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- PDB-2kch: Solution structure of micelle-bound kalata B2 -

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Basic information

Entry
Database: PDB / ID: 2kch
TitleSolution structure of micelle-bound kalata B2
ComponentsKalata-B2
KeywordsPLANT PROTEIN / cyclic cystine knot / Cytolysis / Hemolysis / Knottin / Oxidation / 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-B2
Function and homology information
Biological speciesOldenlandia affinis (plant)
MethodSOLUTION NMR / molecular dynamics
Model detailslowest energy, model 1
AuthorsWang, C.K.
CitationJournal: Biophys.J. / Year: 2009
Title: Despite a conserved cystine knot motif, different cyclotides have different membrane binding modes.
Authors: Wang, C.K. / Colgrave, M.L. / Ireland, D.C. / Kaas, Q. / Craik, D.J.
History
DepositionDec 21, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Database references / Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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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_5551
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) / References: UniProt: P58454

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D 1H-1H NOESY

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Sample preparation

DetailsContents: 2 mM Kalata-B2, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 2 mM / Component: Kalata-B2
Sample conditionsIonic strength: 0 / pH: 5 / Pressure: 0 bar / Temperature: 313 K

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NMR measurement

NMR spectrometerType: Bruker AMX / Manufacturer: Bruker / Model: AMX / Field strength: 600 MHz

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Processing

NMR softwareName: CNS / Developer: Brunger A. T. et.al. / Classification: refinement
RefinementMethod: molecular dynamics / Software ordinal: 1
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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