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Yorodumi- PDB-5s8f: XChem group deposition -- Crystal Structure of the second bromodo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5s8f | ||||||
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Title | XChem group deposition -- Crystal Structure of the second bromodomain of pleckstrin homology domain interacting protein (PHIP) in complex with N00572d (space group C2) | ||||||
Components | PH-interacting protein | ||||||
Keywords | SIGNALING PROTEIN / SGC - Diamond I04-1 fragment screening / bromodomain / PHIP / XChemExplorer | ||||||
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: 1.18 Å | ||||||
Authors | Krojer, T. / Talon, R. / Fairhead, M. / Szykowska, A. / Burgess-Brown, N.A. / Brennan, P.E. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / von Delft, F. | ||||||
Citation | Journal: To Be Published Title: XChem group deposition Authors: Krojer, T. / Talon, R. / Fairhead, M. / Szykowska, A. / Burgess-Brown, N.A. / Brennan, P.E. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / 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 | 5s8f.cif.gz | 69.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5s8f.ent.gz | 51.3 KB | Display | PDB format |
PDBx/mmJSON format | 5s8f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s8/5s8f ftp://data.pdbj.org/pub/pdb/validation_reports/s8/5s8f | HTTPS FTP |
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-Group deposition
ID | G_1002187 (15 entries) |
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Title | XChem group deposition |
Type | changed state |
Description | crystallographic fragment screen of human PHIP(2) |
-Related structure data
Related structure data | 7av9S 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: 15156.185 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-ZHA / ~{ |
#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: 2.1 Å3/Da / Density % sol: 41.49 % / Mosaicity: 0 ° |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.04M potassium phosphate monobasic -- 12% PEG8K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 23, 2016 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.92819 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.18→55.84 Å / Num. obs: 39796 / % possible obs: 95 % / Redundancy: 2.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.033 / Rpim(I) all: 0.023 / Rrim(I) all: 0.041 / Net I/σ(I): 16.5 / Num. measured all: 109783 / Scaling rejects: 1 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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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: 7AV9 Resolution: 1.18→55.84 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.854 / SU ML: 0.035 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.041 / ESU R Free: 0.04 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 62.61 Å2 / Biso mean: 16.158 Å2 / Biso min: 9.43 Å2
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Refinement step | Cycle: final / Resolution: 1.18→55.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.18→1.211 Å / Total num. of bins used: 20
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