB3 Resolution: 1.31→40.28 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.933 / SU R Cruickshank DPI: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.073 / SU Rfree Blow DPI: 0.071 / SU Rfree Cruickshank DPI: 0.066
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Displacement parameters | Biso max: 49.23 Å2 / Biso mean: 16.86 Å2 / Biso min: 8.11 Å2
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Refine analyze | Luzzati coordinate error obs: 0.18 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.31→40.28 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.31→1.34 Å / Total num. of bins used: 51
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Refinement TLS params. | Method: refined / Origin x: -14.2607 Å / Origin y: 12.493 Å / Origin z: 12.6225 Å
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Refinement TLS group | Selection details: { A|* } |