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- PDB-8ulm: Chickpea (Cicer arientinum) nodule-specific cysteine-rich peptide... -

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Basic information

Entry
Database: PDB / ID: 8ulm
TitleChickpea (Cicer arientinum) nodule-specific cysteine-rich peptide NCR13: Solution NMR structure of the isomer with C4:C23, C15:C30, and C10:C28 disulfide bonds
ComponentsNodule cysteine-rich protein 13
KeywordsANTIFUNGAL PROTEIN / antifunal activity / ENDOSYMBIOTIC / DISULFIDE-RICH / ANTIMICROBIAL PROTEIN / NCR peptide
Function / homologyLate nodulin / Late nodulin domain / metal ion binding / Nodule cysteine-rich protein 13
Function and homology information
Biological speciesCicer arietinum (chickpea)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsBuchko, G.W. / Zhou, M. / Shah, D.M. / Velivelli, S.L.S.
Funding support United States, 1items
OrganizationGrant numberCountry
Other government United States
CitationJournal: To Be Published
Title: Solution NMR structures of the Chickpea (Cicer arientinum) nodule-specific cysteine-rich peptide NCR13 in two different disulfide bonding patterns
Authors: Buchko, G.W. / Zhou, M. / Velivelli, S.L.S. / Shah, D.M.
History
DepositionOct 16, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2023Provider: repository / Type: Initial release

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Structure visualization

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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&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1closest to the average

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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 arietinum (chickpea) / Gene: NCR13 / Production host: Komagataella pastoris (fungus) / References: UniProt: A0A0U8SNQ0

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111anisotropic12D 1H-15N HSQC
122anisotropic12D 1H-13C HSQC aliphatic
132anisotropic12D 1H-13C HSQC aromatic
142anisotropic12D 1H-1H NOESY
152anisotropic12D 1H-1H TOCSY
162anisotropic12D 1H-15N HSQC
1101anisotropic13D 1H-15N TOCSY
191anisotropic12D 1H-1H NOESY
181anisotropic12D 1H-1H TOCSY
1111anisotropic13D 1H-13C NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution120 mM sodium acetate, 50 mM sodium chloride, 93% H2O/7% D2ODEF13_B193% H2O/7% D2O
solution220 mM sodium acetate, 50 mM sodium chloride, 100% D2ODEF13_B1100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMsodium acetatenatural abundance1
50 mMsodium chloridenatural abundance1
20 mMsodium acetatenatural abundance2
50 mMsodium chloridenatural abundance2
Sample conditionsIonic strength: 70 mM / Ionic strength err: 2 / Label: 1 / pH: 5.3 / PH err: 0.1 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Felix2007Accelrys Software Inc.processing
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
PokyManthey, Tonelli, Clos II, Rahimi, Markley and Leepeak picking
PSVS3.135Bhattacharya and Montelionedata analysis
TALOS+unknowndata analysis
RefinementMethod: torsion angle dynamics / Software ordinal: 3
Details: It was not possible to verify the disulfide bonding pattern using mass spectrometry or other methods. Therefore the alphafold predicted disulfide pattern was used in the structure ...Details: It was not possible to verify the disulfide bonding pattern using mass spectrometry or other methods. Therefore the alphafold predicted disulfide pattern was used in the structure calculations. The structure was first solved using CYANA and then refined in explicit water adding 10% to the upper bound of the NOE restraints.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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