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- PDB-5gqr: Crystal structure of PXY-CLE41-SERK2 -

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Basic information

Entry
Database: PDB / ID: 5gqr
TitleCrystal structure of PXY-CLE41-SERK2
Components
  • Leucine-rich repeat receptor-like protein kinase TDR
  • Somatic embryogenesis receptor kinase 2
  • TDIF
KeywordsTRANSFERASE / Meristem cell proliferation / SERK / CLE peptides / leucine rich repeat
Function / homology
Function and homology information


procambium histogenesis / phloem development / xylem development / axillary shoot meristem initiation / maintenance of root meristem identity / microsporogenesis / cell-cell signaling involved in cell fate commitment / pollen maturation / phloem or xylem histogenesis / secondary shoot formation ...procambium histogenesis / phloem development / xylem development / axillary shoot meristem initiation / maintenance of root meristem identity / microsporogenesis / cell-cell signaling involved in cell fate commitment / pollen maturation / phloem or xylem histogenesis / secondary shoot formation / brassinosteroid mediated signaling pathway / apoplast / receptor serine/threonine kinase binding / regulation of cell differentiation / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / cell division / signaling receptor binding / protein serine kinase activity / lipid binding / ATP binding / nucleus / plasma membrane
Similarity search - Function
CLAVATA3/ESR (CLE)-related protein 41/42/44 / : / Leucine-rich repeat-containing N-terminal, plant-type / Leucine rich repeat N-terminal domain / Leucine Rich Repeat / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine rich repeat / Leucine-rich repeat, typical subtype ...CLAVATA3/ESR (CLE)-related protein 41/42/44 / : / Leucine-rich repeat-containing N-terminal, plant-type / Leucine rich repeat N-terminal domain / Leucine Rich Repeat / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / 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/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / 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 / Alpha Beta
Similarity search - Domain/homology
CLAVATA3/ESR (CLE)-related protein 44 / Leucine-rich repeat receptor-like protein kinase TDR / Somatic embryogenesis receptor kinase 2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Arabideae (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsChai, J.J. / Zhang, H.Q.
CitationJournal: Mol Plant / Year: 2016
Title: SERK Family Receptor-like Kinases Function as Co-receptors with PXY for Plant Vascular Development
Authors: Zhang, H.Q. / Lin, X.Y. / Han, Z.F. / Wang, J. / Qu, L.J. / Chai, J.J.
History
DepositionAug 8, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 14, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
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_role
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
B: Leucine-rich repeat receptor-like protein kinase TDR
C: TDIF
K: Somatic embryogenesis receptor kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,1947
Polymers87,3093
Non-polymers8854
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4250 Å2
ΔGint5 kcal/mol
Surface area31270 Å2
Unit cell
Length a, b, c (Å)162.422, 162.422, 187.234
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein Leucine-rich repeat receptor-like protein kinase TDR / Protein PHLOEM INTERCALATED WITH XYLEM


Mass: 65853.289 Da / Num. of mol.: 1 / Fragment: UNP residues 32-629
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: TDR / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9FII5, non-specific serine/threonine protein kinase
#2: Protein/peptide TDIF


Mass: 1264.322 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Arabideae (plant) / References: UniProt: Q941C5*PLUS
#3: Protein Somatic embryogenesis receptor kinase 2 / SERK2


Mass: 20191.816 Da / Num. of mol.: 1 / Fragment: UNP residues 30-214
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SERK2 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9XIC7, non-specific serine/threonine protein kinase
#4: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
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

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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: 4.11 Å3/Da / Density % sol: 70.06 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Potassium chloride, 20% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 18060 / % possible obs: 95.13 % / Redundancy: 4.3 % / Rsym value: 0.144 / Net I/σ(I): 6.5

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Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MN8

4mn8


Resolution: 3.5→40.472 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 27.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2759 926 5.14 %
Rwork0.219 --
obs0.2219 18033 95.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.5→40.472 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6104 0 56 0 6160
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016364
X-RAY DIFFRACTIONf_angle_d1.6298663
X-RAY DIFFRACTIONf_dihedral_angle_d18.3052311
X-RAY DIFFRACTIONf_chiral_restr0.124996
X-RAY DIFFRACTIONf_plane_restr0.0081118
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5002-3.68460.38861480.31462400X-RAY DIFFRACTION96
3.6846-3.91530.29331230.25612440X-RAY DIFFRACTION97
3.9153-4.21730.24251410.20722430X-RAY DIFFRACTION97
4.2173-4.64110.26281480.18572430X-RAY DIFFRACTION96
4.6411-5.31140.22221290.18182428X-RAY DIFFRACTION95
5.3114-6.6870.3391250.23562467X-RAY DIFFRACTION94
6.687-40.47430.2521120.21322512X-RAY DIFFRACTION90
Refinement TLS params.Method: refined / Origin x: 58.0206 Å / Origin y: -31.857 Å / Origin z: 14.2508 Å
111213212223313233
T1.1368 Å2-0.0167 Å2-0.0932 Å2-0.4522 Å2-0.037 Å2--0.4786 Å2
L1.1001 °20.9227 °20.7969 °2-1.0532 °20.6576 °2--0.8501 °2
S-0.4574 Å °0.011 Å °0.2322 Å °-0.5223 Å °0.2445 Å °0.1644 Å °-0.3409 Å °-0.0719 Å °0.2108 Å °
Refinement TLS groupSelection details: all

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