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- PDB-5qqf: PanDDA analysis group deposition -- Crystal Structure of Kalirin/... -

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Basic information

Entry
Database: PDB / ID: 5qqf
TitlePanDDA analysis group deposition -- Crystal Structure of Kalirin/Rac1 in complex with MolPort-004-412-710
Components
  • Kalirin
  • Ras-related C3 botulinum toxin substrate 1
KeywordsHydrolase/Transferase / SGC - Diamond I04-1 fragment screening / XChemExplorer / Hydrolase-Transferase complex
Function / homology
Function and homology information


regulation of respiratory burst / regulation of neutrophil migration / negative regulation of interleukin-23 production / localization within membrane / Activated NTRK2 signals through CDK5 / NADPH oxidase complex / negative regulation of receptor-mediated endocytosis / engulfment of apoptotic cell / regulation of hydrogen peroxide metabolic process / ruffle assembly ...regulation of respiratory burst / regulation of neutrophil migration / negative regulation of interleukin-23 production / localization within membrane / Activated NTRK2 signals through CDK5 / NADPH oxidase complex / negative regulation of receptor-mediated endocytosis / engulfment of apoptotic cell / regulation of hydrogen peroxide metabolic process / ruffle assembly / NTRK2 activates RAC1 / Rho GDP-dissociation inhibitor binding / Inactivation of CDC42 and RAC1 / WNT5:FZD7-mediated leishmania damping / respiratory burst / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / PCP/CE pathway / cell projection assembly / RHO GTPases activate CIT / RHO GTPases activate KTN1 / cortical cytoskeleton organization / ruffle organization / hepatocyte growth factor receptor signaling pathway / positive regulation of neutrophil chemotaxis / regulation of nitric oxide biosynthetic process / Azathioprine ADME / regulation of stress fiber assembly / negative regulation of fibroblast migration / sphingosine-1-phosphate receptor signaling pathway / thioesterase binding / Wnt signaling pathway, planar cell polarity pathway / regulation of lamellipodium assembly / Nef and signal transduction / motor neuron axon guidance / Sema4D mediated inhibition of cell attachment and migration / Activation of RAC1 / regulation of small GTPase mediated signal transduction / positive regulation of Rho protein signal transduction / positive regulation of cell-substrate adhesion / Ephrin signaling / MET activates RAP1 and RAC1 / DCC mediated attractive signaling / CD28 dependent Vav1 pathway / lamellipodium assembly / Activation of RAC1 downstream of NMDARs / semaphorin-plexin signaling pathway / NRAGE signals death through JNK / regulation of cell size / Rac protein signal transduction / DSCAM interactions / positive regulation of lamellipodium assembly / establishment or maintenance of cell polarity / small GTPase mediated signal transduction / RHO GTPases activate PAKs / ficolin-1-rich granule membrane / RHOA GTPase cycle / positive regulation of focal adhesion assembly / RHOG GTPase cycle / Sema3A PAK dependent Axon repulsion / EPH-ephrin mediated repulsion of cells / RHO GTPases activate IQGAPs / anatomical structure morphogenesis / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / ephrin receptor signaling pathway / RHO GTPases Activate WASPs and WAVEs / RHO GTPases Activate NADPH Oxidases / extrinsic component of membrane / RHO GTPases activate PKNs / localization / regulation of actin cytoskeleton organization / GPVI-mediated activation cascade / EPHB-mediated forward signaling / positive regulation of microtubule polymerization / G protein activity / positive regulation of stress fiber assembly / positive regulation of substrate adhesion-dependent cell spreading / regulation of cell migration / RAC1 GTPase cycle / neuron migration / actin filament polymerization / small monomeric GTPase / guanyl-nucleotide exchange factor activity / cell-matrix adhesion / substrate adhesion-dependent cell spreading / cell motility / actin filament organization / secretory granule membrane / vesicle-mediated transport / RHO GTPases Activate Formins / VEGFR2 mediated vascular permeability / Translocation of SLC2A4 (GLUT4) to the plasma membrane / positive regulation of endothelial cell migration / Signal transduction by L1 / G alpha (12/13) signalling events / cell projection / central nervous system development / FCERI mediated MAPK activation / MAPK6/MAPK4 signaling / FCGR3A-mediated phagocytosis / axon guidance
Similarity search - Function
Rho GDP/GTP exchange factor Kalirin/TRIO / Dbl Homology Domain; Chain A / Dbl homology (DH) domain / Divergent CRAL/TRIO domain / CRAL-TRIO lipid binding domain profile. / Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p) / CRAL-TRIO lipid binding domain / CRAL-TRIO lipid binding domain superfamily / Spectrin repeat / Spectrin repeat ...Rho GDP/GTP exchange factor Kalirin/TRIO / Dbl Homology Domain; Chain A / Dbl homology (DH) domain / Divergent CRAL/TRIO domain / CRAL-TRIO lipid binding domain profile. / Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p) / CRAL-TRIO lipid binding domain / CRAL-TRIO lipid binding domain superfamily / Spectrin repeat / Spectrin repeat / small GTPase Rho family profile. / Spectrin/alpha-actinin / Spectrin repeats / Small GTPase Rho / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / Immunoglobulin I-set / Immunoglobulin I-set domain / PH domain / Fibronectin type III domain / PH domain profile. / Rho (Ras homology) subfamily of Ras-like small GTPases / Pleckstrin homology domain. / Pleckstrin homology domain / Small GTPase / Ras family / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Small GTP-binding protein domain / PH-like domain superfamily / Immunoglobulin subtype / Immunoglobulin / P-loop containing nucleotide triphosphate hydrolases / Ig-like domain profile. / Immunoglobulin-like domain / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
N-ethyl-N'-1,3-thiazol-2-ylurea / Kalirin / Ras-related C3 botulinum toxin substrate 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 2.26 Å
AuthorsGray, J.L. / Krojer, T. / Talon, R. / Douangamath, A. / Jimenez Antunez, C. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / Brennan, P.E. / von Delft, F.
CitationJournal: 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
DepositionMay 3, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ras-related C3 botulinum toxin substrate 1
B: Kalirin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3064
Polymers41,0722
Non-polymers2332
Water6,107339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint-8 kcal/mol
Surface area15350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.490, 62.490, 341.271
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Ras-related C3 botulinum toxin substrate 1 / Cell migration-inducing gene 5 protein / Ras-like protein TC25 / p21-Rac1


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
#2: Protein Kalirin / / Huntingtin-associated protein-interacting protein / Protein Duo / Serine/threonine-protein kinase ...Huntingtin-associated protein-interacting protein / Protein Duo / Serine/threonine-protein kinase with Dbl- and pleckstrin homology domain


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 / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-N5V / N-ethyl-N'-1,3-thiazol-2-ylurea


Mass: 171.220 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H9N3OS
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 339 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.47 % / Mosaicity: 0.31 °
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1M bis-tris pH 5.5 24% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 2.26→54.12 Å / Num. obs: 19514 / % possible obs: 99.2 % / Redundancy: 10.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.137 / Rpim(I) all: 0.039 / Rrim(I) all: 0.143 / Net I/σ(I): 10.9 / Num. measured all: 208313 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.26-2.398.61.5752309326960.4170.4941.6631.198.1
7.16-54.1214.50.045115107960.9990.0120.04740.7100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0189refinement
Aimless0.7.1data scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5O33

5o33


Resolution: 2.26→56.88 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.924 / SU B: 12.435 / SU ML: 0.268 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.336 / ESU R Free: 0.258 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2699 949 4.9 %RANDOM
Rwork0.1977 ---
obs0.2012 18445 98.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 134.83 Å2 / Biso mean: 52.975 Å2 / Biso min: 27.72 Å2
Baniso -1Baniso -2Baniso -3
1-0.85 Å20.43 Å20 Å2
2--0.85 Å20 Å2
3----2.76 Å2
Refinement stepCycle: final / Resolution: 2.26→56.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2773 0 15 339 3127
Biso mean--58.07 61.01 -
Num. residues----356
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192872
X-RAY DIFFRACTIONr_bond_other_d0.0020.022637
X-RAY DIFFRACTIONr_angle_refined_deg1.571.9743905
X-RAY DIFFRACTIONr_angle_other_deg1.00736111
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8155358
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.05824.919124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.16515477
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4231511
X-RAY DIFFRACTIONr_chiral_restr0.0860.2448
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213210
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02557
X-RAY DIFFRACTIONr_mcbond_it3.7565.3171434
X-RAY DIFFRACTIONr_mcbond_other3.7545.3171435
X-RAY DIFFRACTIONr_mcangle_it5.8567.9611794
LS refinement shellResolution: 2.265→2.323 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 74 -
Rwork0.361 1279 -
all-1353 -
obs--97.2 %

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