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- PDB-6u6g: Solution NMR structure of the nodule-specific cysteine-rich pepti... -

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Basic information

Entry
Database: PDB / ID: 6u6g
TitleSolution NMR structure of the nodule-specific cysteine-rich peptide NCR044 from Medicago truncatula
ComponentsPutative Late nodulin
KeywordsANTIFUNGAL PROTEIN / FUNGAL DISEASE / ANTIFUNGAL AGENT / DEFENSIN-LIKE
Function / homologyLate nodulin / Late nodulin domain / membrane => GO:0016020 / metal ion binding / Putative Late nodulin
Function and homology information
Biological speciesMedicago truncatula (barrel medic)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsVelivelli, S.L.S. / Buchko, G.W. / Shah, D.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Antifungal symbiotic peptide NCR044 exhibits unique structure and multifaceted mechanisms of action that confer plant protection.
Authors: Velivelli, S.L.S. / Czymmek, K.J. / Li, H. / Shaw, J.B. / Buchko, G.W. / Shah, D.M.
History
DepositionAug 29, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 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 1.3Mar 27, 2024Group: Data collection / Source and taxonomy / Structure summary
Category: audit_author / chem_comp_atom ...audit_author / chem_comp_atom / chem_comp_bond / entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative Late nodulin


Theoretical massNumber of molelcules
Total (without water)4,3291
Polymers4,3291
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Don't know what the matrix stuff means below.
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)19 / 100target function
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Putative Late nodulin


Mass: 4329.222 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Medicago truncatula (barrel medic) / Gene: MtrunA17_Chr7g0216231 / Production host: Pichia pastoris (fungus) / References: UniProt: A0A396GSL0

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111anisotropic22D 1H-15N HSQC
121anisotropic13D HNCO
131anisotropic13D HN(CA)CB
141anisotropic13D C(CO)NH
151anisotropic22D 1H-13C HSQC aliphatic
162anisotropic33D 1H-13C NOESY aliphatic
171anisotropic33D 1H-13C NOESY aromatic
191anisotropic23D 1H-15N NOESY
181anisotropic2Deuterium exchange
1101anisotropic23D 1H-13C NOESY aliphatic
1111anisotropic13D H(CCO)NH

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution150 mM sodium chloride, 20 mM sodium acetate, 1 mM [U-99% 13C; U-99% 15N] DEF19, 93% H2O/7% D2ODEF1993% H2O/7% D2O
solution250 mM sodium chloride, 20 mM sodium acetate, 1 mM [U-99% 13C; U-99% 15N] DEF19-2, 100% D2ODEF19-2100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
50 mMsodium chloridenatural abundance1
20 mMsodium acetatenatural abundance1
1 mMDEF19[U-99% 13C; U-99% 15N]1
50 mMsodium chloridenatural abundance2
20 mMsodium acetatenatural abundance2
1 mMDEF19-2[U-99% 13C; U-99% 15N]2
Sample conditionsIonic strength: 70 mM / Ionic strength err: 2 / Label: Condition_1 / pH: 5.4 / PH err: 0.1 / Pressure: 1 atm / Temperature: 293 K / Temperature err: 0.25

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Bruker AVANCEBrukerAVANCE7502
Varian INOVAVarianINOVA7503

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Processing

NMR software
NameVersionDeveloperClassification
Sparky3.13Goddarddata analysis
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure calculation
Felix2007Accelrys Software Inc.processing
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
PSVS1.5Bhattacharya and Montelionedata analysis
RefinementMethod: torsion angle dynamics / Software ordinal: 4
Details: STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING CYANA (AUTOMATED NOESY ASSIGNMENTS). A TOTAL OF 20 STRUCTURES OUT OF 100 WITH LOWEST TARGET FUNCTION FROM THE FINAL CYANA CALCULATION ...Details: STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING CYANA (AUTOMATED NOESY ASSIGNMENTS). A TOTAL OF 20 STRUCTURES OUT OF 100 WITH LOWEST TARGET FUNCTION FROM THE FINAL CYANA CALCULATION WERE TAKEN AND REFINED BY RESTRAINED MOLECULAR DYNAMICS/ENERGY MINIMIZATION IN EXPLICIT WATER (CNS) AFTER ADDING 0% TO THE UPPER BOUNDARY LIMIT OF THE DISTANCE RESTRAINTS AND THE VDW LIMIT TO THE LOWER RESTRAINT. PARAM19 WAS USED FOR THE WATER REFINEMENT CALCULATIONS. Disulfide bond restraints were identified by mass spectrometer and are included in the "NOE" file.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 19

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