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- PDB-5ci6: Crystal structure of Arabidopsis thaliana MPK6 -

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Basic information

Entry
Database: PDB / ID: 5ci6
TitleCrystal structure of Arabidopsis thaliana MPK6
ComponentsMitogen-activated protein kinase 6
KeywordsTRANSFERASE / Kinase / apoenzyme
Function / homology
Function and homology information


preprophase band / priming of cellular response to stress / camalexin biosynthetic process / response to freezing / regulation of unidimensional cell growth / pollen tube guidance / regulation of root meristem growth / induced systemic resistance, jasmonic acid mediated signaling pathway / inflorescence development / plant ovule development ...preprophase band / priming of cellular response to stress / camalexin biosynthetic process / response to freezing / regulation of unidimensional cell growth / pollen tube guidance / regulation of root meristem growth / induced systemic resistance, jasmonic acid mediated signaling pathway / inflorescence development / plant ovule development / phragmoplast / plant-type hypersensitive response / response to ethylene / regulation of stomatal closure / leaf senescence / pollen development / root development / response to fungus / response to abscisic acid / abscisic acid-activated signaling pathway / response to UV-B / response to osmotic stress / response to L-glutamate / MAP kinase activity / mitogen-activated protein kinase / phosphatase binding / response to salt stress / response to cold / response to reactive oxygen species / trans-Golgi network / response to hydrogen peroxide / cell cortex / response to oxidative stress / protein kinase activity / intracellular signal transduction / defense response to bacterium / cell division / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / 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 ...Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / 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
Mitogen-activated protein kinase 6
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsQin, X. / Li, P. / Chen, Z. / Ren, D.
Funding support China, 1items
OrganizationGrant numberCountry
the National Natural Science Foundation of China31125006 China
CitationJournal: Sci Rep / Year: 2016
Title: Analysis of crystal structure of Arabidopsis MPK6 and generation of its mutants with higher activity
Authors: Wang, B. / Qin, X. / Wu, J. / Deng, H. / Li, Y. / Yang, H. / Chen, Z. / Liu, G. / Ren, D.
History
DepositionJul 11, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mitogen-activated protein kinase 6
B: Mitogen-activated protein kinase 6


Theoretical massNumber of molelcules
Total (without water)85,6702
Polymers85,6702
Non-polymers00
Water1086
1
A: Mitogen-activated protein kinase 6


Theoretical massNumber of molelcules
Total (without water)42,8351
Polymers42,8351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mitogen-activated protein kinase 6


Theoretical massNumber of molelcules
Total (without water)42,8351
Polymers42,8351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)150.513, 150.513, 85.624
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: 0 / Auth seq-ID: 32 - 393 / Label seq-ID: 7 - 368

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Mitogen-activated protein kinase 6 / MAP kinase 6


Mass: 42835.035 Da / Num. of mol.: 2 / Fragment: UNP residues 29-395
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: MPK6, At2g43790, F18O19.10 / Production host: Escherichia coli (E. coli)
References: UniProt: Q39026, mitogen-activated protein kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 3.36 Å3/Da / Density % sol: 63.45 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.2 / Details: 0.1 M citrate, 10-12% PEG 20000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97923 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 3, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 24998 / % possible obs: 99.5 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 16.48
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.684 / Mean I/σ(I) obs: 2.15 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
PHENIX1.9-1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ERK

1erk
PDB Unreleased entry


Resolution: 3→42.7 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.907 / SU B: 14.95 / SU ML: 0.281 / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27234 1163 5.2 %RANDOM
Rwork0.22591 ---
obs0.22823 21377 99.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 96.859 Å2
Baniso -1Baniso -2Baniso -3
1-4.16 Å20 Å20 Å2
2--4.16 Å20 Å2
3----8.32 Å2
Refinement stepCycle: LAST / Resolution: 3→42.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5447 0 0 6 5453
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0195570
X-RAY DIFFRACTIONr_bond_other_d0.0060.025298
X-RAY DIFFRACTIONr_angle_refined_deg1.371.9697572
X-RAY DIFFRACTIONr_angle_other_deg1.119312169
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3735678
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.49124.28264
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.58315937
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.7451534
X-RAY DIFFRACTIONr_chiral_restr0.080.2859
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216259
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021257
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 19001 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.14 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 89 -
Rwork0.326 1553 -
obs--100 %

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