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- PDB-2m9o: Solution structure of kalata B7 -

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Basic information

Entry
Database: PDB / ID: 2m9o
TitleSolution structure of kalata B7
ComponentsKalata-B7
KeywordsPLANT PROTEIN / beta hairpin
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 / torsion angle dynamics
AuthorsDaly, N. / Elliott, A. / Craik, D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Cyclotides as templates for peptide GPCR ligand design - discovery of the target receptor of the oxytocic plant peptide kalata B7
Authors: Koehbach, J. / O'Brien, M. / Muttenthaler, M. / Miazzo, M. / Akcan, M. / Elliott, A. / Daly, N. / Harvey, P. / Arrowsmith, S. / Gunasekera, S. / Smith, T. / Wray, S. / Goransson, U. / ...Authors: Koehbach, J. / O'Brien, M. / Muttenthaler, M. / Miazzo, M. / Akcan, M. / Elliott, A. / Daly, N. / Harvey, P. / Arrowsmith, S. / Gunasekera, S. / Smith, T. / Wray, S. / Goransson, U. / Dawson, P. / Craik, D. / Freissmuth, M. / Gruber, C.
History
DepositionJun 18, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 20, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Kalata-B7


Mass: 3097.612 Da / Num. of mol.: 1 / Fragment: UNP residues 76-104 / 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

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Sample preparation

DetailsContents: 1 mM protein, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mM / Component: entity-1
Sample conditionsIonic strength: 0 / pH: 4.0 / Pressure: ambient / Temperature: 290 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
SparkyGoddarddata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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