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- PDB-6dtl: Mitogen-activated protein kinase 6 -

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Basic information

Entry
Database: PDB / ID: 6dtl
TitleMitogen-activated protein kinase 6
ComponentsMitogen-activated protein kinase 6
KeywordsTRANSFERASE / Kinase / plant protein
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 / response to ethylene / plant-type hypersensitive response / regulation of stomatal closure / leaf senescence / response to fungus / pollen development / root development / 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 / defense response to bacterium / protein phosphorylation / cell division / protein serine kinase activity / ATP binding / nucleus / cytosol
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 6
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.753 Å
AuthorsRuble, J.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nat.Plants / Year: 2019
Title: Bipartite anchoring of SCREAM enforces stomatal initiation by coupling MAP kinases to SPEECHLESS.
Authors: Putarjunan, A. / Ruble, J. / Srivastava, A. / Zhao, C. / Rychel, A.L. / Hofstetter, A.K. / Tang, X. / Zhu, J.K. / Tama, F. / Zheng, N. / Torii, K.U.
History
DepositionJun 17, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 24, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 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

Downloads & links

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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)84,3042
Polymers84,3042
Non-polymers00
Water2,126118
1
A: Mitogen-activated protein kinase 6


Theoretical massNumber of molelcules
Total (without water)42,1521
Polymers42,1521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mitogen-activated protein kinase 6


Theoretical massNumber of molelcules
Total (without water)42,1521
Polymers42,1521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)151.589, 151.589, 85.991
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 42152.203 Da / Num. of mol.: 2 / Fragment: UNP residues 32-395
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


Mass: 18.015 Da / Num. of mol.: 118 / 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: 3.38 Å3/Da / Density % sol: 63.64 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / Details: sodium citrate, PEG8000

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 26, 2016
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 29831 / % possible obs: 100 % / Redundancy: 11.1 % / Net I/σ(I): 17.53
Reflection shellResolution: 2.75→2.8 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.753→42.977 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.74
RfactorNum. reflection% reflection
Rfree0.2564 2001 7.17 %
Rwork0.2053 --
obs0.209 27927 93.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.753→42.977 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5811 0 0 118 5929
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045949
X-RAY DIFFRACTIONf_angle_d0.688069
X-RAY DIFFRACTIONf_dihedral_angle_d15.1213634
X-RAY DIFFRACTIONf_chiral_restr0.045890
X-RAY DIFFRACTIONf_plane_restr0.0051053
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7529-2.82170.3188690.2687885X-RAY DIFFRACTION45
2.8217-2.8980.37731030.29511361X-RAY DIFFRACTION70
2.898-2.98320.35541430.26781903X-RAY DIFFRACTION97
2.9832-3.07950.31391520.25221949X-RAY DIFFRACTION100
3.0795-3.18950.27291510.24291963X-RAY DIFFRACTION100
3.1895-3.31720.311540.23481948X-RAY DIFFRACTION100
3.3172-3.46810.25681500.21431959X-RAY DIFFRACTION100
3.4681-3.65090.25911540.21761980X-RAY DIFFRACTION100
3.6509-3.87950.2441520.20111970X-RAY DIFFRACTION100
3.8795-4.17880.27721500.18321957X-RAY DIFFRACTION100
4.1788-4.59890.19081550.16671998X-RAY DIFFRACTION100
4.5989-5.26330.22551510.17421985X-RAY DIFFRACTION100
5.2633-6.62730.26381580.20632008X-RAY DIFFRACTION100
6.6273-42.98270.22351590.1842060X-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)
10.13680.02590.01220.34020.02320.38990.0157-0.0315-0.16980.19310.0415-0.1511-0.03980.32930.34860.26330.0573-0.0185-0.03010.11370.1877-62.4875-22.26296.2508
20.04090.028-0.02320.0185-0.010.00180.10710.12720.151-0.06210.0036-0.2518-0.20460.3540.00010.4933-0.01790.12630.56550.00720.4489-46.8892-17.7712-8.4316
30.02520.0164-0.00010.0227-0.01430.02360.0172-0.03910.06550.0370.0244-0.0193-0.04840.02440.05850.2662-0.0189-0.013-0.0019-0.07540.1746-76.6653-7.179415.5481
40.08370.13790.00380.2974-0.07960.1518-0.0429-0.0109-0.16690.1105-0.0012-0.13840.04990.0703-0.11420.52410.38670.08250.1979-0.11050.3218-60.4578-31.461949.621
50.01540.003-0.00810.0090.00260.00790.0015-0.02290.0139-0.0048-0.0330.0173-0.01670.0172-0.04130.23280.3069-0.04770.2939-0.19240.1814-48.5825-29.099535.5925
60.1119-0.00590.01260.0149-0.01210.02170.0119-0.05950.06880.0460.01810.0066-0.0361-0.0420.12620.03440.3576-0.13290.3441-0.15120.1863-53.0784-39.389532.2073
70.0503-0.05950.04080.0816-0.02560.046-0.0074-0.03930.02350.0276-0.0246-0.0345-0.0290.0112-0.07460.1480.2646-0.08410.279-0.09140.1578-36.0107-46.860436.7643
80.0099-0.0171-0.01080.083-0.00430.0124-0.0076-0.0053-0.01710.0353-0.02830.04080.0282-0.0157-0.03650.00440.326-0.07970.2943-0.03770.1797-41.6892-55.637129.0196
90.0013-0-0.00330.0019-0.0050.01570.00830.02730.0498-0.011-0.0216-0.0267-0.0080.0071-0.02780.05370.1836-0.06710.2313-0.05720.2403-22.7898-54.862325.5951
100.01720.0218-0.0210.0878-0.02490.0261-0.0059-0.00620.0218-0.01370.00660.0712-0.0119-0.03260.0267-0.00740.2050.03690.2378-0.08130.1865-41.3367-63.332820.3925
110.0838-0.01370.03820.01440.01690.0645-0.00390.03760.028-0.0826-0.0633-0.0327-0.0324-0.0273-0.06210.17210.4484-0.11770.34950.03980.1119-43.1402-47.618415.3084
120.0005-0.00050.00760.0120.00760.01210.0877-0.15730.17360.0802-0.0518-0.0447-0.08180.10810.00010.4650.0552-0.11990.4663-0.11650.4226-44.3423-22.656538.5732
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 32 through 279 )
2X-RAY DIFFRACTION2chain 'A' and (resid 280 through 374 )
3X-RAY DIFFRACTION3chain 'A' and (resid 375 through 395 )
4X-RAY DIFFRACTION4chain 'B' and (resid 33 through 103 )
5X-RAY DIFFRACTION5chain 'B' and (resid 104 through 129 )
6X-RAY DIFFRACTION6chain 'B' and (resid 130 through 205 )
7X-RAY DIFFRACTION7chain 'B' and (resid 206 through 242 )
8X-RAY DIFFRACTION8chain 'B' and (resid 243 through 280 )
9X-RAY DIFFRACTION9chain 'B' and (resid 281 through 301 )
10X-RAY DIFFRACTION10chain 'B' and (resid 302 through 318 )
11X-RAY DIFFRACTION11chain 'B' and (resid 319 through 353 )
12X-RAY DIFFRACTION12chain 'B' and (resid 354 through 395 )

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