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- PDB-7th8: Chickpea (Cicer arientinum) nodule-specific cysteine-rich peptide... -

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Basic information

Entry
Database: PDB / ID: 7th8
TitleChickpea (Cicer arientinum) nodule-specific cysteine-rich peptide NCR13: Solution NMR structure of the isomer with C4:C10, C15:C30, and C23:C28 disulfide bonds
ComponentsNodule cysteine-rich protein 13
KeywordsANTIFUNGAL PROTEIN / NCR peptide / antifungal activity / endosymbiotic / disulfide-rich / ANTIMICROBIAL PROTEIN
Biological speciesCicer arientinum (chickpea)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsBuchko, G.W. / Zhou, M. / Shah, D.M. / Velivelli, S.L.S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Chickpea (Cicer arientinum) nodule-specific cysteine-rich peptide NCR13: Solution NMR structure of the isomer with C4:C10, C15:C30, and C23:C28 disulfide bonds
Authors: Buchko, G.W. / Zhou, M. / Shah, D.M. / Velivelli, S.L.S.
History
DepositionJan 10, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nodule cysteine-rich protein 13


Theoretical massNumber of molelcules
Total (without water)3,7421
Polymers3,7421
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry, There is no evidence that NCR013 self-assembles.
TypeNameSymmetry operationNumber
identity operation1_5551
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 protein 13


Mass: 3741.605 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cicer arientinum (chickpea) / Production host: Komagataella pastoris (fungus)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
113anisotropic22D 1H-15N HSQC
122anisotropic22D 1H-1H NOESY
132anisotropic22D 1H-1H TOCSY
143anisotropic13D 1H-15N NOESY
153anisotropic13D 1H-15N TOCSY
1112anisotropic22D 1H-1H COSY
1102anisotropic12D 1H-15N HSQC
192anisotropic12D 1H-13C HSQC aliphatic

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution220 mM sodium acetate, 50 mM sodium chloride, 1 mM [U-98% 15N] Def13_B2, 100% D2ODef13_B2100% D2O
solution320 mM sodium acetate, 50 mM sodium chloride, 1 mM [U-98% 15N] Def13_B2, 93% H2O/7% D2ODef13_B293% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMsodium acetatenatural abundance2
50 mMsodium chloridenatural abundance2
1 mMDef13_B2[U-98% 15N]2
20 mMsodium acetatenatural abundance3
50 mMsodium chloridenatural abundance3
1 mMDef13_B2[U-98% 15N]3
Sample conditionsIonic strength: 70 mM / Ionic strength err: 1 / Label: Def13 / pH: 5.3 / PH err: 0.1 / Pressure: 1 atm / Temperature: 293 K / Temperature err: 0.5

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Bruker AVANCE IIIBrukerAVANCE III7502

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Processing

NMR software
NameVersionDeveloperClassification
Felix75Accelrys Software Inc.processing
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure calculation
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
NMRFAM-SPARKY3.135bobdata analysis
PSVS1.5Bhattacharya and Montelionedata analysis
PdbStatunknownprocessing
RefinementMethod: torsion angle dynamics / Software ordinal: 3
Details: The structure was first solved using CYANA with the deposited structure refined in explicit water
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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