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- PDB-3dbq: Crystal structure of TTK kinase domain -

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Basic information

Entry
Database: PDB / ID: 3dbq
TitleCrystal structure of TTK kinase domain
ComponentsDual specificity protein kinase TTK
KeywordsTRANSFERASE / Mps1 structure / Kinase activation / Phosphorylation / ATP-binding / Kinase / Nucleotide-binding / Phosphoprotein / Polymorphism / Serine/threonine-protein kinase / Tyrosine-protein kinase
Function / homology
Function and homology information


protein localization to meiotic spindle midzone / meiotic spindle assembly checkpoint signaling / kinetochore binding / female meiosis chromosome segregation / protein localization to kinetochore / dual-specificity kinase / spindle organization / mitotic spindle assembly checkpoint signaling / protein serine/threonine/tyrosine kinase activity / mitotic spindle organization ...protein localization to meiotic spindle midzone / meiotic spindle assembly checkpoint signaling / kinetochore binding / female meiosis chromosome segregation / protein localization to kinetochore / dual-specificity kinase / spindle organization / mitotic spindle assembly checkpoint signaling / protein serine/threonine/tyrosine kinase activity / mitotic spindle organization / chromosome segregation / kinetochore / spindle / protein tyrosine kinase activity / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of cell population proliferation / ATP binding / identical protein binding / membrane / nucleus / cytoplasm
Similarity search - Function
Protein kinase Mps1 family / Tetratricopeptide-like helical domain superfamily / 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 Mps1 family / Tetratricopeptide-like helical domain superfamily / 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
Dual specificity protein kinase TTK
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsWang, W. / Yang, Y.T. / Gao, Y.F. / Zhu, S.C. / Wang, F. / Old, W. / Xu, Q.B. / Resing, K. / Ahn, N. / Lei, M. / Liu, X.D.
CitationJournal: J.CELL.MOL.MED. / Year: 2008
Title: Structural and Mechanistic Insights into Mps1 Kinase Activation
Authors: Wang, W. / Yang, Y.T. / Gao, Y.F. / Xu, Q.B. / Wang, F. / Zhu, S.C. / Old, W. / Resing, K. / Ahn, N. / Lei, M. / Liu, X.D.
History
DepositionJun 2, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dual specificity protein kinase TTK


Theoretical massNumber of molelcules
Total (without water)39,2781
Polymers39,2781
Non-polymers00
Water34219
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Dual specificity protein kinase TTK

A: Dual specificity protein kinase TTK


Theoretical massNumber of molelcules
Total (without water)78,5562
Polymers78,5562
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area2180 Å2
ΔGint-18 kcal/mol
Surface area24800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.847, 106.427, 70.682
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Dual specificity protein kinase TTK / Phosphotyrosine picked threonine-protein kinase / PYT


Mass: 39278.004 Da / Num. of mol.: 1 / Fragment: TTK protein kinase, residues 515-857
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTK, MPS1L1
Plasmid details: SF9 cells were transfected with Bacmid DNA using Cellfectin reagent
Plasmid: pFAST-BAC-GST / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: P33981, dual-specificity kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.33
Details: 11% PEG 5000 MME, 100mM NaCl, 0.05M Na2HPO4/KH2PO4, pH 6.33, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 23-ID-B11
SYNCHROTRONAPS 23-ID-B21.00695, 1.00914
Detector
TypeIDDetectorDate
MARMOSAIC 300 mm CCD1CCDJul 25, 2006
MARMOSAIC 300 mm CCD2CCDJul 25, 2006
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.006951
31.009141
ReflectionResolution: 2.5→50 Å / Num. all: 12593 / Num. obs: 11018 / % possible obs: 88.9 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.039 / Net I/σ(I): 40

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Processing

Software
NameVersionClassification
SHARPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.7→42.51 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2852 1106 -RANDOM
Rwork0.2255 ---
all-11300 --
obs-10680 94.5 %-
Displacement parametersBiso mean: 80.6551 Å2
Refinement stepCycle: LAST / Resolution: 2.7→42.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2114 0 0 19 2133
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006555
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.208
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.92276
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.79225
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it6.005
X-RAY DIFFRACTIONc_scbond_it8.996
X-RAY DIFFRACTIONc_mcangle_it8.417
X-RAY DIFFRACTIONc_scangle_it11.447

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