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- PDB-1nb1: High resolution solution structure of kalata B1 -

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Basic information

Entry
Database: PDB / ID: 1nb1
TitleHigh resolution solution structure of kalata B1
Componentskalata B1
KeywordsANTIBIOTIC / cyclotide / cyclic backbone / cystine knot / CCK / insecticidal
Function / homologyCyclotide, moebius, conserved site / Cyclotides Moebius subfamily signature. / Cyclotides profile. / Cyclotide / Cyclotide superfamily / Cyclotide family / killing of cells of another organism / defense response to bacterium / Kalata-B1
Function and homology information
Biological speciesOldenlandia affinis (plant)
MethodSOLUTION NMR / Structures were calculated using torsion angle dynamics, refined in explicit solvent using cartesian dynamics, powell restrained 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 1, 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

Downloads & links

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Assembly

Deposited unit
A: kalata B1


Theoretical massNumber of molelcules
Total (without water)2,9171
Polymers2,9171
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 least restraint violations, structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide kalata B1


Mass: 2917.345 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-29 / Source method: isolated from a natural source / Source: (natural) Oldenlandia affinis (plant) / References: UniProt: P56254

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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 NMR techniques

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Sample preparation

Details
Solution-IDContentsSolvent system
15mM of peptide in 0.5ml90% H2O/10% D2O
25mM of peptide in 0.5ml100% D2O
Sample conditionsIonic strength: 0 / pH: 6.1 / 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 calculated using torsion angle dynamics, refined in explicit solvent using cartesian dynamics, powell restrained 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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