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- PDB-7ckd: Solution structure of NCR169 oxidized form 1 from Medicago truncatula -

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Basic information

Entry
Database: PDB / ID: 7ckd
TitleSolution structure of NCR169 oxidized form 1 from Medicago truncatula
ComponentsNodule Cysteine-Rich (NCR) secreted peptide
KeywordsPLANT PROTEIN / Medicago truncatula / nodule-specific cysteine-rich peptide / antimicrobial peptide / disulfide bond
Function / homologyLate nodulin / Late nodulin domain / defense response to bacterium / lipid binding / membrane / metal ion binding / Nodule Cysteine-Rich (NCR) secreted peptide
Function and homology information
Biological speciesMedicago truncatula (barrel medic)
MethodSOLUTION NMR / na
AuthorsIsozumi, N. / Masubuchi, Y. / Ohki, S.
CitationJournal: Sci Rep / Year: 2021
Title: Structure and antimicrobial activity of NCR169, a nodule-specific cysteine-rich peptide of Medicago truncatula.
Authors: Isozumi, N. / Masubuchi, Y. / Imamura, T. / Mori, M. / Koga, H. / Ohki, S.
History
DepositionJul 16, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.2Oct 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
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nodule Cysteine-Rich (NCR) secreted peptide


Theoretical massNumber of molelcules
Total (without water)4,6311
Polymers4,6311
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4270 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1target function

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Components

#1: Protein/peptide Nodule Cysteine-Rich (NCR) secreted peptide / Nodule-specific cysteine-rich peptide 169


Mass: 4630.519 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Medicago truncatula (barrel medic) / Gene: MTR_7g029760 / Production host: Escherichia coli (E. coli) / References: UniProt: A7KHA7
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H TOCSY
121isotropic12D 1H-1H NOESY
132isotropic12D 1H-15N HSQC
142isotropic13D 1H-15N TOCSY
152isotropic13D 1H-15N NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.7 mM peptide, 90% H2O/10% D2Olabel-free90% H2O/10% D2O
solution20.4 mM [U-99% 15N] peptide, 90% H2O/10% D2O15N_sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.7 mMpeptidenatural abundance1
0.4 mMpeptide[U-99% 15N]2
Sample conditionsIonic strength: 0 mM / Label: condition_1 / pH: 2.2 / Pressure: 1 atm / 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: CYANA / Developer: Guntert P. / Classification: refinement
RefinementMethod: na / Software ordinal: 1
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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