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- PDB-2n92: Solution structure of cecropin P1 with LPS -

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Basic information

Entry
Database: PDB / ID: 2n92
TitleSolution structure of cecropin P1 with LPS
ComponentsCecropin-P1
KeywordsANTIMICROBIAL PROTEIN / antimicrobial peptide / lipopolysaccharide
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 / torsion angle dynamics
Model detailslowest energy, model1
AuthorsBaek, M. / Kamiya, M. / Kushibiki, T. / Nakazumi, T. / Tomisawa, S. / Abe, C. / Kumaki, Y. / Kikukawa, T. / Demura, M. / Kawano, K. / Aizawa, T.
CitationJournal: To be Published
Title: Lipopolysaccharide bound structure of antimicrobial peptide cecropin P1 by NMR spectroscopy
Authors: Baek, M. / Kamiya, M. / Kushibiki, T. / Nakazumi, T. / Tomisawa, S. / Abe, C. / Kumaki, Y. / Kikukawa, T. / Demura, M. / Kawano, K. / Aizawa, T.
History
DepositionNov 4, 2015Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Cecropin-P1


Mass: 3345.914 Da / Num. of mol.: 1 / Fragment: UNP residues 14-44
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-IDType
1132D 1H-15N HSQC
1222D 1H-13C HSQC
1312D 1H-1H TOCSY
1412D 1H-1H COSY
1523D CBCA(CO)NH
1623D C(CO)NH
1723D HNCA
1823D HN(CA)CB
1923D HN(CA)CB
11033D 1H-15N NOESY
11133D 1H-15N TOCSY
11223D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM cp1-1, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-13C; U-15N] cp1-2, 90% H2O/10% D2O90% H2O/10% D2O
31 mM [U-15N] cp1-3, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMcp1-11
1 mMcp1-2[U-13C; U-15N]2
1 mMcp1-3[U-15N]3
Sample conditionsIonic strength: 0 / pH: 5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANArefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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