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- PDB-2bva: Crystal structure of the human P21-activated kinase 4 -

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Basic information

Entry
Database: PDB / ID: 2bva
TitleCrystal structure of the human P21-activated kinase 4
ComponentsP21-ACTIVATED KINASE 4
KeywordsTRANSFERASE / PROTEIN KINASE / STE20 / PAK4 / ATP-BINDING
Function / homology
Function and homology information


signal transduction => GO:0007165 / dendritic spine development / cadherin binding involved in cell-cell adhesion / Activation of RAC1 / stress-activated protein kinase signaling cascade / RHOV GTPase cycle / activation of protein kinase activity / RHOJ GTPase cycle / RHOQ GTPase cycle / regulation of MAPK cascade ...signal transduction => GO:0007165 / dendritic spine development / cadherin binding involved in cell-cell adhesion / Activation of RAC1 / stress-activated protein kinase signaling cascade / RHOV GTPase cycle / activation of protein kinase activity / RHOJ GTPase cycle / RHOQ GTPase cycle / regulation of MAPK cascade / RHOH GTPase cycle / CDC42 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 / 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 / Serine/threonine-protein kinase PAK 4
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsDebreczeni, J.E. / Bunkoczi, G. / Eswaran, J. / Filippakopoulos, P. / Das, S. / Fedorov, O. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. / von Delft, F. / Knapp, S.
CitationJournal: Structure / Year: 2007
Title: Crystal Structures of the P21-Activated Kinases Pak4, Pak5, and Pak6 Reveal Catalytic Domain Plasticity of Active Group II Paks.
Authors: Eswaran, J. / Lee, W.H. / Debreczeni, J.E. / Filippakopoulos, P. / Turnbull, A. / Fedorov, O. / Deacon, S.W. / Peterson, J.R. / Knapp, S.
History
DepositionJun 23, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 14, 2005Provider: 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: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4May 8, 2019Group: Data collection / Derived calculations / Experimental preparation
Category: exptl_crystal_grow / pdbx_seq_map_depositor_info / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_seq_map_depositor_info.one_letter_code_mod / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5May 22, 2019Group: Data collection / Refinement description / Category: pdbx_seq_map_depositor_info / refine
Item: _pdbx_seq_map_depositor_info.one_letter_code_mod / _refine.pdbx_ls_cross_valid_method
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: P21-ACTIVATED KINASE 4
B: P21-ACTIVATED KINASE 4


Theoretical massNumber of molelcules
Total (without water)66,0232
Polymers66,0232
Non-polymers00
Water64936
1
A: P21-ACTIVATED KINASE 4


Theoretical massNumber of molelcules
Total (without water)33,0111
Polymers33,0111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: P21-ACTIVATED KINASE 4


Theoretical massNumber of molelcules
Total (without water)33,0111
Polymers33,0111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)118.110, 118.110, 55.530
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.49972, -0.86616, -0.00676), (-0.86608, 0.49977, -0.01146), (0.0133, 0.00013, -0.99991)
Vector: -0.37658, -0.01682, -18.42605)

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Components

#1: Protein P21-ACTIVATED KINASE 4


Mass: 33011.371 Da / Num. of mol.: 2 / Fragment: KINASE DOMAIN, RESIDUES 300-591
Source method: isolated from a genetically manipulated source
Details: PHOSPHORYLATION ON SER 474 A AND SER 474 B / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX6B-C001 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R (PHAGE RESISTANT)
References: UniProt: Q8NCH5, UniProt: O96013*PLUS, EC: 2.7.1.37
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 3 Å3/Da / Density % sol: 59 %
Crystal growMethod: vapor diffusion, sitting drop / Details: SITTING DROPS, 1.5 M NACL, 10% ETHANOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.968
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 23, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968 Å / Relative weight: 1
ReflectionResolution: 2.3→40.4 Å / Num. obs: 38417 / % possible obs: 99.8 % / Observed criterion σ(I): 3.5 / Redundancy: 2.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.86
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 3.55 / % possible all: 100

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Processing

Software
NameClassification
SHELXL-97refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1U5R

1u5r


Resolution: 2.3→20 Å / Num. parameters: 17176 / Num. restraintsaints: 22479 / Cross valid method: FREE R-VALUE / σ(F): 0
Stereochemistry target values: ENGH AND HUBER BASED ON HIC-UP ENTRY
Details: 1. HYDROGENS WERE ADDED ON RIDING POSITIONS 2. TWIN REFINEMENT: PERFECT MEROHEDRAL TWIN, APPARENT SPACEGROUP P3221, REAL SPACEGROUP P32, TWIN LAW: 010 100 00-1, BASF: 0.5006 3. NCS RESTRAINTS WERE USED
RfactorNum. reflection% reflectionSelection details
Rfree0.2686 1721 4.5 %THIN SHELLS
all0.1917 38368 --
obs0.1878 -99.8 %-
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 13065 / Occupancy sum non hydrogen: 12879
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4251 0 0 36 4287
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_angle_d0.023
X-RAY DIFFRACTIONs_similar_dist0.078
X-RAY DIFFRACTIONs_from_restr_planes0.397
X-RAY DIFFRACTIONs_zero_chiral_vol0.036
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.049
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.044
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps

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