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- PDB-4eku: Crystal Structure of FERM Domain of Proline-rich Tyrosine Kinase 2 -

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Basic information

Entry
Database: PDB / ID: 4eku
TitleCrystal Structure of FERM Domain of Proline-rich Tyrosine Kinase 2
ComponentsProtein-tyrosine kinase 2-beta
KeywordsTRANSFERASE / PROLINE-RICH TYROSINE KINASE 2 / FERM DOMAIN
Function / homology
Function and homology information


regulation of macrophage chemotaxis / neurotransmitter receptor regulator activity / positive regulation of B cell chemotaxis / marginal zone B cell differentiation / regulation of ubiquitin-dependent protein catabolic process / endothelin receptor signaling pathway / negative regulation of myeloid cell differentiation / negative regulation of bone mineralization / cortical cytoskeleton organization / regulation of postsynaptic density assembly ...regulation of macrophage chemotaxis / neurotransmitter receptor regulator activity / positive regulation of B cell chemotaxis / marginal zone B cell differentiation / regulation of ubiquitin-dependent protein catabolic process / endothelin receptor signaling pathway / negative regulation of myeloid cell differentiation / negative regulation of bone mineralization / cortical cytoskeleton organization / regulation of postsynaptic density assembly / activation of Janus kinase activity / chemokine-mediated signaling pathway / apical dendrite / cellular response to fluid shear stress / regulation of release of sequestered calcium ion into cytosol / signal complex assembly / positive regulation of ubiquitin-dependent protein catabolic process / calcium/calmodulin-dependent protein kinase activity / sprouting angiogenesis / Interleukin-2 signaling / Signal regulatory protein family interactions / NMDA selective glutamate receptor complex / positive regulation of cell-matrix adhesion / positive regulation of actin filament polymerization / Golgi organization / negative regulation of potassium ion transport / positive regulation of protein kinase activity / RHOU GTPase cycle / signaling receptor activator activity / peptidyl-tyrosine autophosphorylation / positive regulation of excitatory postsynaptic potential / vascular endothelial growth factor receptor signaling pathway / bone resorption / postsynaptic density, intracellular component / cellular defense response / regulation of cell adhesion / tumor necrosis factor-mediated signaling pathway / cellular response to retinoic acid / ionotropic glutamate receptor binding / positive regulation of endothelial cell migration / ionotropic glutamate receptor signaling pathway / positive regulation of synaptic transmission, glutamatergic / integrin-mediated signaling pathway / regulation of actin cytoskeleton organization / non-membrane spanning protein tyrosine kinase activity / positive regulation of JNK cascade / non-specific protein-tyrosine kinase / peptidyl-tyrosine phosphorylation / positive regulation of neuron projection development / regulation of synaptic plasticity / VEGFA-VEGFR2 Pathway / long-term synaptic potentiation / epidermal growth factor receptor signaling pathway / neuron migration / positive regulation of angiogenesis / lamellipodium / regulation of cell shape / presynapse / cell body / protein autophosphorylation / protein-containing complex assembly / growth cone / protein tyrosine kinase activity / cell cortex / adaptive immune response / negative regulation of neuron apoptotic process / cytoskeleton / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / postsynaptic density / protein phosphorylation / positive regulation of cell migration / negative regulation of cell population proliferation / focal adhesion / neuronal cell body / apoptotic process / positive regulation of cell population proliferation / dendrite / negative regulation of apoptotic process / perinuclear region of cytoplasm / glutamatergic synapse / signal transduction / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Acyl-CoA Binding Protein - #10 / Focal adhesion kinase, targeting (FAT) domain / Focal adhesion kinase, targeting (FAT) domain superfamily / Focal adhesion kinase, N-terminal / FAK1/PYK2, FERM domain C-lobe / Focal adhesion targeting region / FERM N-terminal domain / : / FAK1/PYK2, FERM domain C-lobe / Acyl-CoA Binding Protein ...Acyl-CoA Binding Protein - #10 / Focal adhesion kinase, targeting (FAT) domain / Focal adhesion kinase, targeting (FAT) domain superfamily / Focal adhesion kinase, N-terminal / FAK1/PYK2, FERM domain C-lobe / Focal adhesion targeting region / FERM N-terminal domain / : / FAK1/PYK2, FERM domain C-lobe / Acyl-CoA Binding Protein / FERM central domain / FERM/acyl-CoA-binding protein superfamily / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / FERM central domain / PH-domain like / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / PH-like domain superfamily / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Ubiquitin-like domain superfamily / Roll / Roll / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Up-down Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Protein-tyrosine kinase 2-beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å
AuthorsSavarimuthu, B. / Li, R. / Wang, Y.
CitationJournal: To be Published
Title: Crystal Structure of the Ferm Domain of Proline-rich Tyrosine Kinase 2
Authors: Savarimuthu, B. / Li, R. / Wang, Y.
History
DepositionApr 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein-tyrosine kinase 2-beta


Theoretical massNumber of molelcules
Total (without water)45,3831
Polymers45,3831
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Protein-tyrosine kinase 2-beta

A: Protein-tyrosine kinase 2-beta


Theoretical massNumber of molelcules
Total (without water)90,7662
Polymers90,7662
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-2/31
Buried area1860 Å2
ΔGint-14 kcal/mol
Surface area36670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.971, 112.971, 103.335
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Protein-tyrosine kinase 2-beta / Calcium-dependent tyrosine kinase / CADTK / Calcium-regulated non-receptor proline-rich tyrosine ...Calcium-dependent tyrosine kinase / CADTK / Calcium-regulated non-receptor proline-rich tyrosine kinase / Cell adhesion kinase beta / CAK-beta / CAKB / Focal adhesion kinase 2 / FADK 2 / Proline-rich tyrosine kinase 2 / Related adhesion focal tyrosine kinase / RAFTK


Mass: 45383.102 Da / Num. of mol.: 1 / Fragment: UNP residues 21-409
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FAK2, NM4103, PTK2B, PYK2, RAFTK / Plasmid: PET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: Q14289, non-specific protein-tyrosine kinase

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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: 4.19 Å3/Da / Density % sol: 70.67 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1 M AMMONIUM CITRATE TRIBASIC, pH 7.0, 0.1 M BIS-TRIS PROPANE pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 9, 2009 / Details: ROSENBAUM-ROCH DOUBLE XTAL
RadiationMonochromator: DOUBLE CRYSTAL (Si 111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.25→49.564 Å / Num. all: 12393 / Num. obs: 12393 / % possible obs: 99.94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 11 % / Biso Wilson estimate: 85.6 Å2 / Rmerge(I) obs: 0.113 / Rsym value: 0.113 / Net I/σ(I): 22.8
Reflection shellResolution: 3.25→3.37 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.774 / Mean I/σ(I) obs: 3 / Num. unique all: 715 / Rsym value: 0.744 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2AL6

2al6


Resolution: 3.25→49.564 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.929 / SU B: 29.6 / SU ML: 0.229 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.334 / ESU R Free: 0.341 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2121 546 4.4 %RANDOM
Rwork0.1861 ---
all0.1872 12393 --
obs0.1872 12393 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 90.463 Å2
Baniso -1Baniso -2Baniso -3
1--0.53 Å2-0.27 Å20 Å2
2---0.53 Å20 Å2
3---0.8 Å2
Refinement stepCycle: LAST / Resolution: 3.25→49.564 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2813 0 0 0 2813
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0222868
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2151.9733869
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3375347
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.5824.685143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.73315535
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.121519
X-RAY DIFFRACTIONr_chiral_restr0.1440.2423
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212167
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.9341.51735
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.80122802
X-RAY DIFFRACTIONr_scbond_it2.3331133
X-RAY DIFFRACTIONr_scangle_it4.1284.51067
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.25→3.33 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 44 -
Rwork0.28 853 -
obs--99.89 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.2763-2.5839-1.31418.47513.34293.9530.0840.33840.060.0683-0.17810.6404-0.1987-0.11830.09410.2746-0.09540.11490.5644-0.20770.200839.53613.451-26.805
23.43843.30060.25912.25232.95343.0321-0.24860.47390.00320.23080.2202-0.5851-0.20250.6490.02840.5847-0.0694-0.08350.6715-0.0380.091648.73836.221-8.962
311.7341-0.5832-0.57766.98472.1646.0799-0.1142-0.1352-0.52650.7066-0.38411.97090.5098-0.76590.49830.8562-0.220.54480.5693-0.29440.896520.82914.436-8.248
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A19 - 138
2X-RAY DIFFRACTION2A139 - 264
3X-RAY DIFFRACTION3A265 - 366

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