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- PDB-2jwm: NMR spatial srtucture of ternary complex kalata B7/Mn2+/DPC micelle -

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Basic information

Entry
Database: PDB / ID: 2jwm
TitleNMR spatial srtucture of ternary complex kalata B7/Mn2+/DPC micelle
ComponentsKalata-B7
KeywordsPLANT PROTEIN / cyclotide / cyctine knot / divalent cation-binding site / Cytolysis / Hemolysis / Knottin / Plant defense
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-B7
Function and homology information
Biological speciesOldenlandia affinis (plant)
MethodSOLUTION NMR / simulated annealing
AuthorsNadezhdin, K.D. / Shenkarev, Z.O. / Skjeldal, L. / Arseniev, A.S.
CitationJournal: J.Inorg.Biochem. / Year: 2008
Title: Divalent cation coordination and mode of membrane interaction in cyclotides: NMR spatial structure of ternary complex Kalata B7/Mn(2+)/DPC micelle
Authors: Shenkarev, Z.O. / Nadezhdin, K.D. / Lyukmanova, E.N. / Sobol, V.A. / Skjeldal, L. / Arseniev, A.S.
History
DepositionOct 16, 2007Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Mar 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 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
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-B7


Theoretical massNumber of molelcules
Total (without water)3,0981
Polymers3,0981
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 / 100target function
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide Kalata-B7


Mass: 3097.612 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oldenlandia affinis (plant) / References: UniProt: P58457

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D DQF-COSY
1312D 1H-1H NOESY
2411D 1H
3522D 1H-1H NOESY
3621D invertion-recovery

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Sample preparation

Details
Solution-IDContentsSolvent system
11.6mM kalata B7, 90% H2O/10% D2O90% H2O/10% D2O
20.6mM kalata B7, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
1.6 mMkalata B71
0.6 mMkalata B72
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10 2.6 ambient 303 K
22.6 313 K
35.0 313 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UnityVarianUNITY6001
Bruker DRXBrukerDRX5002

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Processing

NMR software
NameVersionDeveloperClassification
XEASYBartels et al.chemical shift assignment
XEASYBartels et al.peak picking
VNMRVariancollection
VNMRVarianprocessing
XwinNMRBruker Biospincollection
XwinNMRBruker Biospinprocessing
CYANA1.1Guntert, Mumenthaler, Wuthrichstructure solution
CYANA1.1Guntert, Mumenthaler, Wuthrichgeometry optimization
CYANA1.1Guntert, Mumenthaler, Wuthrichdata analysis
MOLMOLKoradi, Billeter, Wuthrichgeometry optimization
MOLMOLKoradi, Billeter, Wuthrichpictures preparation
CYANA1.1Guntert, Mumenthaler, Wuthrichrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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