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- PDB-2m2h: Solution structure of the antimicrobial peptide [Aba3,7,12,16]BTD-2 -

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Basic information

Entry
Database: PDB / ID: 2m2h
TitleSolution structure of the antimicrobial peptide [Aba3,7,12,16]BTD-2
Components[Aba3,7,12,16]BTD-2
KeywordsANTIMICROBIAL PROTEIN / theta-defensin / cyclic peptides / cyclic cystine ladder / disulfide bond / antimicrobial peptide
Function / homology[Aba3,7,12,16]BTD-2
Function and homology information
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
Model detailslowest energy, model1
AuthorsConibear, A.C. / Rosengren, K. / Daly, N.L. / Troiera Henriques, S. / Craik, D.J.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: The cyclic cystine ladder in theta-defensins is important for structure and stability, but not antibacterial activity.
Authors: Conibear, A.C. / Rosengren, K.J. / Daly, N.L. / Henriques, S.T. / Craik, D.J.
History
DepositionDec 20, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2013Group: Database references
Revision 1.2Jul 10, 2013Group: Database references
Revision 1.3Jun 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 / pdbx_nmr_spectrometer / struct_conn
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 / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: [Aba3,7,12,16]BTD-2


Theoretical massNumber of molelcules
Total (without water)2,0191
Polymers2,0191
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 [Aba3,7,12,16]BTD-2


Type: Cyclic peptide / Class: Antimicrobial / Mass: 2018.510 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: solid phase peptide synthesis / References: [Aba3,7,12,16]BTD-2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Head-to-tail (Arg-Gly) cyclic peptide. Residues 3, 7, 12, and 16 are replaced by alpha-aminobutyric acid.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D 1H-1H NOESY
1322D 1H-13C HSQC
1412D DQF-COSY
1522D 1H-1H ECOSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.6 mM [Aba3,7,12,16]BTD, 10 uM DSS, 90% H2O/10% D2O90% H2O/10% D2O
20.7 mM [Aba3,7,12,16]BTD, 10 uM DSS, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
0.6 mM[Aba3,7,12,16]BTD-2-11
10 uMDSS-21
0.7 mM[Aba3,7,12,16]BTD-2-32
10 uMDSS-42
Sample conditionspH: 4 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
CcpNmr2.1CCPNdata analysis
CcpNmr2.1CCPNchemical shift assignment
CcpNmr2.1CCPNpeak picking
TopSpin2.1Bruker Biospincollection
TopSpin2.1Bruker Biospinprocessing
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
CNS2.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
Details: Structures were calculated using the scripts from the RECOORD database. Used to calculate preliminary structures
NMR constraintsNOE constraints total: 110 / NOE intraresidue total count: 52 / NOE long range total count: 8 / NOE medium range total count: 10 / NOE sequential total count: 40 / Hydrogen bond constraints total count: 16 / Protein chi angle constraints total count: 4 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 16 / Protein psi angle constraints total count: 14
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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