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- PDB-6r85: Structure of Arabidopsis thaliana GLR3.3 ligand-binding domain in... -

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Basic information

Entry
Database: PDB / ID: 6r85
TitleStructure of Arabidopsis thaliana GLR3.3 ligand-binding domain in complex with L-glutamate
ComponentsGlutamate receptor 3.3,Glutamate receptor 3.3
KeywordsMEMBRANE PROTEIN / glutamate receptor-like / amino acid-binding
Function / homology
Function and homology information


induced systemic resistance, jasmonic acid mediated signaling pathway / gravitropism / glutamate receptor activity / ligand-gated monoatomic ion channel activity / defense response to fungus / calcium-mediated signaling / cellular response to amino acid stimulus / calcium channel activity / response to wounding / calcium ion transport ...induced systemic resistance, jasmonic acid mediated signaling pathway / gravitropism / glutamate receptor activity / ligand-gated monoatomic ion channel activity / defense response to fungus / calcium-mediated signaling / cellular response to amino acid stimulus / calcium channel activity / response to wounding / calcium ion transport / cell-cell signaling / innate immune response / plasma membrane
Similarity search - Function
Ionotropic glutamate receptor, plant / Plant glutamate receptor, periplasmic ligand-binding domain / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / : / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. ...Ionotropic glutamate receptor, plant / Plant glutamate receptor, periplasmic ligand-binding domain / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / : / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like I
Similarity search - Domain/homology
GLUTAMIC ACID / Glutamate receptor 3.3
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsAlfieri, A. / Pederzoli, R. / Costa, A.
Funding support Italy, 2items
OrganizationGrant numberCountry
Italian Ministry of Education, University and ResearchFIRB 2010 - RBFR10S1LJ_001 grant Italy
University of Milan (Italy)PIANO DI SVILUPPO DI ATENEO 2017 Italy
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: The structural bases for agonist diversity in anArabidopsis thalianaglutamate receptor-like channel.
Authors: Alfieri, A. / Doccula, F.G. / Pederzoli, R. / Grenzi, M. / Bonza, M.C. / Luoni, L. / Candeo, A. / Romano Armada, N. / Barbiroli, A. / Valentini, G. / Schneider, T.R. / Bassi, A. / Bolognesi, ...Authors: Alfieri, A. / Doccula, F.G. / Pederzoli, R. / Grenzi, M. / Bonza, M.C. / Luoni, L. / Candeo, A. / Romano Armada, N. / Barbiroli, A. / Valentini, G. / Schneider, T.R. / Bassi, A. / Bolognesi, M. / Nardini, M. / Costa, A.
History
DepositionMar 31, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 1, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamate receptor 3.3,Glutamate receptor 3.3
B: Glutamate receptor 3.3,Glutamate receptor 3.3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,85815
Polymers53,8922
Non-polymers96713
Water5,675315
1
A: Glutamate receptor 3.3,Glutamate receptor 3.3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4839
Polymers26,9461
Non-polymers5378
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glutamate receptor 3.3,Glutamate receptor 3.3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3756
Polymers26,9461
Non-polymers4295
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.886, 61.280, 64.103
Angle α, β, γ (deg.)75.190, 75.530, 90.020
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Glutamate receptor 3.3,Glutamate receptor 3.3 / Ligand-gated ion channel 3.3


Mass: 26945.777 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: GLR3.3, At1g42540, T8D8.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9C8E7

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Non-polymers , 5 types, 328 molecules

#2: Chemical ChemComp-GLU / GLUTAMIC ACID / Glutamic acid


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO4
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 315 / 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: 2.47 Å3/Da / Density % sol: 50.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 100 mM sodium acetate pH 4.6, 240 mM ammonium sulfate, 30%(w/v) PEG monomethyl ether 2,000.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→59 Å / Num. obs: 33332 / % possible obs: 96.7 % / Redundancy: 3.2 % / CC1/2: 0.99 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.076 / Rrim(I) all: 0.138 / Net I/σ(I): 4.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2-2.053.20.48824020.8340.3180.58494.7
8.94-59.113.40.0523660.9920.0350.06397.1

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.6.2data scaling
REFMAC5refinement
PDB_EXTRACT3.24data extraction
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2→59 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.879 / SU B: 6.454 / SU ML: 0.176 / SU R Cruickshank DPI: 0.2179 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.218 / ESU R Free: 0.193
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2618 1595 4.8 %RANDOM
Rwork0.2067 ---
obs0.2093 31737 96.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 76.41 Å2 / Biso mean: 22.879 Å2 / Biso min: 12.52 Å2
Baniso -1Baniso -2Baniso -3
1-0.54 Å20.13 Å20.13 Å2
2---1.98 Å2-0.76 Å2
3---0.85 Å2
Refinement stepCycle: final / Resolution: 2→59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3679 0 60 315 4054
Biso mean--28.26 31.13 -
Num. residues----477
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0133810
X-RAY DIFFRACTIONr_bond_other_d0.0020.0173586
X-RAY DIFFRACTIONr_angle_refined_deg1.4831.6495157
X-RAY DIFFRACTIONr_angle_other_deg1.2171.5748314
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3645473
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.15622.391184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.16115618
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8391522
X-RAY DIFFRACTIONr_chiral_restr0.0630.2491
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024233
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02785
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 117 -
Rwork0.261 2283 -
all-2400 -
obs--94.56 %

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