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

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Basic information

Entry
Database: PDB / ID: 7xdv
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 brassinosteroid / response to ethylene / brassinosteroid mediated signaling pathway / ethylene-activated signaling pathway / stomatal movement / root development / plasmodesma ...pollen tube reception / filiform apparatus / negative regulation of abscisic acid-activated signaling pathway / response to brassinosteroid / response to ethylene / brassinosteroid mediated signaling pathway / ethylene-activated signaling pathway / stomatal movement / 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 / 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. ...Malectin-like domain / Receptor-like protein kinase ANXUR1-like / Malectin-like domain / 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
ADENOSINE-5'-TRIPHOSPHATE / Receptor-like protein kinase FERONIA
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / struct_ncs_dom_lim
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 / _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
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)72,1426
Polymers71,0792
Non-polymers1,0634
Water3,657203
1
A: Receptor-like protein kinase FERONIA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0713
Polymers35,5401
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-10 kcal/mol
Surface area13910 Å2
MethodPISA
2
B: Receptor-like protein kinase FERONIA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0713
Polymers35,5401
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-9 kcal/mol
Surface area13770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.950, 83.330, 62.050
Angle α, β, γ (deg.)90.000, 93.390, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 28 through 401)
21(chain B and (resid 28 through 320 or resid 401))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11HISHISATPATP(chain A and resid 28 through 401)AA - C28 - 40120
21HISHISGLUGLU(chain B and (resid 28 through 320 or resid 401))BB28 - 32020 - 312
22ATPATPATPATP(chain B and (resid 28 through 320 or resid 401))BE401

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Components

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


Mass: 35539.688 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-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, 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 / Water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 45.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.05M Magnesium chloride hexahydrate, 0.1M HEPES 7.5, 30% v/vPolyethylene glycol monomethyl ether 550

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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: Jan 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 1.97→29.76 Å / Num. obs: 44514 / % possible obs: 99.8 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 12.1
Reflection shellResolution: 1.97→2.02 Å / Num. unique obs: 44474 / CC1/2: 0.998

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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: 1.97→27.059 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.213 1997 4.49 %
Rwork0.1705 42477 -
obs0.1723 44474 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 136 Å2 / Biso mean: 48.1509 Å2 / Biso min: 19.19 Å2
Refinement stepCycle: final / Resolution: 1.97→27.059 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4534 0 64 203 4801
Biso mean--78.84 51.18 -
Num. residues----566
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1728X-RAY DIFFRACTION6.74TORSIONAL
12B1728X-RAY DIFFRACTION6.74TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.97-2.01930.31181380.26263040100
2.0193-2.07380.25741600.23253000100
2.0738-2.13480.2551320.20423023100
2.1348-2.20370.2841390.19353028100
2.2037-2.28240.22581360.18033025100
2.2824-2.37380.21961590.1733041100
2.3738-2.48170.21281310.17023023100
2.4817-2.61250.22271440.17293020100
2.6125-2.7760.23161540.17933004100
2.776-2.99010.22941380.17443057100
2.9901-3.29050.2281390.17793038100
3.2905-3.76560.21351450.15773026100
3.7656-4.74010.19631400.14073082100
4.7401-27.0590.17531420.1753307099
Refinement TLS params.Method: refined / Origin x: 15.8273 Å / Origin y: 6.0604 Å / Origin z: 14.5856 Å
111213212223313233
T0.2095 Å20.008 Å20.002 Å2-0.2257 Å2-0.0322 Å2--0.2437 Å2
L0.3879 °20.0491 °2-0.0838 °2-1.0373 °2-0.529 °2--1.5652 °2
S0.0007 Å °0.0209 Å °0.0079 Å °0.0073 Å °0.0335 Å °0.1387 Å °0.0049 Å °-0.1706 Å °-0.0156 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA26 - 401
2X-RAY DIFFRACTION1allB27 - 401
3X-RAY DIFFRACTION1allC1 - 2
4X-RAY DIFFRACTION1allS1 - 203

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