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- PDB-5lm0: NMR spatial structure of Tk-hefu peptide -

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Basic information

Entry
Database: PDB / ID: 5lm0
TitleNMR spatial structure of Tk-hefu peptide
ComponentsL-2
KeywordsANTIMICROBIAL PROTEIN / PROTEIN MUTANT PLANT DEFENSE PEPTIDE / PROTEIN / anti microbial protein
Function / homologyPlant antimicrobial peptide / Plant antimicrobial peptide / defense response to fungus / L-2
Function and homology information
Biological speciesTriticum kiharae (plant)
MethodSOLUTION NMR / simulated annealing
AuthorsMineev, K.S. / Berkut, A.A. / Novikova, E.V. / Oparin, P.B. / Grishin, E.V. / Arseniev, A.S. / Vassilevski, A.A.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Federation
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Protein Surface Topography as a tool to enhance the selective activity of a potassium channel blocker.
Authors: Berkut, A.A. / Chugunov, A.O. / Mineev, K.S. / Peigneur, S. / Tabakmakher, V.M. / Krylov, N.A. / Oparin, P.B. / Lihonosova, A.F. / Novikova, E.V. / Arseniev, A.S. / Grishin, E.V. / Tytgat, J. ...Authors: Berkut, A.A. / Chugunov, A.O. / Mineev, K.S. / Peigneur, S. / Tabakmakher, V.M. / Krylov, N.A. / Oparin, P.B. / Lihonosova, A.F. / Novikova, E.V. / Arseniev, A.S. / Grishin, E.V. / Tytgat, J. / Efremov, R.G. / Vassilevski, A.A.
History
DepositionJul 28, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.2Sep 25, 2019Group: Data collection / Database references / Category: citation / pdbx_nmr_spectrometer
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.title / _citation.year / _pdbx_nmr_spectrometer.model
Revision 1.3Oct 2, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.4Jun 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-2


Theoretical massNumber of molelcules
Total (without water)3,5651
Polymers3,5651
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area3000 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide L-2 / Tk-hefu


Mass: 3565.082 Da / Num. of mol.: 1 / Fragment: UNP residues 125-152
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Triticum kiharae (plant) / Gene: l-2 / Production host: Escherichia coli (E. coli) / References: UniProt: R4ZAN8

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic1NOESY
121isotropic12D 1H-1H TOCSY
131isotropic13D 1H-15N NOESY
141isotropic13D 1H-15N TOCSY
151isotropic12D 1H-15N HSQC
161isotropic12D 1H-13C HSQC
171isotropic12D DQF-COSY

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Sample preparation

DetailsType: solution
Contents: 1 mM [U-99% 15N] Tk-hefu, 0.001 % sodium azide, 95% H2O/5% D2O
Label: s1 / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMTk-hefu[U-99% 15N]1
0.001 %sodium azidenatural abundance1
Sample conditionsIonic strength: 20 mM / Ionic strength err: 1 / Label: cond1 / pH: 5.7 / PH err: 0.1 / Pressure: AMBIENT Pa / Temperature: 303 K / Temperature err: 0.01

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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
NameVersionDeveloperClassification
CYANA3.97Guntert, Mumenthaler and Wuthrichstructure calculation
TopSpin3.2Bruker Biospinprocessing
CARA1.9.4Keller and Wuthrichchemical shift assignment
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 10

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