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- PDB-5gr9: Crystal structure of PXY-TDIF/CLE41 -

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Basic information

Entry
Database: PDB / ID: 5gr9
TitleCrystal structure of PXY-TDIF/CLE41
Components
  • Leucine-rich repeat receptor-like protein kinase TDR
  • TDIF/CLE41
KeywordsTRANSFERASE / PXY / TDIF / 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 / cell-cell signaling involved in cell fate commitment / phloem or xylem histogenesis / secondary shoot formation / apoplast / receptor serine/threonine kinase binding ...procambium histogenesis / phloem development / xylem development / axillary shoot meristem initiation / maintenance of root meristem identity / cell-cell signaling involved in cell fate commitment / phloem or xylem histogenesis / secondary shoot formation / apoplast / receptor serine/threonine kinase binding / regulation of cell differentiation / non-specific serine/threonine protein kinase / phosphorylation / cell division / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / 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 / 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 ...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 / 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, 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
CLAVATA3/ESR (CLE)-related protein 41 / Leucine-rich repeat receptor-like protein kinase TDR
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Arabidopsis (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.767 Å
AuthorsChai, J.J. / Zhang, H.Q.
CitationJournal: Cell Res. / Year: 2016
Title: Crystal structure of PXY-TDIF complex reveals a conserved recognition mechanism among CLE peptide-receptor pairs
Authors: Zhang, H.Q. / Lin, X.Y. / Han, Z.F. / Qu, L.J. / Chai, J.J.
History
DepositionAug 8, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 23, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_prerelease_seq / pdbx_struct_oper_list / 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 / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Nov 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/CLE41
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,03210
Polymers67,2632
Non-polymers1,7708
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint28 kcal/mol
Surface area25630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.668, 93.668, 228.709
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Leucine-rich repeat receptor-like protein kinase TDR / PXY


Mass: 65982.461 Da / Num. of mol.: 1 / Fragment: UNP residues 31-629
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PXY / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9FII5, non-specific serine/threonine protein kinase
#2: Protein/peptide TDIF/CLE41


Mass: 1280.322 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Arabidopsis (plant) / References: UniProt: Q84W98*PLUS
#3: 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.: 8
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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O

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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: 3.75 Å3/Da / Density % sol: 67.21 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 16% w/v Polyethylene glycol 3350, 2% v/v Tacsimate pH 5.0, 0.1 M Sodium citrate tribasic dihydrate pH 5.5
PH range: 5.0-5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Mar 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.77→50 Å / Num. obs: 26768 / % possible obs: 99.7 % / Redundancy: 5.4 % / Net I/σ(I): 15.5
Reflection shellResolution: 2.77→2.8 Å

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Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MN8

4mn8


Resolution: 2.767→39.905 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 24.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2408 1347 5.03 %
Rwork0.193 --
obs0.1954 26764 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.767→39.905 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4719 0 112 36 4867
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094962
X-RAY DIFFRACTIONf_angle_d1.3396745
X-RAY DIFFRACTIONf_dihedral_angle_d16.4011804
X-RAY DIFFRACTIONf_chiral_restr0.087771
X-RAY DIFFRACTIONf_plane_restr0.005859
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7672-2.86610.30541430.23262455X-RAY DIFFRACTION100
2.8661-2.98080.3271190.23772498X-RAY DIFFRACTION100
2.9808-3.11640.33781240.23822528X-RAY DIFFRACTION100
3.1164-3.28060.28711500.21692462X-RAY DIFFRACTION100
3.2806-3.48610.27811430.21862542X-RAY DIFFRACTION100
3.4861-3.75510.2351240.17512517X-RAY DIFFRACTION100
3.7551-4.13260.1941300.15882541X-RAY DIFFRACTION100
4.1326-4.72980.20241470.14662548X-RAY DIFFRACTION100
4.7298-5.95580.2231430.18222590X-RAY DIFFRACTION100
5.9558-39.90950.23241240.2242736X-RAY DIFFRACTION98

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