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Yorodumi- PDB-5qqn: PanDDA analysis group deposition -- Crystal Structure of Kalirin/... -
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-Basic information
Entry | Database: PDB / ID: 5qqn | ||||||
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Title | PanDDA analysis group deposition -- Crystal Structure of Kalirin/Rac1 in complex with MolPort-010-382-606 | ||||||
Components |
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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 / engulfment of apoptotic cell / NTRK2 activates RAC1 ...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 / engulfment of apoptotic cell / NTRK2 activates RAC1 / Inactivation of CDC42 and RAC1 / NADPH oxidase complex / respiratory burst / WNT5:FZD7-mediated leishmania damping / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / cortical cytoskeleton organization / hepatocyte growth factor receptor signaling pathway / ruffle organization / cell projection assembly / thioesterase binding / regulation of stress fiber assembly / negative regulation of fibroblast migration / RHO GTPases activate CIT / sphingosine-1-phosphate receptor signaling pathway / Nef and signal transduction / motor neuron axon guidance / PCP/CE pathway / positive regulation of neutrophil chemotaxis / regulation of nitric oxide biosynthetic process / RHO GTPases activate KTN1 / Activation of RAC1 / regulation of lamellipodium assembly / Azathioprine ADME / MET activates RAP1 and RAC1 / DCC mediated attractive signaling / positive regulation of cell-substrate adhesion / regulation of small GTPase mediated signal transduction / Wnt signaling pathway, planar cell polarity pathway / Sema4D mediated inhibition of cell attachment and migration / CD28 dependent Vav1 pathway / Ephrin signaling / lamellipodium assembly / positive regulation of Rho protein signal transduction / regulation of cell size / 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 / RHOA GTPase cycle / RHO GTPases Activate NADPH Oxidases / EPH-ephrin mediated repulsion of cells / anatomical structure morphogenesis / ephrin receptor signaling pathway / RHO GTPases Activate WASPs and WAVEs / RHO GTPases activate IQGAPs / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / positive regulation of lamellipodium assembly / positive regulation of substrate adhesion-dependent cell spreading / RHO GTPases activate PKNs / vesicle-mediated transport / Signal transduction by L1 / positive regulation of stress fiber assembly / GPVI-mediated activation cascade / positive regulation of microtubule polymerization / EPHB-mediated forward signaling / RAC1 GTPase cycle / regulation of cell migration / actin filament polymerization / positive regulation of endothelial cell migration / substrate adhesion-dependent cell spreading / cell chemotaxis / cell-matrix adhesion / small monomeric GTPase / secretory granule membrane / VEGFR2 mediated vascular permeability / G protein activity / guanyl-nucleotide exchange factor activity / actin filament organization / axon guidance / Translocation of SLC2A4 (GLUT4) to the plasma membrane / cell motility / RHO GTPases Activate Formins / regulation of actin cytoskeleton organization / FCERI mediated MAPK activation / FCGR3A-mediated phagocytosis / ruffle membrane / neuron migration / MAPK6/MAPK4 signaling / trans-Golgi network / Signaling by SCF-KIT / Regulation of actin dynamics for phagocytic cup formation Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 2.26 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 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5qqn.cif.gz | 93.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5qqn.ent.gz | 69.1 KB | Display | PDB format |
PDBx/mmJSON format | 5qqn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5qqn_validation.pdf.gz | 699 KB | Display | wwPDB validaton report |
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Full document | 5qqn_full_validation.pdf.gz | 703.6 KB | Display | |
Data in XML | 5qqn_validation.xml.gz | 19.9 KB | Display | |
Data in CIF | 5qqn_validation.cif.gz | 29.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qq/5qqn ftp://data.pdbj.org/pub/pdb/validation_reports/qq/5qqn | HTTPS FTP |
-Group deposition
ID | G_1002072 (11 entries) |
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Title | PanDDA analysis group deposition |
Type | changed 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 |
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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
#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 |
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#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: Chemical | ChemComp-N5D / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.56 % / Mosaicity: 0.18 ° |
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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: 100 K | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 2, 2018 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.91587 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.26→170.9 Å / Num. obs: 19972 / % possible obs: 100 % / Redundancy: 17.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.439 / Rpim(I) all: 0.106 / Rrim(I) all: 0.452 / Net I/σ(I): 11.8 / Num. measured all: 350235 / Scaling rejects: 413 | ||||||||||||||||||||||||||||||
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: 5O33 Resolution: 2.26→54.18 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.905 / SU B: 9.512 / SU ML: 0.219 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.332 / ESU R Free: 0.261 / 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: 115.79 Å2 / Biso mean: 43.381 Å2 / Biso min: 24.39 Å2
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Refinement step | Cycle: final / Resolution: 2.26→54.18 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.255→2.314 Å / Total num. of bins used: 20
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