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- PDB-2gj0: Cycloviolacin O14 -

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Basic information

Entry
Database: PDB / ID: 2gj0
TitleCycloviolacin O14
ComponentsCycloviolacin O14
KeywordsPLANT PROTEIN / Cyclotide
Function / homologyCyclotides profile. / Cyclotide / Cyclotide superfamily / Cyclotide family / hemolysis in another organism / defense response / Cycloviolacin-O14
Function and homology information
Biological speciesViola odorata (plant)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics, molecular dynamics, energy minimization
AuthorsIreland, D.C. / Colgrave, M.L. / Craik, D.J.
CitationJournal: Biochem.J. / Year: 2006
Title: A novel suite of cyclotides from Viola odorata: sequence variation and the implications for structure, function and stability
Authors: Ireland, D.C. / Colgrave, M.L. / Craik, D.J.
History
DepositionMar 30, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 11, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cycloviolacin O14


Theoretical massNumber of molelcules
Total (without water)3,2081
Polymers3,2081
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Cycloviolacin O14


Mass: 3207.767 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Viola odorata (plant) / References: UniProt: P85177

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D TOCSY
1212D NOESY
131DQF-COSY
2412D NOESY
152E-COSY
162HSQC
NMR detailsText: Temperature coefficient calculated by TOCSY through temperatures 280-320K

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5mM cycloviolacin O14 in 90% H2O 10% D2O90% H2O/10% D2O
21.5mM cycloviolacin O14 in 100% D2O100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
11 3.5 ambient 290 K
21 3.5 ambient 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker ARXBrukerARX5001
Bruker ARXBrukerARX6002

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Processing

NMR software
NameVersionDeveloperClassification
DIANA1.5Guntert et alrefinement
CNS1.1Brunger et alrefinement
Sparky3.11Goddard and Knellerprocessing
RefinementMethod: simulated annealing, torsion angle dynamics, molecular dynamics, energy minimization
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: 20

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