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- PDB-5hz1: Plant peptide hormone receptor RGFR1 in complex with RGF3 -

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Basic information

Entry
Database: PDB / ID: 5hz1
TitlePlant peptide hormone receptor RGFR1 in complex with RGF3
Components
  • ASP-PTR-TRP-ARG-ALA-LYS-HIS-HIS-PRO-HYP-LYS-ASN-ASN
  • Probable LRR receptor-like serine/threonine-protein kinase At4g26540
KeywordsTRANSFERASE / Plant Receptor
Function / homology
Function and homology information


maintenance of meristem identity / regulation of lateral root development / regulation of root morphogenesis / regulation of root development / maintenance of root meristem identity / regulation of root meristem growth / peptide receptor activity / regulation of asymmetric cell division / growth factor activity / peptide binding ...maintenance of meristem identity / regulation of lateral root development / regulation of root morphogenesis / regulation of root development / maintenance of root meristem identity / regulation of root meristem growth / peptide receptor activity / regulation of asymmetric cell division / growth factor activity / peptide binding / cell differentiation / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of cell population proliferation / positive regulation of gene expression / extracellular space / ATP binding / plasma membrane
Similarity search - Function
Root meristem growth factor 1/2/3 / : / 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 ...Root meristem growth factor 1/2/3 / : / 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, 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
LRR receptor-like serine/threonine-protein kinase RGI3 / Protein GOLVEN 7
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Arabidopsis (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsSong, W. / Han, Z. / Chai, J.
CitationJournal: To Be Published
Title: Plant Receptor
Authors: Song, W. / Han, Z. / Chai, J.
History
DepositionFeb 2, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Probable LRR receptor-like serine/threonine-protein kinase At4g26540
A: ASP-PTR-TRP-ARG-ALA-LYS-HIS-HIS-PRO-HYP-LYS-ASN-ASN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,8345
Polymers70,9672
Non-polymers8673
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint10 kcal/mol
Surface area26610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.466, 183.466, 87.610
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Probable LRR receptor-like serine/threonine-protein kinase At4g26540


Mass: 69202.875 Da / Num. of mol.: 1 / Fragment: UNP residues 57-689 / Mutation: V64T, G81E, M82K, D83Q, N104Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At4g26540, M3E9.30
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: C0LGR3, non-specific serine/threonine protein kinase
#2: Protein/peptide ASP-PTR-TRP-ARG-ALA-LYS-HIS-HIS-PRO-HYP-LYS-ASN-ASN


Mass: 1763.826 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Arabidopsis (plant) / References: UniProt: Q6ID76*PLUS
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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 Å3/Da / Density % sol: 69.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M MES monohydrate pH 6.0, 22% (v/v) polyethylene glycol (PEG) 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: OXFORD RUBY CCD / Detector: CCD / Date: Dec 21, 2014
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.59→99 Å / Num. obs: 33780 / % possible obs: 98.9 % / Redundancy: 5.2 % / Net I/σ(I): 31.8

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACT3.2data extraction
HKL-2000data scaling
PHENIXphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.59→35.42 Å / Cor.coef. Fo:Fc: 0.934 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.363 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflection
Rwork0.2342 --
obs0.2342 33780 98.91 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 214.61 Å2 / Biso mean: 25.686 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-1.15 Å21.15 Å20 Å2
2--1.15 Å2-0 Å2
3----3.73 Å2
Refinement stepCycle: final / Resolution: 2.59→35.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4886 0 56 0 4942
Biso mean--23.67 --
Num. residues----636
LS refinement shellResolution: 2.591→2.659 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.293 2310 -
obs--91.52 %

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