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- PDB-4mna: Crystal structure of the free FLS2 ectodomains -

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Basic information

Entry
Database: PDB / ID: 4mna
TitleCrystal structure of the free FLS2 ectodomains
ComponentsLRR receptor-like serine/threonine-protein kinase FLS2
KeywordsTRANSFERASE / FLS2 / plant immunity / Leucine-rich repeat
Function / homology
Function and homology information


regulation of anion channel activity / defense response by callose deposition in cell wall / transmembrane receptor protein serine/threonine kinase activity / endomembrane system / detection of bacterium / receptor-mediated endocytosis / endosome membrane / non-specific serine/threonine protein kinase / endosome / defense response to bacterium ...regulation of anion channel activity / defense response by callose deposition in cell wall / transmembrane receptor protein serine/threonine kinase activity / endomembrane system / detection of bacterium / receptor-mediated endocytosis / endosome membrane / non-specific serine/threonine protein kinase / endosome / defense response to bacterium / phosphorylation / protein serine kinase activity / ATP binding / membrane / identical protein binding / plasma membrane
Similarity search - Function
Leucine-rich repeat-containing N-terminal, plant-type / Leucine rich repeat N-terminal domain / Leucine Rich Repeat / Leucine-rich repeat, SDS22-like subfamily / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Serine/threonine-protein kinase, active site ...Leucine-rich repeat-containing N-terminal, plant-type / Leucine rich repeat N-terminal domain / Leucine Rich Repeat / Leucine-rich repeat, SDS22-like subfamily / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
LRR receptor-like serine/threonine-protein kinase FLS2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.998 Å
AuthorsChai, J. / Han, Z. / Sun, Y.
CitationJournal: Science / Year: 2013
Title: Structural basis for flg22-induced activation of the Arabidopsis FLS2-BAK1 immune complex.
Authors: Sun, Y. / Li, L. / Macho, A.P. / Han, Z. / Hu, Z. / Zipfel, C. / Zhou, J.M. / Chai, J.
History
DepositionSep 10, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 4, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: LRR receptor-like serine/threonine-protein kinase FLS2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,79310
Polymers72,4251
Non-polymers1,3689
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)189.542, 189.542, 117.751
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein LRR receptor-like serine/threonine-protein kinase FLS2 / Protein FLAGELLIN-SENSING 2 / Protein FLAGELLIN-SENSITIVE 2


Mass: 72425.320 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 25-121, 242-800
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: FLS2, At5g46330, MPL12.13, MPL12.8 / Cell line (production host): high five / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9FL28, non-specific serine/threonine protein kinase
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn

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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

Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1M sodium cacodylate trihydrate pH 5.0, 0.11M Zinc acetate dihydrate, 14.25% (v/v) PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 24, 2012
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.998→50 Å / Num. all: 20910 / Num. obs: 20722 / % possible obs: 99.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 2.9 %

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RGZ

3rgz


Resolution: 3.998→29.728 Å / SU ML: 0.42 / σ(F): 0 / Phase error: 28.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2792 1055 5.1 %RANDOM
Rwork0.2495 ---
all0.251 20854 --
obs0.251 20667 98.89 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.998→29.728 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4890 0 74 0 4964
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085059
X-RAY DIFFRACTIONf_angle_d1.096867
X-RAY DIFFRACTIONf_dihedral_angle_d12.9371893
X-RAY DIFFRACTIONf_chiral_restr0.069833
X-RAY DIFFRACTIONf_plane_restr0.004879
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.9983-4.17980.29731420.2489237098
4.1798-4.39950.28111220.2272244599
4.3995-4.67410.23791460.2008241099
4.6741-5.03340.21011120.1976247699
5.0334-5.5370.25141470.20672430100
5.537-6.33150.32831430.28132468100
6.3315-7.95170.33761230.2752247798
7.9517-29.72830.28121200.2845253698
Refinement TLS params.Method: refined / Origin x: 68.339 Å / Origin y: -71.7339 Å / Origin z: -37.7395 Å
111213212223313233
T0.6474 Å2-0.3386 Å20.0513 Å2-0.6337 Å20.0358 Å2--0.6245 Å2
L1.5028 °20.1872 °20.5324 °2-0.5581 °21.1116 °2--2.365 °2
S0.0318 Å °-0.1085 Å °-0.1272 Å °0.0674 Å °-0.0644 Å °0.0562 Å °0.4264 Å °-0.4626 Å °-0.0979 Å °
Refinement TLS groupSelection details: ALL

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