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- PDB-2mfs: Solution NMR structure of the cactus-derived antimicrobial peptid... -

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Basic information

Entry
Database: PDB / ID: 2mfs
TitleSolution NMR structure of the cactus-derived antimicrobial peptide Ep-AMP1
ComponentsEp-AMP1
KeywordsANTIMICROBIAL PROTEIN / cystine-knot
Biological speciesSynthetic (others)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsRosengren, K. / Goransson, U. / Gunasekera, S. / Aboye, T.L.
CitationJournal: Chembiochem / Year: 2015
Title: A cactus-derived toxin-like cystine knot Peptide with selective antimicrobial activity.
Authors: Aboye, T.L. / Stromstedt, A.A. / Gunasekera, S. / Bruhn, J.G. / El-Seedi, H. / Rosengren, K.J. / Goransson, U.
History
DepositionOct 22, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2015Group: Database references
Revision 1.2May 6, 2015Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / 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_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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: Ep-AMP1


Theoretical massNumber of molelcules
Total (without water)3,6111
Polymers3,6111
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)20 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Ep-AMP1


Mass: 3611.230 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This peptide was assembled using standard Fmoc based solid phase peptide synthesis.
Source: (synth.) Synthetic (others)
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D 1H-1H NOESY
1312D DQF-COSY
1422D 1H-1H TOCSY
1522D 1H-1H NOESY
1622D 1H-13C HSQC
1722D 1H-1H ECOSY

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Sample preparation

Details
Solution-IDContentsSolvent system
16 mg/mL Ep-AMP1, 90% H2O/10% D2O90% H2O/10% D2O
24 mg/mL Ep-AMP1, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
6 mg/mLEp-AMP1-11
4 mg/mLEp-AMP1-22
Sample conditionsIonic strength: 0 / pH: 3 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospincollection
TopSpin2.1Bruker Biospinprocessing
XEASYBartels et al.data analysis
XEASYBartels et al.peak picking
XEASYBartels et al.chemical shift assignment
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Simulated annealing followed by refinement and energy minimization in explicit solvent.
NMR constraintsNOE constraints total: 347 / NOE intraresidue total count: 0 / NOE long range total count: 142 / NOE medium range total count: 51 / NOE sequential total count: 154 / Hydrogen bond constraints total count: 30 / Protein chi angle constraints total count: 7 / Protein phi angle constraints total count: 23 / Protein psi angle constraints total count: 22
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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