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- PDB-8gxt: Antibacterial peptide, mehamycin -

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Basic information

Entry
Database: PDB / ID: 8gxt
TitleAntibacterial peptide, mehamycin
ComponentsAntibacterial peptide
KeywordsANTIMICROBIAL PROTEIN / STRUCTURE FROM XPLOR-NIH
Function / homologyGamma-thionin family / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like superfamily / defense response / extracellular region / Knot1 domain-containing protein
Function and homology information
Biological speciesMeloidogyne hapla (invertebrata)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsIsozumi, N. / Ohki, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Antibacterial peptide, mehamycin
Authors: Ohki, S. / Isozumi, N.
History
DepositionSep 21, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 27, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Database references / Structure summary
Category: database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Antibacterial peptide


Theoretical massNumber of molelcules
Total (without water)7,0841
Polymers7,0841
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Antibacterial peptide


Mass: 7083.510 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Meloidogyne hapla (invertebrata) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1I8C2Q5
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
112isotropic13D 1H-15N NOESY
122isotropic13D 1H-15N TOCSY
132isotropic12D 1H-1H NOESY
142isotropic12D 1H-1H TOCSY

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Sample preparation

DetailsType: solution / Contents: 0.2 mM unlabeled mehamycin, 90% H2O/10% D2O / Details: 0.2 mM, pH 4.5 / Label: unlabeled / Solvent system: 90% H2O/10% D2O
SampleConc.: 0.2 mM / Component: mehamycin / Isotopic labeling: unlabeled
Sample conditionsDetails: the pH was adjusted to 4.5 with DCl and NaOD / Ionic strength: no Not defined / Label: conditions_1 / pH: 4.5 Not defined / PH err: 0.1 / Pressure: 1 bar / Pressure err: 0.01 / Temperature: 298 K / Temperature err: 0.1

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 800 MHz / Details: TCI-cryoprobe

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Processing

NMR software
NameDeveloperClassification
SparkyGoddardpeak picking
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
SparkyGoddardchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 5
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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