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- PDB-2m6a: NMR spatial structure of the antimicrobial peptide Tk-Amp-X2 -

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Basic information

Entry
Database: PDB / ID: 2m6a
TitleNMR spatial structure of the antimicrobial peptide Tk-Amp-X2
ComponentsPredicted proteinProtein structure prediction
KeywordsANTIMICROBIAL PROTEIN
Function / homologyPlant antimicrobial peptide / Plant antimicrobial peptide / defense response to fungus / Uncharacterized protein
Function and homology information
Biological speciesHordeum vulgare subsp. vulgare (domesticated barley)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model1
AuthorsUsmanova, D.R. / Mineev, K.S. / Arseniev, A.S. / Berkut, A.A. / Oparin, P.B. / Grishin, E.V. / Vassilevski, A.A.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structural similarity between defense peptide from wheat and scorpion neurotoxin permits rational functional design
Authors: Berkut, A.A. / Usmanova, D.R. / Peigneur, S. / Oparin, P.B. / Mineev, K.S. / Odintsova, T.I. / Tytgat, J. / Arseniev, A.S. / Grishin, E.V. / Vassilevski, A.A.
History
DepositionMar 28, 2013Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2014Group: Database references
Revision 1.2Nov 29, 2017Group: Derived calculations / Category: struct_conf / struct_conf_type
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Predicted protein


Theoretical massNumber of molelcules
Total (without water)3,5331
Polymers3,5331
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / -structures with the least restraint violations
RepresentativeModel #1

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Components

#1: Protein/peptide Predicted protein / Protein structure prediction


Mass: 3533.104 Da / Num. of mol.: 1 / Fragment: UNP residues 129-154
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hordeum vulgare subsp. vulgare (domesticated barley)
Production host: Escherichia coli (E. coli) / References: UniProt: F2EGM1*PLUS
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: NOESY

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Sample preparation

Sample conditionsPressure: AMBIENT / Temperature units: K

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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
NameDeveloperClassification
CYANA 3.0P.GUNTERT ET AL.refinement
CYANA 3.0structure solution
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 312 / NOE intraresidue total count: 192 / NOE long range total count: 4 / NOE medium range total count: 41 / NOE sequential total count: 75 / Protein chi angle constraints total count: 156 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 108 / Protein psi angle constraints total count: 0
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers submitted total number: 10

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