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- PDB-2nb2: Nigellin-1.1 -

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Basic information

Entry
Database: PDB / ID: 2nb2
TitleNigellin-1.1
Componentsnigellin-1.1
KeywordsANTIMICROBIAL PROTEIN / AMP / antimicrobial peptide / plant antimicrobial peptides / defense peptides / blackseed / antifungal activity / antibacterial activity / hairpin-like peptide / alpha-hairpinin
Function / homologyNigellin-1.1
Function and homology information
Biological speciesNigella sativa L (black cumin)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
Model detailsfewest violations, model1
AuthorsBozin, T.N. / Bocharov, E.V. / Rogozhin, E.A.
CitationJournal: To be Published
Title: A novel type of hairpin-like defense peptides from blackseed (Nigella sativa L.) contains three disulfide bridges
Authors: Rogozhin, E.A. / Kozlov, S.A. / Andreev, Y.A. / Ryazantsev, Y.U. / Grishin, E.V. / Bozin, T.N. / Bocharov, E.V.
History
DepositionJan 20, 2016Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: nigellin-1.1


Theoretical massNumber of molelcules
Total (without water)4,2251
Polymers4,2251
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 / 100target function
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide nigellin-1.1


Mass: 4224.847 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nigella sativa L (black cumin) / References: UniProt: A0A1S4NYD1*PLUS
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-13C HSQC aliphatic
3212D 1H-1H TOCSY
1312D 1H-1H TOCSY
2412D 1H-1H TOCSY
1512D 1H-1H NOESY
1622D DQF-COSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM nigellin-1.1, 50 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
21 mM nigellin-1.1, 50 mM sodium chloride, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
1 mMnigellin-1.1-11
50 mMsodium chloride-21
1 mMnigellin-1.1-32
50 mMsodium chloride-42
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.053.5ambient atm303 K
20.053.5ambient atm310 K
30.053.5ambient atm296 K

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NMR measurement

NMR spectrometerType: Varian Uniform NMR System 700 / Manufacturer: Varian / Model: Uniform NMR System 700 / Field strength: 700 MHz

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Processing

NMR software
NameDeveloperClassification
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichpeak picking
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichrefinement
CYANAGuntert, Mumenthaler and Wuthrichstereospecific assignment
MOLMOLKoradi, Billeter and Wuthrich3d visualization
MOLMOLKoradi, Billeter and Wuthrichdata analysis
MOLMOLKoradi, Billeter and Wuthrichprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
ACMEDelaglio, Zhengrong and Baxcoupling constant measurement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 25

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