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- PDB-4xbu: In vitro Crystal Structure of PAK4 in complex with Inka peptide -

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Basic information

Entry
Database: PDB / ID: 4xbu
TitleIn vitro Crystal Structure of PAK4 in complex with Inka peptide
Components
  • Protein FAM212A
  • Serine/threonine-protein kinase PAK 4
KeywordsTransferase/Peptide / PAK4 / Inka / Transferase-Peptide complex
Function / homology
Function and homology information


dendritic spine development / cadherin binding involved in cell-cell adhesion / protein serine/threonine kinase inhibitor activity / Activation of RAC1 / RHOV GTPase cycle / RHOJ GTPase cycle / RHOQ GTPase cycle / regulation of MAPK cascade / CDC42 GTPase cycle / RHOH GTPase cycle ...dendritic spine development / cadherin binding involved in cell-cell adhesion / protein serine/threonine kinase inhibitor activity / Activation of RAC1 / RHOV GTPase cycle / RHOJ GTPase cycle / RHOQ GTPase cycle / regulation of MAPK cascade / CDC42 GTPase cycle / RHOH GTPase cycle / RHOU 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 / cell cycle / phosphorylation / protein serine kinase activity / focal adhesion / protein serine/threonine kinase activity / apoptotic process / protein kinase binding / Golgi apparatus / signal transduction / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
FAM212 domain / PAK4-inhibitor inka / FAM212 family / p21 activated kinase binding domain / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. / P21-Rho-binding domain / CRIB domain / Transferase(Phosphotransferase) domain 1 ...FAM212 domain / PAK4-inhibitor inka / FAM212 family / p21 activated kinase binding domain / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. / P21-Rho-binding domain / CRIB domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Serine/threonine-protein kinase PAK 4 / PAK4-inhibitor INKA1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsBaskaran, Y. / Ang, K.C. / Anekal, P.V. / Chan, W.L. / Grimes, J.M. / Manser, E. / Robinson, R.C.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Agency for Science, Technology and Research Singapore
CitationJournal: Nat Commun / Year: 2015
Title: An in cellulo-derived structure of PAK4 in complex with its inhibitor Inka1
Authors: Baskaran, Y. / Ang, K.C. / Anekal, P.V. / Chan, W.L. / Grimes, J.M. / Manser, E. / Robinson, R.C.
History
DepositionDec 17, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 2, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2015Group: Database references
Revision 1.2Oct 4, 2017Group: Data collection / Derived calculations
Category: diffrn_detector / diffrn_source / pdbx_struct_oper_list
Item: _diffrn_detector.detector / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase PAK 4
B: Protein FAM212A


Theoretical massNumber of molelcules
Total (without water)39,7062
Polymers39,7062
Non-polymers00
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint-5 kcal/mol
Surface area14130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.620, 65.620, 184.150
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 37046.844 Da / Num. of mol.: 1 / Fragment: UNP residues 286-591
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PAK4, KIAA1142 / Plasmid: pSY5 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star (DE3) pLysS
References: UniProt: O96013, non-specific serine/threonine protein kinase
#2: Protein/peptide Protein FAM212A


Mass: 2658.968 Da / Num. of mol.: 1 / Fragment: UNP residues 167-190 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q96EL1
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.77 % / Description: Bipyramidal
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: Tris-HCl, PEG 8000

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 31, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.06→32.81 Å / Num. obs: 25890 / % possible obs: 100 % / Redundancy: 12.8 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 21.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
xia20.3.6.0data reduction
xia20.3.6.0data scaling
xia20.3.6.0data processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FIE

4fie


Resolution: 2.06→32.81 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.935 / SU B: 4.589 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.177 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24343 1262 4.9 %RANDOM
Rwork0.19856 ---
obs0.20081 24538 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.805 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å2-0 Å20 Å2
2---0.06 Å20 Å2
3---0.12 Å2
Refinement stepCycle: LAST / Resolution: 2.06→32.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2419 0 0 150 2569
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192467
X-RAY DIFFRACTIONr_bond_other_d0.0010.022456
X-RAY DIFFRACTIONr_angle_refined_deg2.0351.9853340
X-RAY DIFFRACTIONr_angle_other_deg0.97135644
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4215304
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.89923.241108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.615445
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3011523
X-RAY DIFFRACTIONr_chiral_restr0.1320.2377
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212738
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02545
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.693.7491222
X-RAY DIFFRACTIONr_mcbond_other3.6743.7481221
X-RAY DIFFRACTIONr_mcangle_it4.8325.5981524
X-RAY DIFFRACTIONr_mcangle_other4.835.61525
X-RAY DIFFRACTIONr_scbond_it4.534.2351245
X-RAY DIFFRACTIONr_scbond_other4.5284.2351245
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.5126.161817
X-RAY DIFFRACTIONr_long_range_B_refined8.12630.7352915
X-RAY DIFFRACTIONr_long_range_B_other8.09130.4712857
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.06→2.113 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 90 -
Rwork0.242 1789 -
obs--99.89 %

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