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- PDB-4ixp: Crystal structure of Maternal Embryonic Leucine Zipper Kinase (MELK) -

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Basic information

Entry
Database: PDB / ID: 4ixp
TitleCrystal structure of Maternal Embryonic Leucine Zipper Kinase (MELK)
ComponentsMaternal embryonic leucine zipper kinaseMELK
KeywordsTRANSFERASE / protein kinase / regulated by phosphorylation
Function / homology
Function and homology information


neural precursor cell proliferation / intrinsic apoptotic signaling pathway in response to oxidative stress / hemopoiesis / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / G2/M transition of mitotic cell cycle / cell cortex / cell population proliferation / protein autophosphorylation / non-specific serine/threonine protein kinase ...neural precursor cell proliferation / intrinsic apoptotic signaling pathway in response to oxidative stress / hemopoiesis / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / G2/M transition of mitotic cell cycle / cell cortex / cell population proliferation / protein autophosphorylation / non-specific serine/threonine protein kinase / intracellular signal transduction / positive regulation of apoptotic process / protein serine kinase activity / protein serine/threonine kinase activity / lipid binding / apoptotic process / calcium ion binding / ATP binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
Maternal embryonic leucine zipper kinase, catalytic domain / : / Maternal embryonic leucine zipper kinase, UBA domain / Kinase associated domain 1 (KA1) / Kinase associated domain 1 / Kinase associated domain 1 (KA1) profile. / KA1 domain/Ssp2, C-terminal / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site ...Maternal embryonic leucine zipper kinase, catalytic domain / : / Maternal embryonic leucine zipper kinase, UBA domain / Kinase associated domain 1 (KA1) / Kinase associated domain 1 / Kinase associated domain 1 (KA1) profile. / KA1 domain/Ssp2, C-terminal / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Maternal embryonic leucine zipper kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.749 Å
AuthorsCao, L.S. / Wang, J. / Wang, Z.X. / Wu, J.W.
CitationJournal: Plos One / Year: 2013
Title: Structural basis for the regulation of maternal embryonic leucine zipper kinase.
Authors: Cao, L.S. / Wang, J. / Chen, Y. / Deng, H. / Wang, Z.X. / Wu, J.W.
History
DepositionJan 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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

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Assembly

Deposited unit
A: Maternal embryonic leucine zipper kinase


Theoretical massNumber of molelcules
Total (without water)40,4241
Polymers40,4241
Non-polymers00
Water70339
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Maternal embryonic leucine zipper kinase

A: Maternal embryonic leucine zipper kinase


Theoretical massNumber of molelcules
Total (without water)80,8482
Polymers80,8482
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565-x,-y+1,z1
Buried area1680 Å2
ΔGint-12 kcal/mol
Surface area30430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.449, 135.449, 153.652
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein Maternal embryonic leucine zipper kinase / MELK / hMELK / Protein kinase Eg3 / pEg3 kinase / Protein kinase PK38 / hPK38 / Tyrosine-protein kinase MELK


Mass: 40423.844 Da / Num. of mol.: 1 / Fragment: N-terminal / Mutation: K40R, D150A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MELK, KIAA0175 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q14680, non-specific serine/threonine protein kinase, non-specific protein-tyrosine kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 5.03 Å3/Da / Density % sol: 75.56 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Sodium Cacodylate, 0.7M Sodium Acetate, 2% PEG 400, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 26, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.749→50 Å / Num. all: 22247 / Num. obs: 22247 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7 % / Biso Wilson estimate: 60.54 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 30
Reflection shellResolution: 2.749→2.8 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.473 / Mean I/σ(I) obs: 4.6 / Num. unique all: 1076 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FE3

3fe3


Resolution: 2.749→34.847 Å / SU ML: 0.42 / σ(F): 1.34 / Phase error: 25.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2323 1134 5.11 %RANDOM
Rwork0.2019 ---
all0.2019 22206 --
obs0.2035 22206 99.87 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.65 Å2 / ksol: 0.343 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.9904 Å2-0 Å20 Å2
2--7.9904 Å2-0 Å2
3----15.9808 Å2
Refinement stepCycle: LAST / Resolution: 2.749→34.847 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2719 0 0 39 2758
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082785
X-RAY DIFFRACTIONf_angle_d1.113763
X-RAY DIFFRACTIONf_dihedral_angle_d15.8431046
X-RAY DIFFRACTIONf_chiral_restr0.072414
X-RAY DIFFRACTIONf_plane_restr0.006473
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7494-2.87450.38731330.30972569X-RAY DIFFRACTION100
2.8745-3.02590.35611490.2682564X-RAY DIFFRACTION100
3.0259-3.21540.29281540.25972576X-RAY DIFFRACTION100
3.2154-3.46340.30731360.23062604X-RAY DIFFRACTION100
3.4634-3.81160.23231380.21522609X-RAY DIFFRACTION100
3.8116-4.36220.20221380.16472642X-RAY DIFFRACTION100
4.3622-5.49250.19341540.16892663X-RAY DIFFRACTION100
5.4925-34.84990.18851320.1892845X-RAY DIFFRACTION100

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