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

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Basic information

Entry
Database: PDB / ID: 7xdw
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: 1.926 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)71,9585
Polymers71,0792
Non-polymers8793
Water2,936163
1
A: Receptor-like protein kinase FERONIA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9913
Polymers35,5401
Non-polymers4522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-5 kcal/mol
Surface area13700 Å2
MethodPISA
2
B: Receptor-like protein kinase FERONIA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9672
Polymers35,5401
Non-polymers4271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.805, 83.163, 62.048
Angle α, β, γ (deg.)90.000, 93.140, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 522 through 815 or resid 901 through 1001))
21(chain B and (resid 522 through 815 or resid 901 through 1001))

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
11ARGARGGLUGLU(chain A and (resid 522 through 815 or resid 901 through 1001))AA522 - 81519 - 312
12ADPADPHOHHOH(chain A and (resid 522 through 815 or resid 901 through 1001))AC - F901 - 1001
21ARGARGGLUGLU(chain B and (resid 522 through 815 or resid 901 through 1001))BB522 - 81519 - 312
22ADPADPHOHHOH(chain B and (resid 522 through 815 or resid 901 through 1001))BE - G901 - 1001

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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-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.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2.24 Å3/Da / Density % sol: 45.09 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1M Potassium chloride, 0.01M Magnesium chloride hexahydrate, 0.05M TRIS hydrochloride pH 8.5, 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: 1.926→61.95 Å / Num. obs: 42862 / % possible obs: 90.2 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 13
Reflection shellResolution: 1.93→2.03 Å / Num. unique obs: 42809 / CC1/2: 0.997

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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: 1.926→61.712 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2074 2107 4.92 %
Rwork0.1866 40702 -
obs0.1877 42809 90.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 159.96 Å2 / Biso mean: 48.2168 Å2 / Biso min: 16 Å2
Refinement stepCycle: final / Resolution: 1.926→61.712 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4506 0 55 163 4724
Biso mean--79.24 45.84 -
Num. residues----562
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1720X-RAY DIFFRACTION8.294TORSIONAL
12B1720X-RAY DIFFRACTION8.294TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.926-1.97050.32091010.2889214272
1.9705-2.01980.2941480.23833006100
2.0198-2.07440.2764710.2328119993
2.0744-2.13550.22371480.2059282498
2.1355-2.20440.23131580.20582991100
2.2044-2.28320.2815810.2016160754
2.2832-2.37460.22771550.19613019100
2.3746-2.48270.25321690.1993297099
2.4827-2.61360.27181580.19282947100
2.6136-2.77730.19581300.1942301199
2.7773-2.99180.21082010.1921295699
2.9918-3.29280.22981250.1923301999
3.2928-3.76920.1881470.1735298599
3.7692-4.74860.1911380.1561302699
4.7486-61.7120.1641770.164300098
Refinement TLS params.Method: refined / Origin x: 13.7122 Å / Origin y: 4.4117 Å / Origin z: 16.705 Å
111213212223313233
T0.1953 Å2-0.0056 Å20.0009 Å2-0.1804 Å2-0.0017 Å2--0.1666 Å2
L0.8724 °20.4051 °2-0.0197 °2-0.5734 °20.0082 °2--0.212 °2
S-0.064 Å °0.0805 Å °-0.0005 Å °-0.0713 Å °0.0536 Å °-0.0169 Å °0.0059 Å °0.0015 Å °0.0001 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA521 - 815
2X-RAY DIFFRACTION1allA901 - 1001
3X-RAY DIFFRACTION1allB522 - 816
4X-RAY DIFFRACTION1allB901
5X-RAY DIFFRACTION1allS1 - 163

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