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- PDB-2kp0: Solution structure of nasonin-1M -

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Basic information

Entry
Database: PDB / ID: 2kp0
TitleSolution structure of nasonin-1M
Componentsnasonin-1M
KeywordsDE NOVO PROTEIN / alpha/beta structure / disulfide bonds
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsKouno, T. / Tian, C. / Luo, L. / Zhu, S. / Mizuguchi, M.
CitationJournal: To be Published
Title: Solution structure of nasonin-1M
Authors: Tian, C. / Kouno, T. / Luo, L. / Mizuguchi, M. / Zhu, S.
History
DepositionOct 4, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Oct 6, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: nasonin-1M


Theoretical massNumber of molelcules
Total (without water)3,6541
Polymers3,6541
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)25 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide nasonin-1M


Mass: 3654.216 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemically synthesized / Source: (synth.) synthetic construct (others)
Compound detailsNASONIN-1M IS A NEWLY DESIGNED PEPTIDE WITH NEUROTOXIC AND ANTIMICROBIAL ACTIVITIES

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Experimental details

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Experiment

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

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Sample preparation

Details
Solution-IDContentsSolvent system
10.25-0.30mM Nasonin-1M; 50mM [U-100% 2H] acetic acid; 20mM sodium chloride; 5% [U-100% 2H] D2O; 95% H2O/5% D2O95% H2O/5% D2O
20.25-0.30mM Nasonin-1M; 50mM [U-100% 2H] acetic acid; 20mM sodium chloride; 100% [U-100% 2H] D2O; 100% D2O100% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMNasonin-1M-10.25-0.301
50 mMacetic acid-2[U-100% 2H]1
20 mMsodium chloride-31
5 %D2O-4[U-100% 2H]1
mMNasonin-1M-50.25-0.302
50 mMacetic acid-6[U-100% 2H]2
20 mMsodium chloride-72
100 %D2O-8[U-100% 2H]2
Sample conditionspH: 3.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
XwinNMRBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardpeak picking
X-PLORBrungerstructure solution
X-PLORBrungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 25 / Representative conformer: 1

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