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- PDB-2mid: Solution structure of the CLAVATA encoded peptide of Arabidopsis ... -

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Basic information

Entry
Database: PDB / ID: 2mid
TitleSolution structure of the CLAVATA encoded peptide of Arabidopsis thaliana - AtCLE10
ComponentsCLAVATA3/ESR (CLE)-related protein 10
KeywordsUNKNOWN FUNCTION / CLE / CLAVATA
Function / homologyCLAVATA3/ESR (CLE)-related protein 9/10/11/12/13 / phloem development / maintenance of root meristem identity / cell-cell signaling involved in cell fate commitment / apoplast / receptor serine/threonine kinase binding / regulation of cell differentiation / CLAVATA3/ESR (CLE)-related protein 10
Function and homology information
Biological speciesArabidopsis thaliana (thale cress)
MethodSOLUTION NMR / simulated annealing
AuthorsBobay, B.G. / DiGennaro, P.M. / Bird, D.M.
CitationJournal: To be Published
Title: Inferring function of CLE peptides from high resolution tertiary structures
Authors: DiGennaro, P.M. / Bobay, B.G. / Bird, D.M.
History
DepositionDec 16, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

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Assembly

Deposited unit
A: CLAVATA3/ESR (CLE)-related protein 10


Theoretical massNumber of molelcules
Total (without water)1,3021
Polymers1,3021
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)10 / 20structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide CLAVATA3/ESR (CLE)-related protein 10 / CLE10p


Mass: 1302.482 Da / Num. of mol.: 1 / Fragment: UNP residues 96-107 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress) / References: UniProt: Q4PSX1

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1312D 1H-1H TOCSY
1412D 1H-1H NOESY

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Sample preparation

DetailsContents: 4 mg/mL peptide, 137 mM sodium chloride, 2.7 mM potassium chloride, 10 mM sodium phosphate, 1.8 mM potassium phosphate, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
4 mg/mLentity-11
137 mMsodium chloride-21
2.7 mMpotassium chloride-31
10 mMsodium phosphate-41
1.8 mMpotassium phosphate-51
Sample conditionsIonic strength: 140 / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
ARIA2.3Linge, O'Donoghue and Nilgesstructure solution
ARIA2.3Linge, O'Donoghue and Nilgesrefinement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificdata analysis
NMRViewJohnson, One Moon Scientificpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 10

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