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- PDB-5wow: Solution NMR structure of cyclotide MCoTI-I -

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Basic information

Entry
Database: PDB / ID: 5wow
TitleSolution NMR structure of cyclotide MCoTI-I
ComponentsTwo inhibitor peptide topologies 2
KeywordsDE NOVO PROTEIN / cyclotide / plant peptide / cyclic cystine knot / grafted peptide / bioactive epitope
Biological speciesMomordica cochinchinensis (spiny bitter cucumber)
MethodSOLUTION NMR / simulated annealing
AuthorsSchroeder, C.I. / Kwon, S.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1047857 Australia
CitationJournal: ACS Chem. Biol. / Year: 2018
Title: Targeted Delivery of Cyclotides via Conjugation to a Nanobody.
Authors: Kwon, S. / Duarte, J.N. / Li, Z. / Ling, J.J. / Cheneval, O. / Durek, T. / Schroeder, C.I. / Craik, D.J. / Ploegh, H.L.
History
DepositionAug 3, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / entity
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity.formula_weight
Revision 1.2Oct 31, 2018Group: Data collection / Database references / Structure summary
Category: citation / entity
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _entity.formula_weight
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Data collection / Derived calculations
Category: pdbx_audit_support / pdbx_nmr_software ...pdbx_audit_support / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name ..._pdbx_audit_support.funding_organization / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Jun 14, 2023Group: Database references / Derived calculations / Other / Category: database_2 / pdbx_database_status / 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 / _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: Two inhibitor peptide topologies 2


Theoretical massNumber of molelcules
Total (without water)4,2481
Polymers4,2481
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
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 Two inhibitor peptide topologies 2


Mass: 4247.842 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Momordica cochinchinensis (spiny bitter cucumber)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H TOCSY
121isotropic12D 1H-1H NOESY
131isotropic12D 1H-15N HSQC
141isotropic12D DQF-COSY
151isotropic12D 1H-13C HSQC
282isotropic12D 1H-1H TOCSY
272isotropic12D 1H-13C HSQC
262isotropic12D 1H-1H E COSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.5 mM MCoTI-HA, 90% H2O/10% D2OH2O90% H2O/10% D2O
solution20.5 mM MCoTI-HA, 100% D2OD2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMMCoTI-HAnatural abundance1
0.5 mMMCoTI-HAnatural abundance2
Sample conditions
Conditions-IDIonic strength unitsLabelpHPressure (kPa)Temperature (K)
1Not definedconditions_13.0 ambient atm298 K
2Not definedconditions_23.0 ambient atm298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz / Details: equipped with a cryoprobe

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Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CcpNMRCCPNchemical shift assignment
CcpNMRCCPNpeak picking
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
RefinementMethod: simulated annealing / 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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