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- PDB-5tos: Botrytis-induced kinase 1 (BIK1) from Arabidopsis thaliana -

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Basic information

Entry
Database: PDB / ID: 5tos
TitleBotrytis-induced kinase 1 (BIK1) from Arabidopsis thaliana
ComponentsSerine/threonine-protein kinase BIK1
KeywordsTRANSFERASE / serine/threonine-protein kinase / BIK1 / PAMP-triggered immunity
Function / homology
Function and homology information


regulation of salicylic acid biosynthetic process / regulation of defense response to bacterium / regulation of jasmonic acid biosynthetic process / protein serine/threonine kinase activity => GO:0004674 / regulation of stomatal movement / response to fungus / pattern recognition receptor signaling pathway / endomembrane system / defense response to fungus / response to molecule of bacterial origin ...regulation of salicylic acid biosynthetic process / regulation of defense response to bacterium / regulation of jasmonic acid biosynthetic process / protein serine/threonine kinase activity => GO:0004674 / regulation of stomatal movement / response to fungus / pattern recognition receptor signaling pathway / endomembrane system / defense response to fungus / response to molecule of bacterial origin / kinase activity / protein autophosphorylation / endosome membrane / non-specific serine/threonine protein kinase / endosome / defense response to bacterium / protein phosphorylation / innate immune response / protein serine kinase activity / protein serine/threonine kinase activity / nucleolus / Golgi apparatus / ATP binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / 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
Serine/threonine-protein kinase BIK1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsHurlburt, N.K. / Lal, N.K. / Fisher, A.J.
CitationJournal: Cell Host Microbe / Year: 2018
Title: The Receptor-like Cytoplasmic Kinase BIK1 Localizes to the Nucleus and Regulates Defense Hormone Expression during Plant Innate Immunity.
Authors: Lal, N.K. / Nagalakshmi, U. / Hurlburt, N.K. / Flores, R. / Bak, A. / Sone, P. / Ma, X. / Song, G. / Walley, J. / Shan, L. / He, P. / Casteel, C. / Fisher, A.J. / Dinesh-Kumar, S.P.
History
DepositionOct 18, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Serine/threonine-protein kinase BIK1
B: Serine/threonine-protein kinase BIK1


Theoretical massNumber of molelcules
Total (without water)88,4792
Polymers88,4792
Non-polymers00
Water2,828157
1
A: Serine/threonine-protein kinase BIK1


Theoretical massNumber of molelcules
Total (without water)44,2391
Polymers44,2391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Serine/threonine-protein kinase BIK1


Theoretical massNumber of molelcules
Total (without water)44,2391
Polymers44,2391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)114.190, 72.090, 93.880
Angle α, β, γ (deg.)90.00, 108.41, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Serine/threonine-protein kinase BIK1 / Protein BOTRYTIS-INDUCED KINASE 1


Mass: 44239.418 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: BIK1, At2g39660, F12L6.32, F17A14.3 / Plasmid: pET His6 TEV LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: O48814, non-specific serine/threonine protein kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.08 Å3/Da / Density % sol: 41 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 7 / Details: 245 mM ammonium tartrate, 12.5% PEG 3350 pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 29382 / % possible obs: 96.6 % / Redundancy: 2.92 % / Biso Wilson estimate: 26.8 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 9.73
Reflection shellResolution: 2.35→2.41 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.575 / Mean I/σ(I) obs: 1.93 / CC1/2: 0.883 / % possible all: 95.1

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OH4, 3UIM

4oh4

3uim


Resolution: 2.35→33.543 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 29.3
RfactorNum. reflection% reflection
Rfree0.268 1448 4.93 %
Rwork0.238 --
obs0.2395 29352 96.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.35→33.543 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4514 0 0 157 4671
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024616
X-RAY DIFFRACTIONf_angle_d0.5896248
X-RAY DIFFRACTIONf_dihedral_angle_d12.982776
X-RAY DIFFRACTIONf_chiral_restr0.042686
X-RAY DIFFRACTIONf_plane_restr0.003798
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3483-2.43220.34271600.28722727X-RAY DIFFRACTION96
2.4322-2.52960.30611520.27242799X-RAY DIFFRACTION98
2.5296-2.64460.33531380.26752817X-RAY DIFFRACTION98
2.6446-2.7840.30741560.26182747X-RAY DIFFRACTION96
2.784-2.95830.30591570.26032758X-RAY DIFFRACTION96
2.9583-3.18660.281130.24332858X-RAY DIFFRACTION98
3.1866-3.5070.27181500.23132798X-RAY DIFFRACTION97
3.507-4.01370.22621510.22392778X-RAY DIFFRACTION96
4.0137-5.05410.24661400.20672810X-RAY DIFFRACTION97
5.0541-33.54610.2621310.24942812X-RAY DIFFRACTION94
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)
14.1874-1.4825-1.5873.54750.01835.0356-0.4832-0.4503-0.30080.26530.11030.11290.92260.48650.17930.56190.08940.02320.54340.10970.461134.6027-6.31826.4242
23.091-1.4924-0.392.839-0.26973.1368-0.03110.1353-0.57320.121-0.00420.04140.41820.36510.02170.3010.0103-0.01070.2928-0.00830.293529.35134.070316.0275
34.1268-0.4251-0.69562.28390.13925.26670.16960.7456-0.2905-0.2937-0.209-0.09920.30470.20820.02760.36470.02520.00960.4094-0.0260.256820.044211.70822.5096
41.9756-0.64880.48852.4687-0.29897.15760.0989-0.31620.14110.16230.1857-0.0217-0.81150.6442-0.35820.5009-0.180.02120.6238-0.00950.433234.682937.648230.6163
54.4992.06760.13762.52481.0452.5945-0.0268-0.39790.47570.0185-0.1020.0246-0.30120.12970.15140.3255-0.0197-0.00690.313-0.02340.301221.162426.711231.263
64.09360.41170.08962.66580.35556.19960.1258-0.63880.31470.2962-0.3490.1526-0.0366-0.53870.19050.3506-0.06620.0460.4866-0.05020.27935.756419.998137.8079
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 52 through 114 )
2X-RAY DIFFRACTION2chain 'A' and (resid 115 through 192 )
3X-RAY DIFFRACTION3chain 'A' and (resid 193 through 360 )
4X-RAY DIFFRACTION4chain 'B' and (resid 52 through 127 )
5X-RAY DIFFRACTION5chain 'B' and (resid 128 through 218 )
6X-RAY DIFFRACTION6chain 'B' and (resid 219 through 360 )

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