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- PDB-1df6: 1H NMR SOLUTION STRUCTURE OF CYCLOVIOLACIN O1 -

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Basic information

Entry
Database: PDB / ID: 1df6
Title1H NMR SOLUTION STRUCTURE OF CYCLOVIOLACIN O1
ComponentsCYCLOVIOLACIN O1
KeywordsPLANT PROTEIN / CYCLIC CYSTINE KNOT / BACKBONE CYCLIC / 3-10 HELIX / DOUBLE-STRANDED ANTI- PARALLEL BETA-SHEET / HAIRPIN BENDS / LOOPS
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 / DISTANCE GEOMETRY, SIMULATED ANNEALING, MOLECULAR DYNAMICS
AuthorsCraik, D.J. / Daly, N.L. / Bond, T. / Waine, C.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: Plant cyclotides: A unique family of cyclic and knotted proteins that defines the cyclic cystine knot structural motif.
Authors: Craik, D.J. / Daly, N.L. / Bond, T. / Waine, C.
History
DepositionNov 17, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 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
Revision 1.4Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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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)16 / 50STRUCTURES WITH ACCEPTABLE COVALENT GEOMETRY,STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS,STRUCTURES WITH THE LOWEST ENERGY
RepresentativeModel #16fewest violations,lowest 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 / Details: LEAVES, STEMS AND FLOWERS / Source: (natural) Viola odorata (plant) / References: UniProt: P82230
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121DQF-COSY
131TOCSY
142E-COSY
1522D NOESY
162TOCSY
NMR detailsText: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D HOMONUCLEAR TECHNIQUES.

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Sample preparation

Details
Solution-IDContents
11.6MM CYCLOVIOLACIN O1 1H
21.6MM CYCLOVIOLACIN O1 1H
Sample conditionspH: 3.6 / Pressure: AMBIENT / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AMX / Manufacturer: Bruker / Model: AMX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR1.3BRUKERcollection
XwinNMR1.3BRUKERdata analysis
XwinNMR1.3BRUKERprocessing
X-PLOR3.1BRUNGERrefinement
X-PLOR3.1BRUNGERstructure solution
RefinementMethod: DISTANCE GEOMETRY, SIMULATED ANNEALING, MOLECULAR DYNAMICS
Software ordinal: 1
Details: THE STRUCTURES WERE GENERATED USING 564 INTER-PROTON DISTANCE RESTRAINTS DERIVED FROM 230 INTRA-RESIDUAL, 141 SEQUENTIAL, 108 MEDIUM RANGE AND 85 LONG RANGE NOE INTENSITIES. THESE DISTANCE ...Details: THE STRUCTURES WERE GENERATED USING 564 INTER-PROTON DISTANCE RESTRAINTS DERIVED FROM 230 INTRA-RESIDUAL, 141 SEQUENTIAL, 108 MEDIUM RANGE AND 85 LONG RANGE NOE INTENSITIES. THESE DISTANCE RESTRAINTS WERE SUPPLEMENTED WITH 17 BACKBONE AND 7 SIDE-CHAIN DIHEDRAL ANGLE RESTRAINTS FROM SPIN-SPIN COUPLING CONSTANTS.
NMR representativeSelection criteria: fewest violations,lowest energy
NMR ensembleConformer selection criteria: STRUCTURES WITH ACCEPTABLE COVALENT GEOMETRY,STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS,STRUCTURES WITH THE LOWEST ENERGY
Conformers calculated total number: 50 / Conformers submitted total number: 16

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