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- PDB-5qhs: PanDDA analysis group deposition of models with modelled events (... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5qhs | ||||||
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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 FF000014a | ||||||
![]() | Protein FAM83B | ||||||
![]() | PROTEIN BINDING / PanDDA / SGC - Diamond I04-1 fragment screening / DUF1669 domain / XChemExplorer | ||||||
Function / homology | ![]() phosphatidylinositol 3-kinase catalytic subunit binding / 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 / Signaling by EGFR / cell population proliferation / protein kinase binding ...phosphatidylinositol 3-kinase catalytic subunit binding / 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 / Signaling by EGFR / cell population proliferation / protein kinase binding / signal transduction / membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | 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. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 46.4 KB | Display | ![]() |
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PDB format | ![]() | 35.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-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 |
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Links
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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.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Chemical | #3: Chemical | ChemComp-GQV / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.51 % / Mosaicity: 0 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 27.3% Tacsimate pH 7.0, 0.15 M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 3, 2017 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.95→51.41 Å / Num. obs: 15563 / % possible obs: 100 % / Redundancy: 12.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.033 / Rrim(I) all: 0.116 / Net I/σ(I): 14 / Num. measured all: 188277 / Scaling rejects: 82 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5LZK Resolution: 1.95→50.77 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.927 / SU B: 4.486 / SU ML: 0.121 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.167 / ESU R Free: 0.161 / 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: 94.32 Å2 / Biso mean: 34.551 Å2 / Biso min: 7.23 Å2
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Refinement step | Cycle: final / Resolution: 1.95→50.77 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.948→1.999 Å / Total num. of bins used: 20
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