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- PDB-2zmd: Crystal structure of human Mps1 catalytic domain T686A mutant in ... -

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Basic information

Entry
Database: PDB / ID: 2zmd
TitleCrystal structure of human Mps1 catalytic domain T686A mutant in complex with SP600125 inhibitor
ComponentsDual specificity protein kinase TTK
KeywordsTRANSFERASE / kinase / Mps1 / SP600125 / T686A / ATP-binding / Nucleotide-binding / Phosphoprotein / 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 / spindle / kinetochore / protein tyrosine kinase activity / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of cell population proliferation / ATP binding / membrane / identical protein binding / 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
2,6-DIHYDROANTHRA/1,9-CD/PYRAZOL-6-ONE / Chem-7PE / Dual specificity protein kinase TTK
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.88 Å
AuthorsChu, M.L.H. / Chavas, L.M.G. / Douglas, K.T. / Eyers, P.A. / Tabernero, L.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Crystal structure of the catalytic domain of the mitotic checkpoint kinase Mps1 in complex with SP600125.
Authors: Chu, M.L. / Chavas, L.M. / Douglas, K.T. / Eyers, P.A. / Tabernero, L.
History
DepositionApr 16, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 13, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 2023Group: 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: Dual specificity protein kinase TTK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8493
Polymers44,3181
Non-polymers5312
Water46826
1


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

A: Dual specificity protein kinase TTK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,6986
Polymers88,6372
Non-polymers1,0614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area6060 Å2
ΔGint-22.7 kcal/mol
Surface area24360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.600, 105.170, 111.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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


Mass: 44318.363 Da / Num. of mol.: 1 / Fragment: UNP residues 510-857, Catalytic domain / Mutation: T686A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTK, MPS1L1 / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P33981, dual-specificity kinase
#2: Chemical ChemComp-537 / 2,6-DIHYDROANTHRA/1,9-CD/PYRAZOL-6-ONE / 1,9-Pyrazoloanthrone


Mass: 220.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H8N2O / Comment: inhibitor*YM
#3: Chemical ChemComp-7PE / 2-(2-(2-(2-(2-(2-ETHOXYETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHANOL / POLYETHYLENE GLYCOL FRAGMENT / Polyethylene glycol


Mass: 310.384 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30O7
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.34 Å3/Da / Density % sol: 47.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG300, HEPES, pH6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 94 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 11, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.88→59.76 Å / Num. obs: 9729 / % possible obs: 99.8 % / Observed criterion σ(I): 1 / Redundancy: 3.1 % / Biso Wilson estimate: 84.702 Å2 / Rmerge(I) obs: 0.107 / Rsym value: 0.072 / Net I/σ(I): 11.7
Reflection shellResolution: 2.88→3.04 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.798 / Mean I/σ(I) obs: 1.5 / Num. unique all: 1397 / Rsym value: 0.535 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CrystalCleardata collection
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ZMC

2zmc


Resolution: 2.88→40.49 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.892 / SU B: 17.078 / SU ML: 0.307 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 1.253 / ESU R Free: 0.37 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2605 468 4.8 %RANDOM
Rwork0.22122 ---
obs0.22314 9261 99.61 %-
all-9729 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.441 Å2
Baniso -1Baniso -2Baniso -3
1--3.78 Å20 Å20 Å2
2--0.73 Å20 Å2
3---3.05 Å2
Refinement stepCycle: LAST / Resolution: 2.88→40.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2111 0 33 26 2170
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0222191
X-RAY DIFFRACTIONr_bond_other_d0.0010.021503
X-RAY DIFFRACTIONr_angle_refined_deg1.0231.9792956
X-RAY DIFFRACTIONr_angle_other_deg0.78633698
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5375256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.77825.6100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.00315410
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.639156
X-RAY DIFFRACTIONr_chiral_restr0.0620.2320
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022342
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02396
X-RAY DIFFRACTIONr_nbd_refined0.1940.2458
X-RAY DIFFRACTIONr_nbd_other0.1650.21589
X-RAY DIFFRACTIONr_nbtor_refined0.1740.21071
X-RAY DIFFRACTIONr_nbtor_other0.0820.21107
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1220.244
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.20.223
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1830.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1310.24
X-RAY DIFFRACTIONr_mcbond_it0.3321.51715
X-RAY DIFFRACTIONr_mcbond_other0.031.5516
X-RAY DIFFRACTIONr_mcangle_it0.37322106
X-RAY DIFFRACTIONr_scbond_it0.35431128
X-RAY DIFFRACTIONr_scangle_it0.5374.5850
LS refinement shellResolution: 2.88→2.955 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 33 -
Rwork0.318 675 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -44.4735 Å / Origin y: -23.2215 Å / Origin z: -13.8241 Å
111213212223313233
T-0.0296 Å2-0.0781 Å2-0.0135 Å2--0.1073 Å20.038 Å2---0.0559 Å2
L1.5702 °20.3517 °22.7308 °2-0.2012 °21.1315 °2--6.9565 °2
S-0.4133 Å °-0.2052 Å °0.6208 Å °0.094 Å °-0.2434 Å °-0.3869 Å °0.0729 Å °-0.4919 Å °0.6567 Å °

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