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- PDB-2eri: Solution structure of circulin B -

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Basic information

Entry
Database: PDB / ID: 2eri
TitleSolution structure of circulin B
ComponentsCirculin B
KeywordsANTIBIOTIC / cystine knot / beta hairpin / beta turn
Function / homologyCyclotide, bracelet, conserved site / Cyclotides bracelet subfamily signature. / Cyclotides profile. / Cyclotide / Cyclotide superfamily / Cyclotide family / defense response to bacterium / Circulin-B
Function and homology information
Biological speciesChassalia parviflora (plant)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsCraik, D.J. / Daly, N.L.
CitationJournal: INT.J.PEPT.PROTEIN RES. / Year: 2005
Title: Structure of circullin B and implications for antimicrobial activity of the cyclotides
Authors: Koltay, A. / Daly, N.L. / Gustafson, K.R. / Craik, D.J.
History
DepositionOct 24, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 15, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Circulin B


Theoretical massNumber of molelcules
Total (without water)3,3111
Polymers3,3111
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 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Circulin B / CIRB


Mass: 3310.995 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chassalia parviflora (plant) / Production host: Escherichia coli (E. coli) / References: UniProt: P56879

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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
141E-COSY

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Sample preparation

DetailsContents: 1mM circulin B pH 3.5; 70% H2O, 20% CD3CN, 10% D2 / Solvent system: 70% H2O, 20% CD3CN, 10% D2O
Sample conditionsIonic strength: 1 / pH: 3.5 / Pressure: ambient / Temperature: 295 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker ARXBrukerARX5001
Bruker DMXBrukerDMX7502

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Brukercollection
XEASY1.3.7Eccles et aldata analysis
DYANA1.5Guntert et alstructure solution
CNS1.1Brungerstructure solution
CNS1.1refinement
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: 50 / Conformers submitted total number: 20

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