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Yorodumi- PDB-5rkp: PanDDA analysis group deposition -- Crystal Structure of PHIP in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5rkp | ||||||
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Title | PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z1079512010 | ||||||
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: 1.35 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 | 5rkp.cif.gz | 69.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5rkp.ent.gz | 50.2 KB | Display | PDB format |
PDBx/mmJSON format | 5rkp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rk/5rkp ftp://data.pdbj.org/pub/pdb/validation_reports/rk/5rkp | 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-UWS / |
#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: 1.74 Å3/Da / Density % sol: 29.31 % / 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: 0.97622 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 28, 2019 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97622 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.35→54.87 Å / Num. obs: 25855 / % possible obs: 95.6 % / Redundancy: 3 % / Biso Wilson estimate: 17.36 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.035 / Rrim(I) all: 0.063 / Net I/σ(I): 10.7 / Num. measured all: 76596 / Scaling rejects: 4 | ||||||||||||||||||||||||||||||
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: 3MB3 Resolution: 1.35→54.87 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.927 / SU R Cruickshank DPI: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.073 / SU Rfree Blow DPI: 0.077 / SU Rfree Cruickshank DPI: 0.071
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Displacement parameters | Biso max: 62.03 Å2 / Biso mean: 21.45 Å2 / Biso min: 11.92 Å2
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Refine analyze | Luzzati coordinate error obs: 0.19 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.35→54.87 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.35→1.36 Å / Total num. of bins used: 51
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Refinement TLS params. | Method: refined / Origin x: -14.278 Å / Origin y: 12.527 Å / Origin z: 12.7965 Å
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Refinement TLS group | Selection details: { A|* } |