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- PDB-2liy: Plant peptide hormone regulating stomatal density -

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Basic information

Entry
Database: PDB / ID: 2liy
TitlePlant peptide hormone regulating stomatal density
ComponentsEPIDERMAL PATTERNING FACTOR-like protein 9
KeywordsHORMONE / Plant peptide hormone / EPFL family / stomatal density / positive regulator
Function / homology
Function and homology information


regulation of stomatal complex development / positive regulation of stomatal complex development / guard cell differentiation / stomatal complex patterning / stomatal complex development / apoplast / receptor serine/threonine kinase binding / cell-cell signaling / signaling receptor binding / protein kinase binding
Similarity search - Function
Stomagen / Stomagen / Stomagen, C-terminal domain superfamily / Stomagen, C-terminal domain / Stomagen / N-terminal domain of TfIIb / Single Sheet / Mainly Beta
Similarity search - Domain/homology
EPIDERMAL PATTERNING FACTOR-like protein 9
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model 1
AuthorsOhki, S.
CitationJournal: Nat Commun / Year: 2011
Title: The NMR structure of stomagen reveals the basis of stomatal density regulation by plant peptide hormones
Authors: Ohki, S. / Takeuchi, M. / Mori, M.
History
DepositionSep 2, 2011Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Sep 5, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EPIDERMAL PATTERNING FACTOR-like protein 9


Theoretical massNumber of molelcules
Total (without water)5,1311
Polymers5,1311
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 96structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide EPIDERMAL PATTERNING FACTOR-like protein 9 / EPF-like protein 9


Mass: 5130.784 Da / Num. of mol.: 1 / Fragment: UNP residues 58-102
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: EPFL9 / Cell (production host): BY-2 / Production host: Tomato mosaic virus / References: UniProt: Q9SV72
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCO
1313D HNCA
1413D HN(CA)CB
1513D CBCA(CO)NH
1613D (H)CCH-TOCSY
1712D 1H-1H TOCSY
1812D 1H-1H NOESY
1913D 1H-15N NOESY

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Sample preparation

DetailsContents: 0.5mM [U-99% 13C; U-99% 15N] D2O-1, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 0.5 mM / Component: D2O-1 / Isotopic labeling: [U-99% 13C; U-99% 15N]
Sample conditionsIonic strength: 0.1 / pH: 5.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR softwareName: CNS / Developer: Brunger A.T. et.al. / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 666 / NOE intraresidue total count: 352 / NOE long range total count: 110 / NOE medium range total count: 54 / NOE sequential total count: 140
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 96 / Conformers submitted total number: 20 / Representative conformer: 1

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