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- PDB-7deh: Solution structure of cecropin P1 in dodecylphosphocholine micelles -

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Basic information

Entry
Database: PDB / ID: 7deh
TitleSolution structure of cecropin P1 in dodecylphosphocholine micelles
ComponentsCecropin-P1
KeywordsANTIMICROBIAL PROTEIN / cecropin P1 / calmodulin-fusion / antimicrobial peptides
Function / homologyantimicrobial peptide secretion / Cecropin family signature. / Cecropin / Cecropin family / antibacterial humoral response / defense response to bacterium / extracellular region / Cecropin-P1
Function and homology information
Biological speciesAscaris suum (pig roundworm)
MethodSOLUTION NMR / simulated annealing
AuthorsGu, H. / Kumeta, H. / Aizawa, T.
CitationJournal: Acs Omega / Year: 2022
Title: Three-Dimensional Structure of the Antimicrobial Peptide Cecropin P1 in Dodecylphosphocholine Micelles and the Role of the C-Terminal Residues
Authors: Gu, H. / Kato, T. / Kumeta, H. / Kumaki, Y. / Tsukamoto, T. / Kikukawa, T. / Demura, M. / Ishida, H. / Vogel, H.J. / Aizawa, T.
History
DepositionNov 4, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 17, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cecropin-P1


Theoretical massNumber of molelcules
Total (without water)3,3461
Polymers3,3461
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area3110 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20all calculated structures submitted
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Cecropin-P1


Mass: 3345.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ascaris suum (pig roundworm) / Gene: ASCEC-1 / Production host: Escherichia coli (E. coli) / References: UniProt: P14661

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111anisotropic12D 1H-15N HSQC
1101anisotropic12D 1H-13C HSQC
121anisotropic12D 1H-1H NOESY
1111anisotropic13D 1H-13C NOESY
1121anisotropic13D CBCA(CO)NH
191anisotropic13D C(CO)NH
161anisotropic13D HNCA
151anisotropic13D HN(CA)CB
131anisotropic13D HN(CO)CA
141anisotropic13D HNCO
171anisotropic13D HBHA(CO)NH
181anisotropic13D (H)CCH-TOCSY

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Sample preparation

DetailsType: solution
Contents: 1 mM [U-13C; U-15N] Cecropin P1, 40 mM [U-2H] DPC, 90% H2O/10% D2O
Label: 15N13C_sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMCecropin P1[U-13C; U-15N]1
40 mMDPC[U-2H]1
Sample conditionsIonic strength: 42 mM / Label: conditions_1 / pH: 5.0 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Agilent Direct Drive / Manufacturer: Agilent / Model: Direct Drive / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
SparkyGoddardchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxchemical shift calculation
VNMRVariancollection
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / Conformers submitted total number: 20

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