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- PDB-1r1f: Solution Structure of the Cyclotide Palicourein: Implications for... -

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Basic information

Entry
Database: PDB / ID: 1r1f
TitleSolution Structure of the Cyclotide Palicourein: Implications for the development of pharmaceutical and agricultural applications
ComponentsPalicourein
KeywordsPLANT PROTEIN / Palicourein / Cyclotide
Function / homologyCyclotide / Cyclotide superfamily / Cyclotide family / defense response / Palicourein
Function and homology information
Biological speciesPalicourea condensata (plant)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
AuthorsBarry, D.G. / Daly, N.L. / Bokesch, H.R. / Gustafson, K.R. / Craik, D.J.
CitationJournal: STRUCTURE / Year: 2004
Title: Solution structure of the cyclotide palicourein: implications for the development of a pharmaceutical framework.
Authors: Barry, D.G. / Daly, N.L. / Bokesch, H.R. / Gustafson, K.R. / Craik, D.J.
History
DepositionSep 23, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation / Refinement description
Category: database_2 / diffrn ...database_2 / diffrn / diffrn_radiation / diffrn_radiation_wavelength / pdbx_nmr_exptl_sample / pdbx_nmr_refine / pdbx_nmr_sample_details / pdbx_nmr_software / pdbx_nmr_spectrometer / 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_refine.software_ordinal / _pdbx_nmr_sample_details.contents / _pdbx_nmr_sample_details.label / _pdbx_nmr_sample_details.solvent_system / _pdbx_nmr_sample_details.type / _pdbx_nmr_software.authors / _pdbx_nmr_software.classification / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag
Remark 999SEQUENCE The sequence of the protein was not deposited into any sequence database.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Palicourein


Theoretical massNumber of molelcules
Total (without water)3,9321
Polymers3,9321
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50lowest energy structures
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Palicourein


Mass: 3932.447 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Palicourea condensata (plant) / References: UniProt: P84645

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D TOCSY
1212D NOESY
232E-COSY

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Sample preparation

DetailsType: solution / Contents: 3.8 mM Palicourein, 90% H2O, 10% D2O / Label: sample_1 / Solvent system: 90% H2O/10% D2O
SampleConc.: 3.8 mM / Component: Palicourein / Isotopic labeling: natural abundance
Sample conditionspH: 4.0 / Pressure: ambient / Temperature: 295 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX7501
Bruker ARXBrukerARX5002

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Processing

NMR software
NameDeveloperClassification
DYANAGuntert, Braun and Wuthrichstructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: lowest energy structures / Conformers calculated total number: 50 / Conformers submitted total number: 20

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