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- PDB-7xdy: Crystal structure of a receptor like kinase from Arabidopsis -

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Basic information

Entry
Database: PDB / ID: 7xdy
TitleCrystal structure of a receptor like kinase from Arabidopsis
ComponentsReceptor-like protein kinase FERONIA
KeywordsPLANT PROTEIN / receptor-like kinase
Function / homology
Function and homology information


pollen tube reception / filiform apparatus / negative regulation of abscisic acid-activated signaling pathway / response to ethylene / response to brassinosteroid / brassinosteroid mediated signaling pathway / stomatal movement / ethylene-activated signaling pathway / root development / plasmodesma ...pollen tube reception / filiform apparatus / negative regulation of abscisic acid-activated signaling pathway / response to ethylene / response to brassinosteroid / brassinosteroid mediated signaling pathway / stomatal movement / ethylene-activated signaling pathway / root development / plasmodesma / abscisic acid-activated signaling pathway / defense response to fungus / transmembrane receptor protein tyrosine kinase activity / post-embryonic development / circadian regulation of gene expression / negative regulation of cell growth / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / plasma membrane
Similarity search - Function
Malectin-like domain / Receptor-like protein kinase ANXUR1-like / Malectin-like domain / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / 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. ...Malectin-like domain / Receptor-like protein kinase ANXUR1-like / Malectin-like domain / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / 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
ADENOSINE-5'-DIPHOSPHATE / Receptor-like protein kinase FERONIA
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsKong, Y.Q. / Ming, Z.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31700052 China
CitationJournal: Plant Commun. / Year: 2023
Title: Structural and biochemical basis of Arabidopsis FERONIA receptor kinase-mediated early signaling initiation.
Authors: Kong, Y. / Chen, J. / Jiang, L. / Chen, H. / Shen, Y. / Wang, L. / Yan, Y. / Zhou, H. / Zheng, H. / Yu, F. / Ming, Z.
History
DepositionMar 29, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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 1.2Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Receptor-like protein kinase FERONIA
B: Receptor-like protein kinase FERONIA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,9266
Polymers71,0232
Non-polymers9034
Water1,38777
1
A: Receptor-like protein kinase FERONIA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9633
Polymers35,5121
Non-polymers4522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
ΔGint-16 kcal/mol
Surface area13600 Å2
MethodPISA
2
B: Receptor-like protein kinase FERONIA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9633
Polymers35,5121
Non-polymers4522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area890 Å2
ΔGint-15 kcal/mol
Surface area13510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.795, 83.248, 62.322
Angle α, β, γ (deg.)90.000, 93.040, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Receptor-like protein kinase FERONIA / Protein SIRENE


Mass: 35511.676 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: FER, AAK1, SIR, SRN, At3g51550, F26O13.190
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9SCZ4, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.25 Å3/Da / Density % sol: 45.43 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1M Tris pH8.0, 30% v/v Polyethylene glycol 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979183 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 1.957→62.234 Å / Num. obs: 32641 / % possible obs: 88.2 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 8.3
Reflection shellResolution: 1.96→2.15 Å / Num. unique obs: 28740 / CC1/2: 0.994

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Processing

Software
NameVersionClassification
PHENIX1.15_3459refinement
PDB_EXTRACT3.27data extraction
autoPROCdata reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QKW

2qkw


Resolution: 2.28→61.708 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 28.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.247 1363 4.76 %
Rwork0.1971 27281 -
obs0.1996 28644 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 146.77 Å2 / Biso mean: 50.3043 Å2 / Biso min: 21.75 Å2
Refinement stepCycle: final / Resolution: 2.28→61.708 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4494 0 56 77 4627
Biso mean--86.84 49.6 -
Num. residues----560
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2802-2.36170.3014820.2859275299
2.3617-2.45630.34041350.2699269399
2.4563-2.56810.25991460.22782726100
2.5681-2.70340.27151330.22882714100
2.7034-2.87280.27151340.21642737100
2.8728-3.09460.26861530.21112705100
3.0946-3.4060.27291760.20292701100
3.406-3.89880.25181180.1824276399
3.8988-4.91180.20271650.1667269699
4.9118-61.7080.23341210.1797279498

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