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- PDB-5z33: Crystal structure of Mitogen-activated Protein Kinase Mps1 in Mag... -

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Basic information

Entry
Database: PDB / ID: 5z33
TitleCrystal structure of Mitogen-activated Protein Kinase Mps1 in Magnaporthe oryzae
ComponentsMitogen-activated protein kinase
KeywordsTRANSFERASE / Mps1 / MAPK / Phosphorylation / Magnaporthe oryzae
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 / negative regulation of glucose mediated signaling pathway / MAP kinase activity / mitogen-activated protein kinase / positive regulation of calcium-mediated signaling / protein serine kinase activity / 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
Mitogen-activated protein kinase MPS1
Similarity search - Component
Biological speciesMagnaporthe oryzae (rice blast fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsZhou, F. / Liu, J.F. / Zhang, G.Z.
Funding support China, 2items
OrganizationGrant numberCountry
National Key Research and Development PlanNo.2017YFD0200500 China
National Key Research and Development PlanNo.2017YFD0201100 China
CitationJournal: To Be Published
Title: Crystal structure of Mitogen-activated Protein Kinase Mps1 in Magnaporthe oryzae
Authors: Zhou, F. / Peng, J.B. / Zhao, Y.X. / Chen, X. / Zhang, Y.Y. / Peng, Y.L. / Liu, J.F. / Zhang, G.Z.
History
DepositionJan 5, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mitogen-activated protein kinase


Theoretical massNumber of molelcules
Total (without water)48,3131
Polymers48,3131
Non-polymers00
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area18210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.549, 74.549, 158.561
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


Mass: 48312.816 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnaporthe oryzae (strain P131) (fungus)
Strain: P131 / Gene: MPS1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: G4N374, mitogen-activated protein kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSequence reference G4N374 (G4N374_MAGO7) was derived from a different strain Magnaporthe oryzae ...Sequence reference G4N374 (G4N374_MAGO7) was derived from a different strain Magnaporthe oryzae (strain 70-15 / ATCC MYA-4617 / FGSC 8958) (TaxID 242507).

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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: 2.63 Å3/Da / Density % sol: 53.28 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: Sodium cacodylate trihydrate, tacsimate, spermine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 31, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.99→79.28 Å / Num. obs: 379824 / % possible obs: 99.9 % / Redundancy: 10.6 % / Net I/σ(I): 12.8
Reflection shellResolution: 1.99→2.1 Å

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.99→59.795 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.31 / Phase error: 20.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2217 1989 5.56 %
Rwork0.1866 --
obs0.1886 35781 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.99→59.795 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3013 0 0 151 3164
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073081
X-RAY DIFFRACTIONf_angle_d1.0484173
X-RAY DIFFRACTIONf_dihedral_angle_d6.6121852
X-RAY DIFFRACTIONf_chiral_restr0.054454
X-RAY DIFFRACTIONf_plane_restr0.007548
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9901-2.03980.27871400.24082359X-RAY DIFFRACTION100
2.0398-2.0950.2181430.22222371X-RAY DIFFRACTION100
2.095-2.15660.27711400.21142391X-RAY DIFFRACTION100
2.1566-2.22620.24131380.2032391X-RAY DIFFRACTION100
2.2262-2.30580.25131400.19942380X-RAY DIFFRACTION100
2.3058-2.39810.22141390.19982395X-RAY DIFFRACTION100
2.3981-2.50730.2351420.19782373X-RAY DIFFRACTION100
2.5073-2.63950.25341450.1982410X-RAY DIFFRACTION100
2.6395-2.80480.21431370.19872395X-RAY DIFFRACTION100
2.8048-3.02140.23081430.20342420X-RAY DIFFRACTION100
3.0214-3.32540.25661390.19412422X-RAY DIFFRACTION100
3.3254-3.80660.20571420.17662454X-RAY DIFFRACTION100
3.8066-4.79560.17541440.15772462X-RAY DIFFRACTION100
4.7956-59.8220.23281570.1852569X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.14930.87521.04082.283-0.92496.2345-0.07390.7237-0.2471-0.4383-0.1252-0.45410.11050.81610.16310.27920.0974-0.00060.53680.04350.488146.046-36.19222.033
24.0615-0.09342.5261.48370.52453.4919-0.05480.1992-0.089-0.17730.05420.0983-0.05510.2435-0.01170.2120.05190.02470.30080.00770.251548.972-34.334.582
33.52292.3044-3.93114.0895-3.64455.42290.0639-0.403-0.65850.3110.02240.75610.7011-0.6517-0.01810.3751-0.0995-0.03530.74150.20540.63338.284-46.83940.978
45.6471-1.29251.55534.8339-2.40377.83620.03240.1826-0.7024-0.27080.55161.07290.816-1.0461-0.60430.3658-0.0068-0.05130.43520.05530.546648.938-52.43944.596
51.4563-0.60190.92491.1203-0.48761.73660.0328-0.2812-0.19290.13210.10540.20130.2552-0.1948-0.12550.29920.03570.02190.36230.02320.330448.734-44.1747.37
67.3155-4.2635-2.0722.4911.08321.95810.23990.2661-1.3639-0.3103-0.45510.59850.3789-0.71640.33540.6068-0.0822-0.18790.4498-0.03450.706119.133-1.52845.04
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 85 )
2X-RAY DIFFRACTION2chain 'A' and (resid 86 through 162 )
3X-RAY DIFFRACTION3chain 'A' and (resid 163 through 186 )
4X-RAY DIFFRACTION4chain 'A' and (resid 187 through 207 )
5X-RAY DIFFRACTION5chain 'A' and (resid 208 through 360 )
6X-RAY DIFFRACTION6chain 'A' and (resid 394 through 412 )

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