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- PDB-1y8g: Catalytic and ubiqutin-associated domains of MARK2/PAR-1: Inactiv... -

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Basic information

Entry
Database: PDB / ID: 1y8g
TitleCatalytic and ubiqutin-associated domains of MARK2/PAR-1: Inactive double mutant with selenomethionine
ComponentsMAP/Microtubule affinity-regulating kinase 2
KeywordsSIGNALING PROTEIN / TRANSFERASE / SERINE/THREONINE PROTEIN KINASE / MARK / PAR-1 / KIN1 / UBA DOMAIN
Function / homology
Function and homology information


establishment or maintenance of cell polarity regulating cell shape / microtubule bundle / basal cortex / regulation of microtubule binding / tau-protein kinase / establishment or maintenance of epithelial cell apical/basal polarity / regulation of postsynapse organization / regulation of cytoskeleton organization / regulation of axonogenesis / establishment of cell polarity ...establishment or maintenance of cell polarity regulating cell shape / microtubule bundle / basal cortex / regulation of microtubule binding / tau-protein kinase / establishment or maintenance of epithelial cell apical/basal polarity / regulation of postsynapse organization / regulation of cytoskeleton organization / regulation of axonogenesis / establishment of cell polarity / tau-protein kinase activity / axon development / lateral plasma membrane / regulation of microtubule cytoskeleton organization / molecular function activator activity / actin filament / neuron migration / tau protein binding / microtubule cytoskeleton organization / Wnt signaling pathway / positive regulation of neuron projection development / postsynapse / peptidyl-serine phosphorylation / protein autophosphorylation / non-specific serine/threonine protein kinase / intracellular signal transduction / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / dendrite / lipid binding / glutamatergic synapse / magnesium ion binding / ATP binding / membrane / nucleus / plasma membrane / cytoplasm
Similarity search - Function
: / Kinase associated domain 1 (KA1) / Kinase associated domain 1 / Kinase associated domain 1 (KA1) profile. / KA1 domain/Ssp2, C-terminal / Ubiquitin-associated (UBA) domain / UBA/TS-N domain / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. ...: / Kinase associated domain 1 (KA1) / Kinase associated domain 1 / Kinase associated domain 1 (KA1) profile. / KA1 domain/Ssp2, C-terminal / Ubiquitin-associated (UBA) domain / UBA/TS-N domain / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / Helicase, Ruva Protein; domain 3 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic 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 MARK2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / other / Resolution: 2.501 Å
AuthorsPanneerselvam, S. / Marx, A. / Mandelkow, E.-M. / Mandelkow, E.
CitationJournal: Structure / Year: 2006
Title: Structure of the catalytic and ubiquitin-associated domains of the protein kinase MARK/Par-1.
Authors: Panneerselvam, S. / Marx, A. / Mandelkow, E.M. / Mandelkow, E.
History
DepositionDec 12, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MAP/Microtubule affinity-regulating kinase 2
B: MAP/Microtubule affinity-regulating kinase 2


Theoretical massNumber of molelcules
Total (without water)76,1412
Polymers76,1412
Non-polymers00
Water2,846158
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-15 kcal/mol
Surface area29240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.822, 118.822, 105.380
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Cell settinghexagonal
Space group name H-MP61

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Components

#1: Protein MAP/Microtubule affinity-regulating kinase 2 / E.C.2.7.1.37 / PAR-1 / Kin1 / serine/threonine kinase Emk


Mass: 38070.352 Da / Num. of mol.: 2
Fragment: catalytic and ubiquitin-associated domains, residues 39-364
Mutation: T208A, S212A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: MARK2 / Plasmid: pDEST17 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) pLysS
References: EMBL: 2052191, UniProt: O08679*PLUS, EC: 2.7.1.37
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2.86 Å3/Da / Density % sol: 56.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 5000 MME, TACSIMATE, BIS-TRIS, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8031 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 14, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8031 Å / Relative weight: 1
ReflectionResolution: 2.501→46.3 Å / Num. all: 29259 / Num. obs: 29259 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.26 % / Biso Wilson estimate: 58.7 Å2 / Rsym value: 0.099 / Net I/σ(I): 17.9
Reflection shellResolution: 2.501→2.54 Å / % possible all: 100

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
MLPHAREphasing
REFMAC5.2refinement
RefinementMethod to determine structure: other
Starting model: partially refined model of a similar construct obtained by combination of MR and MIR

Resolution: 2.501→46.3 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.9 / SU B: 9.664 / SU ML: 0.212 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.415 / ESU R Free: 0.292 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26834 1514 5.2 %RANDOM
Rwork0.19776 ---
all0.20136 29259 --
obs0.20136 29259 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.887 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å20.18 Å20 Å2
2--0.35 Å20 Å2
3----0.53 Å2
Refinement stepCycle: LAST / Resolution: 2.501→46.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4913 0 0 158 5071
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0225010
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5271.9826742
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2495600
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.03523.957230
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.69615969
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.371534
X-RAY DIFFRACTIONr_chiral_restr0.1030.2742
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023692
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2320.22383
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3180.23414
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2263
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.170.276
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1870.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.9361.53089
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.46824855
X-RAY DIFFRACTIONr_scbond_it2.24932185
X-RAY DIFFRACTIONr_scangle_it3.3684.51887
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.501→2.566 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 112 -
Rwork0.295 2057 -
obs--99.86 %

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