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- PDB-3ose: Structure of the Kinase Associated Domain 1 (KA1) from MARK1 kinase -

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Basic information

Entry
Database: PDB / ID: 3ose
TitleStructure of the Kinase Associated Domain 1 (KA1) from MARK1 kinase
ComponentsSerine/threonine-protein kinase MARK1
KeywordsLIPID BINDING PROTEIN / Kinase Associated-1(KA1) Domain / TRANSFERASE / MEMBRANE ASSOCIATION / KINASE
Function / homology
Function and homology information


establishment of mitochondrion localization / regulation of dendrite development / phosphatidic acid binding / tau-protein kinase / negative regulation of epithelial to mesenchymal transition / regulation of neuron projection development / tau-protein kinase activity / phosphatidylserine binding / cytoskeleton organization / phosphatidylinositol-4,5-bisphosphate binding ...establishment of mitochondrion localization / regulation of dendrite development / phosphatidic acid binding / tau-protein kinase / negative regulation of epithelial to mesenchymal transition / regulation of neuron projection development / tau-protein kinase activity / phosphatidylserine binding / cytoskeleton organization / phosphatidylinositol-4,5-bisphosphate binding / neuron migration / tau protein binding / Wnt signaling pathway / microtubule cytoskeleton organization / microtubule cytoskeleton / peptidyl-serine phosphorylation / cytoskeleton / non-specific serine/threonine protein kinase / intracellular signal transduction / protein phosphorylation / negative regulation of gene expression / protein serine kinase activity / protein serine/threonine kinase activity / dendrite / positive regulation of gene expression / magnesium ion binding / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
: / Kinase associated domain 1, KA1 / Kinase associated domain 1 (KA1) / Kinase associated domain 1 / Kinase associated domain 1 (KA1) profile. / KA1 domain/Ssp2, C-terminal / UBA/TS-N domain / TATA-Binding Protein / Ubiquitin associated domain / Ubiquitin-associated domain ...: / Kinase associated domain 1, KA1 / Kinase associated domain 1 (KA1) / Kinase associated domain 1 / Kinase associated domain 1 (KA1) profile. / KA1 domain/Ssp2, C-terminal / UBA/TS-N domain / TATA-Binding Protein / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / 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 / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Serine/threonine-protein kinase MARK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsMoravcevic, K. / Lemmon, M.A.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2010
Title: Kinase Associated-1 Domains Drive MARK/PAR1 Kinases to Membrane Targets by Binding Acidic Phospholipids.
Authors: Moravcevic, K. / Mendrola, J.M. / Schmitz, K.R. / Wang, Y.H. / Slochower, D. / Janmey, P.A. / Lemmon, M.A.
History
DepositionSep 8, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine-protein kinase MARK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3734
Polymers14,1961
Non-polymers1773
Water1,69394
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Serine/threonine-protein kinase MARK1
hetero molecules

A: Serine/threonine-protein kinase MARK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7478
Polymers28,3932
Non-polymers3546
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area2760 Å2
ΔGint-61 kcal/mol
Surface area10570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.843, 69.843, 54.446
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Serine/threonine-protein kinase MARK1 / MAP/microtubule affinity-regulating kinase 1


Mass: 14196.317 Da / Num. of mol.: 1
Fragment: Kinase Associated-1 (KA1) Domain, residues 683-795
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MARK1, KIAA1477, MARK / Production host: Escherichia coli (E. coli)
References: UniProt: Q9P0L2, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.7 Å3/Da / Density % sol: 54.45 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1 M Na acetate, pH 4.6, 0.04 M CaCl2, and 15-25% (w/v) PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97951 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 16, 2008
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. all: 18863 / Num. obs: 18599 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 7.2 % / Rsym value: 0.068
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 29.8 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→40 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.949 / Cross valid method: THROUGHOUT / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19452 876 5.1 %RANDOM
Rwork0.1749 ---
all0.1759 16337 --
obs0.1759 16298 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.915 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.01 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.7→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms805 0 9 94 908
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.022763
X-RAY DIFFRACTIONr_angle_refined_deg1.2381.9651010
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.614585
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.82224.28635
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.0615144
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.608156
X-RAY DIFFRACTIONr_chiral_restr0.0850.2110
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021658
X-RAY DIFFRACTIONr_mcbond_it0.6881.5470
X-RAY DIFFRACTIONr_mcangle_it1.3942742
X-RAY DIFFRACTIONr_scbond_it2.4343293
X-RAY DIFFRACTIONr_scangle_it4.0864.5268
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.228 61 -
Rwork0.206 1178 -
obs--99.92 %

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