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Yorodumi- PDB-5qhi: PanDDA analysis group deposition of models with modelled events (... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5qhi | ||||||
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Title | PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of human FAM83B in complex with FMOPL000271a | ||||||
Components | Protein FAM83B | ||||||
Keywords | PROTEIN BINDING / PanDDA / SGC - Diamond I04-1 fragment screening / DUF1669 domain / XChemExplorer | ||||||
Function / homology | Function and homology information phosphatidylinositol 3-kinase catalytic subunit binding / Signaling by EGFR / phosphatidylinositol 3-kinase regulatory subunit binding / RND1 GTPase cycle / RND2 GTPase cycle / RND3 GTPase cycle / positive regulation of epidermal growth factor receptor signaling pathway / epidermal growth factor receptor binding / cell population proliferation / protein kinase binding ...phosphatidylinositol 3-kinase catalytic subunit binding / Signaling by EGFR / phosphatidylinositol 3-kinase regulatory subunit binding / RND1 GTPase cycle / RND2 GTPase cycle / RND3 GTPase cycle / positive regulation of epidermal growth factor receptor signaling pathway / epidermal growth factor receptor binding / cell population proliferation / protein kinase binding / signal transduction / membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.73 Å | ||||||
Authors | Pinkas, D.M. / Bufton, J.C. / Fox, A.E. / Talon, R. / Krojer, T. / Douangamath, A. / Collins, P. / Zhang, R. / von Delft, F. / Bountra, C. ...Pinkas, D.M. / Bufton, J.C. / Fox, A.E. / Talon, R. / Krojer, T. / Douangamath, A. / Collins, P. / Zhang, R. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / Bullock, A.N. | ||||||
Citation | Journal: To Be Published Title: PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) Authors: Pinkas, D.M. / Bufton, J.C. / Fox, A.E. / Talon, R. / Krojer, T. / Douangamath, A. / Collins, P. / Zhang, R. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / Bullock, A.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5qhi.cif.gz | 90.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5qhi.ent.gz | 68.3 KB | Display | PDB format |
PDBx/mmJSON format | 5qhi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5qhi_validation.pdf.gz | 462.7 KB | Display | wwPDB validaton report |
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Full document | 5qhi_full_validation.pdf.gz | 465.2 KB | Display | |
Data in XML | 5qhi_validation.xml.gz | 18.2 KB | Display | |
Data in CIF | 5qhi_validation.cif.gz | 26.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qh/5qhi ftp://data.pdbj.org/pub/pdb/validation_reports/qh/5qhi | HTTPS FTP |
-Group deposition
ID | G_1002046 (11 entries) |
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Title | PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) |
Type | changed state |
Description | Human FAM83B DUF1669 domain screened against DSPL and OxXChem Libraries by X-ray Crystallography at the XChem facility of Diamond Light Source beamline I04-1 |
-Related structure data
Related structure data | 5lzkS S: Starting model for refinement |
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Similar structure data | |
Experimental dataset #1 | Data set type: other data / Details: Complete PanDDA analysis / Metadata reference: 10.5281/zenodo.1247291 |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 20783.109 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FAM83B, C6orf143 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5T0W9 #2: Chemical | ChemComp-IOD / #3: Chemical | ChemComp-EDO / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-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: 41.33 % / Mosaicity: 0 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.8M NaP monobasic, 0.8M KP dibasic, 0.1M HEPES pH 7.5 5%(w/v) PEG10K |
-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: Jul 9, 2016 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.92819 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.73→31.93 Å / Num. obs: 35382 / % possible obs: 98.8 % / Redundancy: 3.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.069 / Rrim(I) all: 0.129 / Net I/σ(I): 8.1 / Num. measured all: 118553 / Scaling rejects: 0 | ||||||||||||||||||||||||||||||
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: 5LZK Resolution: 1.73→62.67 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.468 / SU ML: 0.105 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.124 / ESU R Free: 0.123 / 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: 160.93 Å2 / Biso mean: 24.7 Å2 / Biso min: 11.11 Å2
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Refinement step | Cycle: final / Resolution: 1.73→62.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.73→1.775 Å / Total num. of bins used: 20
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