[English] 日本語
Yorodumi- PDB-5qu9: PanDDA analysis group deposition of ground-state model of Kalirin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5qu9 | ||||||
---|---|---|---|---|---|---|---|
Title | PanDDA analysis group deposition of ground-state model of Kalirin/Rac1 screened against a customized urea fragment library by X-ray Crystallography at the XChem facility of Diamond Light Source beamline I04-1 | ||||||
Components |
| ||||||
Keywords | HYDROLASE/TRANSFERASE / SGC - Diamond I04-1 fragment screening / XChemExplorer / HYDROLASE-TRANSFERASE complex | ||||||
Function / homology | Function and homology information regulation of respiratory burst / negative regulation of interleukin-23 production / regulation of neutrophil migration / localization within membrane / Activated NTRK2 signals through CDK5 / negative regulation of receptor-mediated endocytosis / regulation of hydrogen peroxide metabolic process / ruffle assembly / NTRK2 activates RAC1 / NADPH oxidase complex ...regulation of respiratory burst / negative regulation of interleukin-23 production / regulation of neutrophil migration / localization within membrane / Activated NTRK2 signals through CDK5 / negative regulation of receptor-mediated endocytosis / regulation of hydrogen peroxide metabolic process / ruffle assembly / NTRK2 activates RAC1 / NADPH oxidase complex / engulfment of apoptotic cell / Inactivation of CDC42 and RAC1 / WNT5:FZD7-mediated leishmania damping / cortical cytoskeleton organization / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / respiratory burst / hepatocyte growth factor receptor signaling pathway / ruffle organization / cell projection assembly / thioesterase binding / negative regulation of fibroblast migration / regulation of stress fiber assembly / RHO GTPases activate CIT / Nef and signal transduction / sphingosine-1-phosphate receptor signaling pathway / PCP/CE pathway / regulation of nitric oxide biosynthetic process / motor neuron axon guidance / RHO GTPases activate KTN1 / regulation of lamellipodium assembly / Azathioprine ADME / Activation of RAC1 / positive regulation of neutrophil chemotaxis / positive regulation of cell-substrate adhesion / MET activates RAP1 and RAC1 / DCC mediated attractive signaling / Wnt signaling pathway, planar cell polarity pathway / Sema4D mediated inhibition of cell attachment and migration / regulation of small GTPase mediated signal transduction / CD28 dependent Vav1 pathway / Ephrin signaling / lamellipodium assembly / positive regulation of Rho protein signal transduction / regulation of cell size / DSCAM interactions / establishment or maintenance of cell polarity / Activation of RAC1 downstream of NMDARs / small GTPase-mediated signal transduction / Rho GDP-dissociation inhibitor binding / extrinsic component of membrane / NRAGE signals death through JNK / Rac protein signal transduction / RHO GTPases activate PAKs / positive regulation of focal adhesion assembly / semaphorin-plexin signaling pathway / Sema3A PAK dependent Axon repulsion / ficolin-1-rich granule membrane / RHOG GTPase cycle / EPH-ephrin mediated repulsion of cells / RHO GTPases Activate NADPH Oxidases / RHOA GTPase cycle / RHO GTPases Activate WASPs and WAVEs / anatomical structure morphogenesis / ephrin receptor signaling pathway / RHO GTPases activate IQGAPs / localization / positive regulation of lamellipodium assembly / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / positive regulation of substrate adhesion-dependent cell spreading / RHO GTPases activate PKNs / positive regulation of microtubule polymerization / regulation of cell migration / vesicle-mediated transport / positive regulation of stress fiber assembly / GPVI-mediated activation cascade / EPHB-mediated forward signaling / RAC1 GTPase cycle / actin filament polymerization / cell chemotaxis / substrate adhesion-dependent cell spreading / cell-matrix adhesion / guanyl-nucleotide exchange factor activity / small monomeric GTPase / positive regulation of endothelial cell migration / G protein activity / secretory granule membrane / VEGFR2 mediated vascular permeability / Signal transduction by L1 / actin filament organization / cell motility / axon guidance / Translocation of SLC2A4 (GLUT4) to the plasma membrane / RHO GTPases Activate Formins / regulation of actin cytoskeleton organization / FCERI mediated MAPK activation / FCGR3A-mediated phagocytosis / neuron migration / MAPK6/MAPK4 signaling / trans-Golgi network / Signaling by SCF-KIT Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 2 Å | ||||||
Authors | Gray, J.L. / Krojer, T. / Talon, R. / Douangamath, A. / Jimenez Antunez, C. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / Brennan, P.E. / von Delft, F. | ||||||
Citation | Journal: To Be Published Title: PanDDA analysis group deposition of ground-state model Authors: Gray, J.L. / Krojer, T. / Talon, R. / Douangamath, A. / Jimenez Antunez, C. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / Brennan, P.E. / von Delft, F. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5qu9.cif.gz | 160.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5qu9.ent.gz | 125.3 KB | Display | PDB format |
PDBx/mmJSON format | 5qu9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qu/5qu9 ftp://data.pdbj.org/pub/pdb/validation_reports/qu/5qu9 | HTTPS FTP |
---|
-Group deposition
ID | G_1002111 (1 entries) |
---|---|
Title | PanDDA analysis group deposition of ground-state model |
Type | ground state |
Description | Kalirin/Rac1 complex screened against a customized urea fragment library by X-ray Crystallography at the XChem facility of Diamond Light Source beamline I04-1 |
-Related structure data
Related structure data | 5o33S S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 19797.844 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RAC1, TC25, MIG5 / Production host: Escherichia coli (E. coli) / References: UniProt: P63000, small monomeric GTPase |
---|---|
#2: Protein | Mass: 21274.471 Da / Num. of mol.: 1 / Mutation: None Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KALRN, DUET, DUO, HAPIP, TRAD / Production host: Escherichia coli (E. coli) References: UniProt: O60229, non-specific serine/threonine protein kinase |
#3: Chemical | ChemComp-EDO / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.84 % / Mosaicity: 0 ° |
---|---|
Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1M bis-tris pH 5.5 24% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 277 K | |||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1 Å | |||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 3, 2018 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.91→342.64 Å / Num. obs: 32694 / % possible obs: 100 % / Redundancy: 33.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.514 / Rpim(I) all: 0.087 / Rrim(I) all: 0.521 / Net I/σ(I): 10.4 / Num. measured all: 1106790 / Scaling rejects: 2217 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / % possible all: 100
|
-Phasing
Phasing | Method: molecular replacement |
---|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 5O33 Resolution: 2→55.008 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.26 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 113.15 Å2 / Biso mean: 30.5209 Å2 / Biso min: 6.09 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→55.008 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|