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- PDB-1pt4: Solution structure of the Moebius cyclotide kalata B2 -

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Basic information

Entry
Database: PDB / ID: 1pt4
TitleSolution structure of the Moebius cyclotide kalata B2
Componentskalata B2
KeywordsANTIBIOTIC / cyclotide / kalata / circular protein / cyclic cystine knot / CCK
Function / homologyCyclotide, moebius, conserved site / Cyclotides Moebius subfamily signature. / Cyclotides profile. / Cyclotide / Cyclotide superfamily / Cyclotide family / defense response / killing of cells of another organism / Kalata-B2
Function and homology information
Biological speciesOldenlandia affinis (plant)
MethodSOLUTION NMR / Simulated annealing using both torsion angle, Cartesian dynamics.
AuthorsJennings, C.V. / Anderson, M.A. / Daly, N.L. / Rosengren, K.J. / Craik, D.J.
CitationJournal: Biochemistry / Year: 2005
Title: Isolation, Solution Structure, and Insecticidal Activity of Kalata B2, a Circular Protein with a Twist: Do Mobius Strips Exist in Nature?(,)
Authors: Jennings, C.V. / Rosengren, K.J. / Daly, N.L. / Plan, M. / Stevens, J. / Scanlon, M.J. / Waine, C. / Norman, D.G. / Anderson, M.A. / Craik, D.J.
History
DepositionJun 23, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 10, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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
Revision 1.4Oct 30, 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: kalata B2


Theoretical massNumber of molelcules
Total (without water)2,9801
Polymers2,9801
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 lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide kalata B2


Mass: 2980.400 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oldenlandia affinis (plant) / Strain: DC / References: UniProt: P58454
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
2112D TOCSY
2212D NOESY
231DQF-COSY
2422D TOCSY
2522D NOESY
1612D TOCSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

Details
Solution-IDContentsSolvent system
12mM kalata B2 in 0.5ml70% H2O, 20% CH3CN, 10% D2O
22mM kalata B2 in 0.5ml80% D2O, 20% CH3CN
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
104ambient 290 K
204ambient 298 K

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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 ARXBrukerARX5001
Bruker DMXBrukerDMX7502

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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
CNS1refinement
RefinementMethod: Simulated annealing using both torsion angle, Cartesian dynamics.
Software ordinal: 1
Details: Structure was calculated using torsion angle dynamics within CNS and subsequently refined and energy minimised in a water shell using Cartesian dynamics in CNS according to protocols by Linge and Nilges (ARIA).
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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