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- PDB-1zmw: Catalytic and ubiqutin-associated domains of MARK2/PAR-1: T208A/S... -

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Basic information

Entry
Database: PDB / ID: 1zmw
TitleCatalytic and ubiqutin-associated domains of MARK2/PAR-1: T208A/S212A inactive double mutant
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 / establishment of cell polarity / regulation of axonogenesis / tau-protein kinase activity ...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 / establishment of cell polarity / regulation of axonogenesis / tau-protein kinase activity / axon development / regulation of cytoskeleton organization / lateral plasma membrane / regulation of microtubule cytoskeleton organization / molecular function activator activity / actin filament / neuron migration / tau protein binding / Wnt signaling pathway / positive regulation of neuron projection development / microtubule cytoskeleton organization / 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 / glutamatergic synapse / lipid binding / dendrite / 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 / MOLECULAR REPLACEMENT / Resolution: 2.802 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
DepositionMay 11, 2005Deposition 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 / Category: database_2 / diffrn_source / 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_ref_seq_dif.details
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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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)75,2032
Polymers75,2032
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint-13 kcal/mol
Surface area29380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.302, 119.302, 105.694
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Cell settinghexagonal
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B

NCS domain segments:

Component-ID: 1 / Refine code: 3

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11TYRTYRTYRTYRAA53 - 13116 - 94
21TYRTYRTYRTYRBB53 - 13116 - 94
12GLYGLYGLUGLUAA135 - 30998 - 272
22GLYGLYGLUGLUBB135 - 30998 - 272
13TYRTYRTYRTYRAA323 - 363286 - 326
23TYRTYRGLYGLYBB323 - 362286 - 325

NCS ensembles :
ID
1
2
3

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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 / serine/threonine-protein kinase MARK2 / ELKL Motif Kinase / EMK1


Mass: 37601.406 Da / Num. of mol.: 2 / Fragment: CATALYTIC AND UBIQUITIN-ASSOCIATED DOMAINS / 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): BL21AI / References: UniProt: O08679, EC: 2.7.1.37

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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: 2.9 Å3/Da / Density % sol: 57.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 3350, Ammonium Sulphate, 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: 0.8043 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 21, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8043 Å / Relative weight: 1
ReflectionResolution: 2.802→73.88 Å / Num. all: 21073 / Num. obs: 21073 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.102 / Net I/σ(I): 17.1
Reflection shellResolution: 2.802→2.85 Å / Mean I/σ(I) obs: 2.78 / % possible all: 100

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.2refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Y8G

1y8g


Resolution: 2.802→73.88 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.886 / SU B: 13.791 / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.93 / ESU R Free: 0.37 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26243 1092 5.2 %RANDOM
Rwork0.20321 ---
all0.20619 21073 --
obs0.20619 21073 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.89 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20.13 Å20 Å2
2--0.25 Å20 Å2
3----0.38 Å2
Refinement stepCycle: LAST / Resolution: 2.802→73.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4885 0 0 0 4885
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0224982
X-RAY DIFFRACTIONr_angle_refined_deg1.931.9826710
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6695600
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.55723.85226
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.8515949
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2631534
X-RAY DIFFRACTIONr_chiral_restr0.1210.2742
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023676
X-RAY DIFFRACTIONr_nbd_refined0.2450.22252
X-RAY DIFFRACTIONr_nbtor_refined0.330.23396
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2155
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.160.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1360.25
X-RAY DIFFRACTIONr_mcbond_it0.9491.53081
X-RAY DIFFRACTIONr_mcangle_it1.53224847
X-RAY DIFFRACTIONr_scbond_it2.47432154
X-RAY DIFFRACTIONr_scangle_it3.8564.51863
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
1316tight positional0.070.05
2636tight positional0.060.05
3160tight positional0.080.05
1331loose positional0.625
2646loose positional0.365
3169loose positional0.525
1316tight thermal0.670.5
2636tight thermal0.470.5
3160tight thermal1.10.5
1331loose thermal2.110
2646loose thermal1.910
3169loose thermal2.5210
LS refinement shellResolution: 2.802→2.875 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 86 -
Rwork0.313 1461 -
obs--99.68 %

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