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- PDB-1znu: Structure of cyclotide Kalata B1 in DPC micelles solution -

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Basic information

Entry
Database: PDB / ID: 1znu
TitleStructure of cyclotide Kalata B1 in DPC micelles solution
ComponentsKalata B1
KeywordsPLANT PROTEIN / ANTIBIOTIC / Cyclotide / cyclic peptide / knottin / cystine knot / antimicrobial peptide
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 / simulated annealing in torsion angle space
AuthorsShenkarev, Z.O. / Nadezhdin, K.D. / Sobol, V.A. / Sobol, A.G. / Skjeldal, L. / Arseniev, A.S.
CitationJournal: Febs J. / Year: 2006
Title: Conformation and mode of membrane interaction in cyclotides. Spatial structure of kalata B1 bound to a dodecylphosphocholine micelle.
Authors: Shenkarev, Z.O. / Nadezhdin, K.D. / Sobol, V.A. / Sobol, A.G. / Skjeldal, L. / Arseniev, A.S.
History
DepositionMay 12, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Feb 5, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / database_2 ...atom_site / database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kalata B1


Theoretical massNumber of molelcules
Total (without water)2,9171
Polymers2,9171
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 / 100structures with the least restraint violations, target function
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide Kalata B1


Mass: 2917.345 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oldenlandia affinis (plant) / References: UniProt: P56254
Has protein modificationY

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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
142long-range HMQC
NMR detailsText: This structure was determined from 1H homonuclear data in combination with 3JHBC' measured for Cys residues in D2O solution.

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Sample preparation

Details
Solution-IDContentsSolvent system
13.6mM Kalata B1, 216mM perdeuterated DPC, 90% H2O, 10% D2O90% H2O/10% D2O
23.6mM Kalata B1, 100% D2O100% D2O
Sample conditionsIonic strength: 0 / pH: 2.8 / Pressure: ambient / Temperature: 313 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 DRXBrukerDRX5001
Varian UNITYVarianUNITY6002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA1.01Guntert,P.structure solution
XwinNMR2.6Brukerprocessing
VNMR6.1cVarianprocessing
XEASYxBartels,C.data analysis
CYANA1.01P.Guntertrefinement
RefinementMethod: simulated annealing in torsion angle space / Software ordinal: 1 / Details: No energy minimization was done
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations, target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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