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Yorodumi- PDB-8bw3: PanDDA analysis -- Crystal Structure of PHIP in complex with Z198... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8bw3 | |||||||||
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Title | PanDDA analysis -- Crystal Structure of PHIP in complex with Z198194396 synthetic derivative | |||||||||
Components | PH-interacting protein | |||||||||
Keywords | SIGNALING PROTEIN / brodomain / automated chemistry / reaction product | |||||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | |||||||||
Authors | Grosjean, H. / Aimon, A. / Hassell-Hart, S. / Bradshaw, W.J. / Krojer, T. / Talon, R. / Douangamath, A. / Koekemoer, L. / Biggin, P.C. / Spencer, J. / von Delft, F. | |||||||||
Funding support | United Kingdom, 1items
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Citation | Journal: To Be Published Title: PanDDA analysis -- Crystal Structure of PHIP in complex with Z198194396 synthetic derivative Authors: Grosjean, H. / Aimon, A. / Hassell-Hart, S. / Bradshaw, W.J. / 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 | 8bw3.cif.gz | 90.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8bw3.ent.gz | 51.5 KB | Display | PDB format |
PDBx/mmJSON format | 8bw3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8bw3_validation.pdf.gz | 751.7 KB | Display | wwPDB validaton report |
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Full document | 8bw3_full_validation.pdf.gz | 752.4 KB | Display | |
Data in XML | 8bw3_validation.xml.gz | 8.4 KB | Display | |
Data in CIF | 8bw3_validation.cif.gz | 11.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bw/8bw3 ftp://data.pdbj.org/pub/pdb/validation_reports/bw/8bw3 | HTTPS FTP |
-Related structure data
Related structure data | 8bw2C 8bw4C 7av9S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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-Y3V / ( |
#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: 1.7 Å3/Da / Density % sol: 27.44 % |
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Crystal grow | Temperature: 277.5 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: 20% PEG 8000, 0.04M POTASSIUM PHOSPHATE |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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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 / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9127 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→54.4 Å / Num. obs: 28411 / % possible obs: 96.7 % / Redundancy: 2.9 % / CC1/2: 0.996 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 1.3→1.32 Å / Mean I/σ(I) obs: 0.6 / Num. unique obs: 1239 / CC1/2: 0.417 / % possible all: 87.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7AV9 Resolution: 1.3→54.4 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.884 / SU ML: 0.067 / Cross valid method: FREE R-VALUE / ESU R: 0.073 / ESU R Free: 0.067 Details: Hydrogens have been added in their riding positions
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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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.35 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→54.4 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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