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- PDB-1wn8: NMR Structure of OaNTR -

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Basic information

Entry
Database: PDB / ID: 1wn8
TitleNMR Structure of OaNTR
ComponentsKalata B3/B6
KeywordsPLANT PROTEIN / helix
Function / homologyCyclotide, moebius, conserved site / Cyclotides Moebius subfamily signature. / Cyclotides profile. / Cyclotide / Cyclotide superfamily / Cyclotide family / hemolysis in another organism / defense response / Kalata-B3/B6
Function and homology information
MethodSOLUTION NMR / simulated annealing, molecular dynamics
AuthorsDutton, J.L. / Renda, R.F. / Waine, C. / Clark, R.J. / Daly, N.L. / Jennings, C.V. / Anderson, M.A. / Craik, D.J.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Conserved structural and sequence elements implicated in the processing of gene-encoded circular proteins
Authors: Dutton, J.L. / Renda, R.F. / Waine, C. / Clark, R.J. / Daly, N.L. / Jennings, C.V. / Anderson, M.A. / Craik, D.J.
History
DepositionJul 28, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 14, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 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 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kalata B3/B6


Theoretical massNumber of molelcules
Total (without water)2,4421
Polymers2,4421
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 lowest energy
RepresentativeModel #8closest to the average

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Components

#1: Protein/peptide Kalata B3/B6 / OaNTR protein


Mass: 2441.924 Da / Num. of mol.: 1 / Fragment: N-terminal repeat / Source method: obtained synthetically
Details: syn peptide based on N-terminal repeat sequence of cyclotide precursors from the plant Oldenlandia affinis
References: UniProt: P58455

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
131DQF-COSY
1422D NOESY
152E-COSY
1622D TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
15mM peptide, 90% H2O, 10% D2O, pH 3.690% H2O/10% D2O
25mM peptide, 100% D2O, pH 3.6100% D2O
Sample conditionspH: 3.6 / Pressure: ambient / Temperature: 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 DMXBrukerDMX7501
Bruker AMXBrukerAMX5002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Brukercollection
X-PLOR3.851Brungerstructure solution
CNS1refinement
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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