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- PDB-2msq: Solution study of cBru9a -

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Basic information

Entry
Database: PDB / ID: 2msq
TitleSolution study of cBru9a
ComponentsConotoxin cBru9a
KeywordsTOXIN / conotoxins / cyclic peptides / cyclization / cystine knot / drug design
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model1
AuthorsAkcan, M. / Clark, R.J. / Daly, N.L. / Conibear, A.C. / de Faoite, A.C. / Heghinian, M.C. / Adams, D.J. / Mari, F. / Craik, D.J.
CitationJournal: Biopolymers / Year: 2015
Title: Transforming conotoxins into cyclotides: Backbone cyclization of P-superfamily conotoxins.
Authors: Akcan, M. / Clark, R.J. / Daly, N.L. / Conibear, A.C. / de Faoite, A. / Heghinian, M.D. / Sahil, T. / Adams, D.J. / Mari, F. / Craik, D.J.
History
DepositionAug 5, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 22, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2015Group: Database references
Revision 1.2Feb 3, 2016Group: Database references
Revision 1.3Jun 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_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_spectrometer.model / _struct_conn.pdbx_dist_value / _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: Conotoxin cBru9a


Theoretical massNumber of molelcules
Total (without water)2,8091
Polymers2,8091
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 / 50target function
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Conotoxin cBru9a


Mass: 2809.191 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: P-superfamily conotoxin Bru9a cyclised with a Gly-Leu-Pro linker
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D 1H-1H NOESY

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Sample preparation

DetailsContents: 0.05-0.2 mM cBru9a, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
SampleUnits: mM / Component: cBru9a-1 / Conc. range: 0.05-0.2
Sample conditionsPressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 900 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1 / Details: 10000 steps
NMR constraintsNOE constraints total: 217 / NOE intraresidue total count: 75 / NOE long range total count: 33 / NOE medium range total count: 18 / NOE sequential total count: 91 / Hydrogen bond constraints total count: 0 / Protein chi angle constraints total count: 7 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 25 / Protein psi angle constraints total count: 0
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 50 / Conformers submitted total number: 20

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