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- PDB-2j0i: CRYSTAL STRUCTURE OF THE HUMAN P21-ACTIVATED KINASE 4 -

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Basic information

Entry
Database: PDB / ID: 2j0i
TitleCRYSTAL STRUCTURE OF THE HUMAN P21-ACTIVATED KINASE 4
ComponentsSERINE/THREONINE-PROTEIN KINASE PAK 4
KeywordsTRANSFERASE / PROTEIN KINASE / PHOSPHORYLATION / NUCLEOTIDE-BINDING / PAK4 / STE20 / KINASE / ATP-BINDING / ALTERNATIVE SPLICING / SERINE/THREONINE-PROTEIN KINASE
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 / regulation of MAPK cascade / RHOH GTPase cycle / CDC42 GTPase cycle / RHOU GTPase cycle ...dendritic spine development / cadherin binding involved in cell-cell adhesion / Activation of RAC1 / RHOV GTPase cycle / RHOJ GTPase cycle / RHOQ GTPase cycle / regulation of MAPK cascade / RHOH GTPase cycle / CDC42 GTPase cycle / RHOU GTPase cycle / RHOG GTPase cycle / cellular response to organic cyclic compound / 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 / focal adhesion / protein serine kinase activity / 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 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 ...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
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsDebreczeni, J.E. / Eswaran, J. / Ugochukwu, E. / Papagrigoriou, E. / Turnbull, A. / von Delft, F. / Arrowsmith, C. / Weigelt, J. / Edwards, A. / Sundstrom, M. / Knapp, S.
CitationJournal: To be Published
Title: Crystal Structure of the Human P21-Activated Kinase 4
Authors: Debreczeni, J.E. / Eswaran, J. / Ugochukwu, E. / Papagrigoriou, E. / Turnbull, A. / von Delft, F. / Arrowsmith, C. / Weigelt, J. / Edwards, A. / Sundstrom, M. / Knapp, S.
History
DepositionAug 3, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 17, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.4Jan 31, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.5May 8, 2019Group: Data collection / Derived calculations / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / struct_conn
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _struct_conn.pdbx_leaving_atom_flag
Revision 1.6Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SERINE/THREONINE-PROTEIN KINASE PAK 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4845
Polymers34,2361
Non-polymers2484
Water3,693205
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)63.514, 63.514, 178.478
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 / HUMAN P21-ACTIVATED KINASE 4 / PAK-4 / P21-ACTIVATED KINASE 4


Mass: 34235.691 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, RESIDUES 291-591
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria)
References: UniProt: O96013, EC: 2.7.1.37, non-specific serine/threonine protein kinase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 2.67 Å3/Da / Density % sol: 53.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 150 UL SITTING DROPS, 4DEG, 0.2M K3(CIT), 0.1M BIS-TRIS PROPANE PH 6.5, 20% PEG3350, 10% ETHYLENE GLYCOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.976
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 16, 2006 / Details: MIRRORS
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.6→43.55 Å / Num. obs: 49277 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 7.33 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 13.34
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.62 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CDZ

2cdz


Resolution: 1.6→43.56 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.2 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.215 2460 5 %RANDOM
Rwork0.172 ---
obs0.174 46301 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.95 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å20 Å2
2--0.28 Å20 Å2
3----0.55 Å2
Refinement stepCycle: LAST / Resolution: 1.6→43.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2255 0 16 205 2476
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222333
X-RAY DIFFRACTIONr_bond_other_d0.0010.021602
X-RAY DIFFRACTIONr_angle_refined_deg1.1471.9853166
X-RAY DIFFRACTIONr_angle_other_deg0.89533918
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2195295
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.8423.77698
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.33815.037404
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9971517
X-RAY DIFFRACTIONr_chiral_restr0.0690.2362
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022557
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02445
X-RAY DIFFRACTIONr_nbd_refined0.1990.2450
X-RAY DIFFRACTIONr_nbd_other0.190.21687
X-RAY DIFFRACTIONr_nbtor_refined0.1650.21156
X-RAY DIFFRACTIONr_nbtor_other0.0820.21150
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1170.2144
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0980.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2870.226
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1430.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.41651585
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.21872370
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.7959940
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.34612793
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.281 176
Rwork0.175 3201

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