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- PDB-2n0v: Backbone 1H, Chemical Shift Assignments for Cn-APM1 -

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Basic information

Entry
Database: PDB / ID: 2n0v
TitleBackbone 1H, Chemical Shift Assignments for Cn-APM1
ComponentsAntimicrobial peptide 1
KeywordsANTIMICROBIAL PROTEIN
Function / homologydefense response to Gram-negative bacterium / defense response to Gram-positive bacterium / extracellular space / Antimicrobial peptide 1
Function and homology information
Biological speciesCocos nucifera (coconut palm)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsSantana, M.J. / Oliveira, A.L. / Queiroz Jr., L.K. / Mandal, S.M. / Matos, C.O. / Dias, R.O. / Franco, O.L. / Liao, L.M.
CitationJournal: Febs Lett. / Year: 2015
Title: Structural insights into Cn-AMP1, a short disulfide-free multifunctional peptide from green coconut water.
Authors: Santana, M.J. / de Oliveira, A.L. / Queiroz Junior, L.H. / Mandal, S.M. / Matos, C.O. / Dias, R.O. / Franco, O.L. / Liao, L.M.
History
DepositionMar 17, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 23, 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 / pdbx_nmr_spectrometer / 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 / _pdbx_nmr_spectrometer.model / _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: Antimicrobial peptide 1


Theoretical massNumber of molelcules
Total (without water)8751
Polymers8751
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Antimicrobial peptide 1 / Cn-AMP1


Mass: 875.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Cocos nucifera (coconut palm) / References: UniProt: P86705

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1212D 1H-1H TOCSY
NMR detailsText: The structure was determined using a combination of NOE and residual dipolar coupling data

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Sample preparation

DetailsContents: 1.0 mM Peptide, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 1.0 mM / Component: Peptide-1
Sample conditionspH: 3.97 / Pressure: ambient / Temperature: 298.15 K

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NMR measurement

NMR spectrometerType: Bruker Avance III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.38Schwieters, Kuszewski, Tjandra and Clorechemical shift assignment
X-PLOR NIH2.38Schwieters, Kuszewski, Tjandra and Cloredata analysis
X-PLOR NIHrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 118 / NOE intraresidue total count: 43 / NOE long range total count: 0 / NOE medium range total count: 42 / NOE sequential total count: 33
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0.5 Å / Maximum upper distance constraint violation: 0.5 Å / Representative conformer: 1
NMR ensemble rmsDistance rms dev: 0.43 Å / Distance rms dev error: 0.16 Å

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