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- PDB-2mif: Solution structure of the CLAVATA-like encoded peptide of Meloido... -

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Entry
Database: PDB / ID: 2mif
TitleSolution structure of the CLAVATA-like encoded peptide of Meloidogyne hapla - MhCLE4
ComponentsCLAVATA-like encoded peptide of Meloidogyne hapla - MhCLE4
KeywordsUNKNOWN FUNCTION / CLE / CLAVATA
Biological speciesMeloidogyne hapla (invertebrata)
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 13, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 24, 2014Provider: 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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Assembly

Deposited unit
A: CLAVATA-like encoded peptide of Meloidogyne hapla - MhCLE4


Theoretical massNumber of molelcules
Total (without water)1,2221
Polymers1,2221
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 CLAVATA-like encoded peptide of Meloidogyne hapla - MhCLE4


Mass: 1222.242 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Meloidogyne hapla (invertebrata)

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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
NameDeveloperClassification
ARIALinge, O'Donoghue and Nilgesrefinement
ARIALinge, O'Donoghue and Nilgesstructure solution
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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