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- PDB-4z63: The plant peptide hormone receptor in arabidopsis -

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Basic information

Entry
Database: PDB / ID: 4z63
TitleThe plant peptide hormone receptor in arabidopsis
Components
  • Phytosulfokine
  • Phytosulfokine receptor 1
KeywordsHORMONE / hormone receptor
Function / homology
Function and homology information


regulation of defense response / peptide receptor activity / guanylate cyclase / guanylate cyclase activity / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity ...regulation of defense response / peptide receptor activity / guanylate cyclase / guanylate cyclase activity / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / Rho-dependent protein serine/threonine kinase activity / ribosomal protein S6 kinase activity / histone H2BS14 kinase activity / histone H3T6 kinase activity / histone H3T45 kinase activity / histone H3S10 kinase activity / histone H3T11 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / protein serine/threonine kinase activity / innate immune response / protein serine kinase activity / ATP 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 / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily ...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 profile. / 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
Phytosulfokine receptor 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Arabidopsis (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.514 Å
AuthorsChai, J. / Wang, J. / Han, Z.
CitationJournal: Nature / Year: 2015
Title: Allosteric receptor activation by the plant peptide hormone phytosulfokine
Authors: Wang, J. / Li, H. / Han, Z. / Zhang, H. / Wang, T. / Lin, G. / Chang, J. / Yang, W. / Chai, J.
History
DepositionApr 3, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 2, 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_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
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phytosulfokine receptor 1
P: Phytosulfokine
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,72211
Polymers70,7312
Non-polymers1,9919
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint28 kcal/mol
Surface area26160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.892, 92.892, 242.492
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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Components

#1: Protein Phytosulfokine receptor 1 / AtPSKR1 / Phytosulfokine LRR receptor kinase 1


Mass: 69884.008 Da / Num. of mol.: 1 / Fragment: UNP residues 24-648
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PSKR1, PSKR, At2g02220, F5O4.1
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: Q9ZVR7, non-specific serine/threonine protein kinase
#2: Protein/peptide Phytosulfokine


Mass: 846.879 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Arabidopsis (plant)
#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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 9
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


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.84 Å3/Da / Density % sol: 67.93 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1M Bis-Tris 5.5, 2.0M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: BRUKER SMART 6500 / Detector: CCD / Date: Dec 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→99 Å / Num. obs: 36369 / % possible obs: 98.4 % / Redundancy: 5.3 % / Net I/σ(I): 26

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Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Z5W

4z5w


Resolution: 2.514→33.544 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 29.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2755 1817 5 %
Rwork0.2287 --
obs0.231 36369 98.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.514→33.544 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4805 0 125 145 5075
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085037
X-RAY DIFFRACTIONf_angle_d1.4816832
X-RAY DIFFRACTIONf_dihedral_angle_d16.2131865
X-RAY DIFFRACTIONf_chiral_restr0.123784
X-RAY DIFFRACTIONf_plane_restr0.008873
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5139-2.58180.35081270.26732588X-RAY DIFFRACTION97
2.5818-2.65780.31911330.26722647X-RAY DIFFRACTION99
2.6578-2.74350.35641380.28072630X-RAY DIFFRACTION99
2.7435-2.84150.25961450.23582642X-RAY DIFFRACTION100
2.8415-2.95530.38781330.25332660X-RAY DIFFRACTION100
2.9553-3.08970.36181610.25652647X-RAY DIFFRACTION100
3.0897-3.25240.29261450.25882667X-RAY DIFFRACTION100
3.2524-3.4560.30311430.25612667X-RAY DIFFRACTION99
3.456-3.72250.33411290.26552590X-RAY DIFFRACTION96
3.7225-4.09660.22631220.21272428X-RAY DIFFRACTION89
4.0966-4.6880.19761380.16022730X-RAY DIFFRACTION99
4.688-5.90110.21681660.19222735X-RAY DIFFRACTION99
5.9011-33.54740.27191370.23172921X-RAY DIFFRACTION98

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