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- PDB-1nbj: High-resolution solution structure of cycloviolacin O1 -

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Basic information

Entry
Database: PDB / ID: 1nbj
TitleHigh-resolution solution structure of cycloviolacin O1
Componentscycloviolacin O1
KeywordsPLANT PROTEIN / cyclotide / cyclic backbone / cystine knot / CCK
Function / homologyCyclotide, bracelet, conserved site / Cyclotides bracelet subfamily signature. / Cyclotides profile. / Cyclotide / Cyclotide superfamily / Cyclotide family / defense response / Cycloviolacin-O1
Function and homology information
Biological speciesViola odorata (plant)
MethodSOLUTION NMR / Structures were generated using torsion angle dynamics, refined in explicit water using Cartesian dynamics, restrained powell minimisation
AuthorsRosengren, K.J. / Daly, N.L. / Plan, M.R. / Waine, C. / Craik, D.J.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Twists, Knots, and Rings in Proteins. STRUCTURAL DEFINITION OF THE CYCLOTIDE FRAMEWORK.
Authors: Rosengren, K.J. / Daly, N.L. / Plan, M.R. / Waine, C. / Craik, D.J.
History
DepositionDec 2, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 18, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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
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: cycloviolacin O1


Theoretical massNumber of molelcules
Total (without water)3,1421
Polymers3,1421
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 / 50structures with the least restraint violations, structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide cycloviolacin O1


Mass: 3141.686 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Viola odorata (plant) / References: UniProt: P82230

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DQF-COSY
1212D TOCSY
1322D TOCSY
1412D NOESY
1522D NOESY
162E-COSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques

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Sample preparation

Details
Solution-IDContentsSolvent system
11.3mM in total volume of 0.5ml90% H2O/10% D2O
21.3mM in total volume of 0.5ml100% D2O
Sample conditionsIonic strength: 0 / pH: 5.5 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX7501
Bruker ARXBrukerARX5002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
XEASY1.3.7Eccles C., Guntert P., Billeter M. and Wuthrich K.data analysis
DYANA1.5Guntert P., Mumenthaler C. and Wuthrich K.structure solution
CNS1Brunger A.T., Adams P.D., Clore G.M., DeLano W.L., Gros P., Grosse-Kunstleve R.W., Jiang J.S., Kuszewski J., Nilges M., Pannu N.S., Read R.J., Rice L.M., Simonson T. and Warren G.L.refinement
RefinementMethod: Structures were generated using torsion angle dynamics, refined in explicit water using Cartesian dynamics, restrained powell minimisation
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations, structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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