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- PDB-7xbr: Crystal structure of phosphorylated AtMKK5 -

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Basic information

Entry
Database: PDB / ID: 7xbr
TitleCrystal structure of phosphorylated AtMKK5
Components(Mitogen-activated protein kinase kinase 5) x 2
KeywordsTRANSFERASE / Mitogen-activated protein kinase kinase 5 / Arabidopsis thaliana / Phosphoserine / Phosphothreonine
Function / homology
Function and homology information


positive regulation of ethylene biosynthetic process / regulation of unidimensional cell growth / regulation of root meristem growth / floral organ abscission / inflorescence development / plant-type hypersensitive response / regulation of stomatal closure / defense response to other organism / mitogen-activated protein kinase kinase / abscisic acid-activated signaling pathway ...positive regulation of ethylene biosynthetic process / regulation of unidimensional cell growth / regulation of root meristem growth / floral organ abscission / inflorescence development / plant-type hypersensitive response / regulation of stomatal closure / defense response to other organism / mitogen-activated protein kinase kinase / abscisic acid-activated signaling pathway / MAP kinase kinase activity / protein tyrosine kinase activity / cell division / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / cytoplasm
Similarity search - Function
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 kinase 5
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsPei, C.J. / Luo, Z.P. / Wu, J.W. / Wang, Z.X.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: Acta Biochim.Biophys.Sin. / Year: 2022
Title: Crystal structure of the phosphorylated Arabidopsis MKK5 reveals activation mechanism of MAPK kinases.
Authors: Pei, C.J. / He, Q.X. / Luo, Z. / Yao, H. / Wang, Z.X. / Wu, J.W.
History
DepositionMar 22, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 8, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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: Mitogen-activated protein kinase kinase 5
B: Mitogen-activated protein kinase kinase 5
C: Mitogen-activated protein kinase kinase 5
D: Mitogen-activated protein kinase kinase 5
E: Mitogen-activated protein kinase kinase 5
F: Mitogen-activated protein kinase kinase 5
G: Mitogen-activated protein kinase kinase 5
H: Mitogen-activated protein kinase kinase 5


Theoretical massNumber of molelcules
Total (without water)266,9798
Polymers266,9798
Non-polymers00
Water00
1
A: Mitogen-activated protein kinase kinase 5
D: Mitogen-activated protein kinase kinase 5
G: Mitogen-activated protein kinase kinase 5
H: Mitogen-activated protein kinase kinase 5


Theoretical massNumber of molelcules
Total (without water)133,4904
Polymers133,4904
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5330 Å2
ΔGint-42 kcal/mol
Surface area47160 Å2
MethodPISA
2
B: Mitogen-activated protein kinase kinase 5
C: Mitogen-activated protein kinase kinase 5
E: Mitogen-activated protein kinase kinase 5
F: Mitogen-activated protein kinase kinase 5


Theoretical massNumber of molelcules
Total (without water)133,4904
Polymers133,4904
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5250 Å2
ΔGint-37 kcal/mol
Surface area46390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.666, 198.572, 202.824
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Mitogen-activated protein kinase kinase 5 / AtMAP2Kalpha / AtMEK5 / AtMKK5 / MAP kinase kinase 5


Mass: 33392.402 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: MKK5 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8RXG3, mitogen-activated protein kinase kinase
#2: Protein Mitogen-activated protein kinase kinase 5 / AtMAP2Kalpha / AtMEK5 / AtMKK5 / MAP kinase kinase 5


Mass: 33312.422 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: MKK5 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8RXG3, mitogen-activated protein kinase kinase
Has ligand of interestN

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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: 3.16 Å3/Da / Density % sol: 61.02 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M Bis-Tris Propane (pH 7.0), 2.8 M NaAc (pH 7.0) and 0.4M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 55113 / % possible obs: 96.7 % / Redundancy: 7.5 % / CC1/2: 0.99 / Rmerge(I) obs: 0.167 / Net I/σ(I): 15.6
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 7.6 % / Rmerge(I) obs: 1.697 / Mean I/σ(I) obs: 1.86 / Num. unique obs: 5452 / CC1/2: 0.872 / % possible all: 97.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BF2

4bf2


Resolution: 3.2→49.13 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.922 / SU B: 21.706 / SU ML: 0.359 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.456 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2456 2647 4.8 %RANDOM
Rwork0.2093 ---
obs0.211 52111 96.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 269.23 Å2 / Biso mean: 101.07 Å2 / Biso min: 33.81 Å2
Baniso -1Baniso -2Baniso -3
1-6.03 Å2-0 Å20 Å2
2---4.35 Å20 Å2
3----1.68 Å2
Refinement stepCycle: final / Resolution: 3.2→49.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16581 0 0 0 16581
Num. residues----2075
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01316963
X-RAY DIFFRACTIONr_bond_other_d0.0010.01515729
X-RAY DIFFRACTIONr_angle_refined_deg1.671.63523054
X-RAY DIFFRACTIONr_angle_other_deg1.41.57536136
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.82552060
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.47421.43944
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.673152788
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.77815137
X-RAY DIFFRACTIONr_chiral_restr0.0820.22181
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219109
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024021
X-RAY DIFFRACTIONr_mcbond_it10.92110.4158285
X-RAY DIFFRACTIONr_mcbond_other10.91910.4158284
X-RAY DIFFRACTIONr_mcangle_it15.99815.61110330
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 179 -
Rwork0.325 3814 -
all-3993 -
obs--97.44 %

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