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- PDB-2mp9: Solution structure of an potent antifungal peptide Cm-p5 derived ... -

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Basic information

Entry
Database: PDB / ID: 2mp9
TitleSolution structure of an potent antifungal peptide Cm-p5 derived from C. muricatus
ComponentsAntifungal peptide
KeywordsANTIMICROBIAL PROTEIN / helical peptide / antimicrobial
Function / homologydefense response to fungus / killing of cells of another organism / Antifungal peptide
Function and homology information
Biological speciesCenchritis muricatus (invertebrata)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model1
AuthorsSun, Z.J. / Heffron, G. / Mcbeth, C. / Wagner, G. / Otero-Gonzales, A.J. / Starnbach, M.N.
CitationJournal: Faseb J. / Year: 2015
Title: Cm-p5: an antifungal hydrophilic peptide derived from the coastal mollusk Cenchritis muricatus (Gastropoda: Littorinidae).
Authors: Lopez-Abarrategui, C. / McBeth, C. / Mandal, S.M. / Sun, Z.J. / Heffron, G. / Alba-Menendez, A. / Migliolo, L. / Reyes-Acosta, O. / Garcia-Villarino, M. / Nolasco, D.O. / Falcao, R. / ...Authors: Lopez-Abarrategui, C. / McBeth, C. / Mandal, S.M. / Sun, Z.J. / Heffron, G. / Alba-Menendez, A. / Migliolo, L. / Reyes-Acosta, O. / Garcia-Villarino, M. / Nolasco, D.O. / Falcao, R. / Cherobim, M.D. / Dias, S.C. / Brandt, W. / Wessjohann, L. / Starnbach, M. / Franco, O.L. / Otero-Gonzalez, A.J.
History
DepositionMay 14, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_conn / struct_ref_seq_dif
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_software.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Antifungal peptide


Theoretical massNumber of molelcules
Total (without water)1,4861
Polymers1,4861
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 20structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Antifungal peptide / Cm-p1


Mass: 1485.734 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Cenchritis muricatus (invertebrata) / References: UniProt: B3EWI7
Sequence detailsTWO C-TERMINAL RESIDUES LF WAS APPENDED TO THE NATURAL SEQUENCE

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Solution structure of an potent antifungal peptide Cm-p5 derived from C. muricatus determined in 40% TFE
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1212D 1H-1H TOCSY
1312D 1H-15N HSQC
1412D 1H-13C HSQC
NMR detailsText: natural abundance heteronuclear HSQC

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Sample preparation

DetailsContents: 4 mM Cm-p5, 40 % TFE, trifluoroethanol/water / Solvent system: trifluoroethanol/water
Sample
Conc. (mg/ml)ComponentSolution-ID
4 mMCm-p5-11
40 %TFE-21
Sample conditionsPressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Agilent DD2 / Manufacturer: Agilent / Model: DD2 / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CARAKeller and Wuthrichchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 131 / NOE intraresidue total count: 67 / NOE long range total count: 0 / NOE medium range total count: 22 / NOE sequential total count: 42
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 10 / Maximum lower distance constraint violation: 0 Å / Maximum upper distance constraint violation: 0.25 Å
NMR ensemble rmsDistance rms dev: 0.0597 Å / Distance rms dev error: 0.0006 Å

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