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- PDB-8ztc: Crystal structure of Mps1-AMP complex -

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Basic information

Entry
Database: PDB / ID: 8ztc
TitleCrystal structure of Mps1-AMP complex
ComponentsMitogen-activated protein kinase MPS1
KeywordsSIGNALING PROTEIN / M. oryzae / kinase / AMP / complex
Function / homology
Function and homology information


negative regulation of mitotic cytokinesis / positive regulation of developmental process / positive regulation of calcium ion import across plasma membrane / JUN kinase activity / negative regulation of glucose mediated signaling pathway / response to stress / mitogen-activated protein kinase / positive regulation of calcium-mediated signaling / ATP binding / nucleus / cytoplasm
Similarity search - Function
Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / : / 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. ...Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / : / 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
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / Mitogen-activated protein kinase MPS1
Similarity search - Component
Biological speciesPyricularia oryzae (rice blast fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsKong, Z. / Li, S. / Zhang, X. / Wang, D. / Liu, J.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China) China
CitationJournal: J.Agric.Food Chem. / Year: 2024
Title: Combinatorial Targeting of Common Docking and ATP Binding Sites on Mps1 MAPK for Management of Pathogenic Fungi.
Authors: Kong, Z. / Li, S. / Li, J. / Chen, Y. / Chen, M. / Zhang, X. / Wang, D. / Liu, J.
History
DepositionJun 7, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 23, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mitogen-activated protein kinase MPS1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7752
Polymers48,4281
Non-polymers3471
Water1,22568
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area640 Å2
ΔGint-2 kcal/mol
Surface area18530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.733, 76.733, 162.689
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Mitogen-activated protein kinase MPS1 / MAPK MPS1


Mass: 48427.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyricularia oryzae (rice blast fungus) / Gene: MPS1, PgNI_01373 / Production host: Escherichia coli (E. coli)
References: UniProt: O13352, mitogen-activated protein kinase
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 3.22 Å3/Da / Density % sol: 61.77 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 20% (v/v) Tacsimate, pH 6.0, 0.05 M sodium cacodylate trihydrate, pH 6.5, and 1.0 mM Spermine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 7, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.26→50 Å / Num. obs: 26616 / % possible obs: 99.5 % / Redundancy: 18.73 % / CC1/2: 0.9993 / Rmerge(I) obs: 0.0838 / Net I/σ(I): 44.54
Reflection shellResolution: 2.26→2.32 Å / Rmerge(I) obs: 0.7175 / Mean I/σ(I) obs: 5.14 / Num. unique obs: 1942 / CC1/2: 0.8914

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
autoPXdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.26→29.22 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2517 1238 4.66 %
Rwork0.1963 --
obs0.1989 26551 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.26→29.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2989 0 23 68 3080
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043082
X-RAY DIFFRACTIONf_angle_d0.6124179
X-RAY DIFFRACTIONf_dihedral_angle_d6.89416
X-RAY DIFFRACTIONf_chiral_restr0.044455
X-RAY DIFFRACTIONf_plane_restr0.006544
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.26-2.350.29671190.25682675X-RAY DIFFRACTION97
2.35-2.460.34221350.2452803X-RAY DIFFRACTION100
2.46-2.590.26091260.24422770X-RAY DIFFRACTION100
2.59-2.750.28561320.24332804X-RAY DIFFRACTION100
2.75-2.960.30341580.24862775X-RAY DIFFRACTION100
2.96-3.260.28841430.23432797X-RAY DIFFRACTION100
3.26-3.730.27291560.20912807X-RAY DIFFRACTION100
3.73-4.70.20661200.15892878X-RAY DIFFRACTION100
4.7-29.220.21411490.15933004X-RAY DIFFRACTION100

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