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- PDB-8x5z: The Crystal Structure of PAK1 kinase domain from Biortus. -

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Basic information

Entry
Database: PDB / ID: 8x5z
TitleThe Crystal Structure of PAK1 kinase domain from Biortus.
ComponentsSerine/threonine-protein kinase PAK 1
KeywordsSIGNALING PROTEIN / Serine/threonine-protein kinase / Transferase
Function / homology
Function and homology information


negative regulation of cell proliferation involved in contact inhibition / protein localization to cytoplasmic stress granule / positive regulation of microtubule nucleation / hepatocyte growth factor receptor signaling pathway / RHO GTPases Activate ROCKs / gamma-tubulin binding / Activation of RAC1 / CD28 dependent Vav1 pathway / Ephrin signaling / positive regulation of intracellular estrogen receptor signaling pathway ...negative regulation of cell proliferation involved in contact inhibition / protein localization to cytoplasmic stress granule / positive regulation of microtubule nucleation / hepatocyte growth factor receptor signaling pathway / RHO GTPases Activate ROCKs / gamma-tubulin binding / Activation of RAC1 / CD28 dependent Vav1 pathway / Ephrin signaling / positive regulation of intracellular estrogen receptor signaling pathway / DSCAM interactions / RHOV GTPase cycle / regulation of axonogenesis / branching morphogenesis of an epithelial tube / Fc-gamma receptor signaling pathway involved in phagocytosis / RHOJ GTPase cycle / RHOQ GTPase cycle / exocytosis / RHO GTPases activate PAKs / stimulatory C-type lectin receptor signaling pathway / regulation of MAPK cascade / RHOH GTPase cycle / CDC42 GTPase cycle / RHOU GTPase cycle / Sema3A PAK dependent Axon repulsion / Generation of second messenger molecules / intercalated disc / Smooth Muscle Contraction / RAC3 GTPase cycle / RAC2 GTPase cycle / ephrin receptor signaling pathway / localization / positive regulation of microtubule polymerization / RHO GTPases activate PKNs / positive regulation of JUN kinase activity / positive regulation of stress fiber assembly / ruffle / RAC1 GTPase cycle / EPHB-mediated forward signaling / collagen binding / CD209 (DC-SIGN) signaling / neuron projection morphogenesis / VEGFR2 mediated vascular permeability / Signal transduction by L1 / actin filament / regulation of actin cytoskeleton organization / FCERI mediated MAPK activation / MAPK6/MAPK4 signaling / wound healing / G beta:gamma signalling through CDC42 / Regulation of actin dynamics for phagocytic cup formation / ruffle membrane / Z disc / cell-cell junction / cell migration / lamellipodium / positive regulation of peptidyl-serine phosphorylation / chromosome / actin cytoskeleton organization / nuclear membrane / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / positive regulation of cell migration / intracellular signal transduction / chromatin remodeling / positive regulation of protein phosphorylation / axon / phosphorylation / protein phosphorylation / focal adhesion / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / dendrite / apoptotic process / DNA damage response / positive regulation of cell population proliferation / protein-containing complex / nucleoplasm / ATP binding / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
p21 activated kinase binding domain / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. / P21-Rho-binding domain / CRIB domain / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain ...p21 activated kinase binding domain / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. / P21-Rho-binding domain / CRIB 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. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Serine/threonine-protein kinase PAK 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWang, F. / Cheng, W. / Lv, Z. / Ju, C. / Ni, C.
Funding support China, 1items
OrganizationGrant numberCountry
Not funded China
CitationJournal: To Be Published
Title: The Crystal Structure of PAK1 kinase domain from Biortus.
Authors: Wang, F. / Cheng, W. / Lv, Z. / Ju, C. / Ni, C.
History
DepositionNov 20, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 6, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine-protein kinase PAK 1


Theoretical massNumber of molelcules
Total (without water)33,3531
Polymers33,3531
Non-polymers00
Water4,918273
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.823, 103.262, 122.182
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-763-

HOH

21A-853-

HOH

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Components

#1: Protein Serine/threonine-protein kinase PAK 1


Mass: 33353.215 Da / Num. of mol.: 1 / Mutation: K299R,E503D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PAK1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13153
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 273 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.45 Å3/Da / Density % sol: 49.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M SPG pH6.0, 25% PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.1806 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1806 Å / Relative weight: 1
ReflectionResolution: 1.8→47.56 Å / Num. obs: 30827 / % possible obs: 100 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 18.3
Reflection shellResolution: 1.8→1.84 Å / Rmerge(I) obs: 0.77 / Num. unique obs: 1779

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→46.36 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.904 / SU ML: 0.088 / Cross valid method: FREE R-VALUE / ESU R: 0.114 / ESU R Free: 0.117
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2161 1533 4.978 %
Rwork0.1684 29262 -
all0.171 --
obs-30795 99.958 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 33.321 Å2
Baniso -1Baniso -2Baniso -3
1-3.023 Å20 Å2-0 Å2
2---1.358 Å20 Å2
3----1.665 Å2
Refinement stepCycle: LAST / Resolution: 1.8→46.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2298 0 0 273 2571
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0122343
X-RAY DIFFRACTIONr_bond_other_d0.0020.0162211
X-RAY DIFFRACTIONr_angle_refined_deg1.4581.6443173
X-RAY DIFFRACTIONr_angle_other_deg0.4961.5575177
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.485294
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.583512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.6610440
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.53410102
X-RAY DIFFRACTIONr_chiral_restr0.0750.2366
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022607
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02409
X-RAY DIFFRACTIONr_nbd_refined0.2210.2462
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1880.22101
X-RAY DIFFRACTIONr_nbtor_refined0.1720.21174
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.21247
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1980.2189
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1630.212
X-RAY DIFFRACTIONr_nbd_other0.2070.244
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2420.222
X-RAY DIFFRACTIONr_mcbond_it3.173.4261170
X-RAY DIFFRACTIONr_mcbond_other3.1663.4271170
X-RAY DIFFRACTIONr_mcangle_it4.2925.1161460
X-RAY DIFFRACTIONr_mcangle_other4.2915.1191461
X-RAY DIFFRACTIONr_scbond_it4.1623.971173
X-RAY DIFFRACTIONr_scbond_other4.1593.9681172
X-RAY DIFFRACTIONr_scangle_it6.3895.741711
X-RAY DIFFRACTIONr_scangle_other6.3885.7431712
X-RAY DIFFRACTIONr_lrange_it8.08949.2912714
X-RAY DIFFRACTIONr_lrange_other7.97642.7372633
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.8-1.8470.3181010.26421400.26622410.9210.9381000.234
1.847-1.8970.2331030.23220700.23221740.9610.95599.9540.2
1.897-1.9520.2651090.2220330.22221440.9540.96299.90670.188
1.952-2.0120.2481130.219470.20320600.9510.9711000.17
2.012-2.0780.2271010.18819320.1920340.9610.97599.95080.162
2.078-2.1510.227870.17718360.1819240.9690.97999.9480.155
2.151-2.2320.2770.16618060.16718840.9670.98299.94690.146
2.232-2.3230.219920.16217190.16518110.9720.9841000.142
2.323-2.4260.188880.15816350.15917230.9780.9841000.14
2.426-2.5440.209910.15515850.15816760.9710.9861000.138
2.544-2.6810.222700.15815050.16115750.9720.9851000.145
2.681-2.8430.228840.17714420.1815260.9660.9791000.168
2.843-3.0380.206860.16813440.17114300.970.9821000.162
3.038-3.2810.255650.17512450.17913110.9580.9899.92370.173
3.281-3.5920.235650.17411740.17712390.9650.9821000.179
3.592-4.0130.2720.15610410.15911130.9770.9861000.167
4.013-4.6280.175420.1329540.1349960.9830.9891000.149
4.628-5.6540.157390.1548090.1548480.9870.9861000.173
5.654-7.9370.323290.1816540.1866830.9580.9811000.206
7.937-46.360.173190.1583910.1594130.9760.9899.27360.192

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