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- PDB-8yhk: The Crystal Structure of P21-Activated Kinases Pak4 from Biortus -

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Basic information

Entry
Database: PDB / ID: 8yhk
TitleThe Crystal Structure of P21-Activated Kinases Pak4 from Biortus
ComponentsSerine/threonine-protein kinase PAK 4
KeywordsTRANSFERASE / Kinase / Serine/threonine-protein kinase / Apoptosis / ATP-binding
Function / homology
Function and homology information


dendritic spine development / cadherin binding involved in cell-cell adhesion / Activation of RAC1 / RHOV GTPase cycle / RHOJ GTPase cycle / RHOQ GTPase cycle / RHOU GTPase cycle / regulation of MAPK cascade / CDC42 GTPase cycle / RHOH GTPase cycle ...dendritic spine development / cadherin binding involved in cell-cell adhesion / Activation of RAC1 / RHOV GTPase cycle / RHOJ GTPase cycle / RHOQ GTPase cycle / RHOU GTPase cycle / regulation of MAPK cascade / CDC42 GTPase cycle / RHOH GTPase cycle / cellular response to organic cyclic compound / RHOG GTPase cycle / RAC2 GTPase cycle / RAC3 GTPase cycle / negative regulation of endothelial cell apoptotic process / cytoskeleton organization / RAC1 GTPase cycle / regulation of cell growth / adherens junction / positive regulation of angiogenesis / cell migration / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / protein serine kinase activity / focal adhesion / protein serine/threonine kinase activity / apoptotic process / Golgi apparatus / signal transduction / ATP binding / 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 / Protein kinase domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. ...p21 activated kinase binding domain / CRIB domain superfamily / P21-Rho-binding domain / : / CRIB domain profile. / P21-Rho-binding domain / CRIB domain / Protein kinase 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
TRIETHYLENE GLYCOL / Serine/threonine-protein kinase PAK 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsWang, F. / Cheng, W. / Lv, Z. / Qi, J. / Wu, B.
Funding support China, 1items
OrganizationGrant numberCountry
Not funded China
CitationJournal: To Be Published
Title: The Crystal Structure of P21-Activated Kinases Pak4 from Biortus
Authors: Wang, F. / Cheng, W. / Lv, Z. / Qi, J. / Wu, B.
History
DepositionFeb 28, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 13, 2024Provider: 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 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1622
Polymers34,0121
Non-polymers1501
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area70 Å2
ΔGint-0 kcal/mol
Surface area14400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.274, 146.274, 43.680
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Serine/threonine-protein kinase PAK 4 / p21-activated kinase 4 / PAK-4


Mass: 34011.586 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PAK4, KIAA1142 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O96013, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 3.43 Å3/Da / Density % sol: 64.19 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.4 M Potassium sodium tartrate tetrahydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.95373 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 10, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 3.3→48.76 Å / Num. obs: 7176 / % possible obs: 95.1 % / Redundancy: 11 % / CC1/2: 0.996 / Net I/σ(I): 9.6
Reflection shellResolution: 3.3→3.56 Å / Num. unique obs: 1460 / CC1/2: 0.809

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Processing

Software
NameVersionClassification
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMAC5.8.0267refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→46.299 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.88 / SU B: 47.589 / SU ML: 0.602 / Cross valid method: FREE R-VALUE / ESU R Free: 0.64
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.3186 351 4.906 %
Rwork0.2494 6803 -
all0.253 --
obs-7154 94.455 %
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: 102.959 Å2
Baniso -1Baniso -2Baniso -3
1--8.992 Å20 Å20 Å2
2---8.992 Å2-0 Å2
3---17.983 Å2
Refinement stepCycle: LAST / Resolution: 3.3→46.299 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2328 0 10 11 2349
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0132385
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152366
X-RAY DIFFRACTIONr_angle_refined_deg1.1951.6423226
X-RAY DIFFRACTIONr_angle_other_deg0.9821.5775444
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0085293
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.31220.8125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.53615431
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8461522
X-RAY DIFFRACTIONr_chiral_restr0.0350.2302
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022641
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02531
X-RAY DIFFRACTIONr_nbd_refined0.1790.2498
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1570.22364
X-RAY DIFFRACTIONr_nbtor_refined0.1430.21131
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0680.21146
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.258
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0980.29
X-RAY DIFFRACTIONr_nbd_other0.1250.232
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0350.21
X-RAY DIFFRACTIONr_mcbond_it2.51810.7881175
X-RAY DIFFRACTIONr_mcbond_other2.51910.7871174
X-RAY DIFFRACTIONr_mcangle_it4.41316.1811467
X-RAY DIFFRACTIONr_mcangle_other4.41216.1821468
X-RAY DIFFRACTIONr_scbond_it2.24211.1631208
X-RAY DIFFRACTIONr_scbond_other2.24111.1611209
X-RAY DIFFRACTIONr_scangle_it4.04816.6281759
X-RAY DIFFRACTIONr_scangle_other4.04616.6251760
X-RAY DIFFRACTIONr_lrange_it7.523126.3482554
X-RAY DIFFRACTIONr_lrange_other7.522126.3432555
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.3860.453280.446485X-RAY DIFFRACTION93.7843
3.386-3.4790.514240.461491X-RAY DIFFRACTION99.8062
3.479-3.5790.425220.383463X-RAY DIFFRACTION94.1748
3.579-3.6890.354210.386455X-RAY DIFFRACTION94.2574
3.689-3.810.327210.354461X-RAY DIFFRACTION98.7705
3.81-3.9440.434230.305419X-RAY DIFFRACTION92.0833
3.944-4.0920.242250.282414X-RAY DIFFRACTION97.5556
4.092-4.2590.414280.236393X-RAY DIFFRACTION95.0339
4.259-4.4480.31230.21377X-RAY DIFFRACTION93.4579
4.448-4.6650.246160.214375X-RAY DIFFRACTION98.2412
4.665-4.9170.313220.207353X-RAY DIFFRACTION91.0194
4.917-5.2140.304180.232313X-RAY DIFFRACTION92.9775
5.214-5.5730.331100.25312X-RAY DIFFRACTION90.1961
5.573-6.0180.414180.235291X-RAY DIFFRACTION96.2617
6.018-6.5910.201140.182277X-RAY DIFFRACTION92.9712
6.591-7.3650.21270.138250X-RAY DIFFRACTION90.493
7.365-8.4970.15480.128231X-RAY DIFFRACTION94.8413
8.497-10.3890.1580.145195X-RAY DIFFRACTION94.8598
10.389-14.6190.207100.15151X-RAY DIFFRACTION88.4615
14.619-46.2990.6150.3497X-RAY DIFFRACTION90.2655

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