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- PDB-6xn9: Solution NMR structure of recifin, a cysteine-rich tyrosyl-DNA Ph... -

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Basic information

Entry
Database: PDB / ID: 6xn9
TitleSolution NMR structure of recifin, a cysteine-rich tyrosyl-DNA Phosphodiesterase I modulatory peptide from the marine sponge Axinella sp.
ComponentsRecifin modulatory peptide
KeywordsTOXIN / cystine-rich peptide / protein knot / tyrosyl-DNA Phosphodiesterase I inhibitor / marine natural product
Biological speciesAxinella sp. 1 TF-2017 (invertebrata)
MethodSOLUTION NMR / simulated annealing
AuthorsSchroeder, C.I. / Rosengren, K.J. / O'Keefe, B.R.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)FT160100055 Australia
CitationJournal: J.Am.Chem.Soc. / Year: 2020
Title: Recifin A, Initial Example of the Tyr-Lock Peptide Structural Family, Is a Selective Allosteric Inhibitor of Tyrosyl-DNA Phosphodiesterase I.
Authors: Krumpe, L.R.H. / Wilson, B.A.P. / Marchand, C. / Sunassee, S.N. / Bermingham, A. / Wang, W. / Price, E. / Guszczynski, T. / Kelley, J.A. / Gustafson, K.R. / Pommier, Y. / Rosengren, K.J. / ...Authors: Krumpe, L.R.H. / Wilson, B.A.P. / Marchand, C. / Sunassee, S.N. / Bermingham, A. / Wang, W. / Price, E. / Guszczynski, T. / Kelley, J.A. / Gustafson, K.R. / Pommier, Y. / Rosengren, K.J. / Schroeder, C.I. / O'Keefe, B.R.
History
DepositionJul 2, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 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 / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Recifin modulatory peptide


Theoretical massNumber of molelcules
Total (without water)4,9241
Polymers4,9241
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: All NOEs consistent with monomeric structure
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with acceptable covalent geometry
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Recifin modulatory peptide


Mass: 4924.441 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Axinella sp. 1 TF-2017 (invertebrata)
Has ligand of interestN
Has protein modificationY

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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 NOESY
121isotropic12D 1H-1H TOCSY
132isotropic12D 1H-1H NOESY
142isotropic12D 1H-1H TOCSY
152isotropic12D 1H-13C HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution14 mg/mL recifin, 90% H2O/10% D2OH2O_sample90% H2O/10% D2O
solution24 mg/mL recifin, 100% D2OD2O_sample100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
4 mg/mLrecifinnatural abundance1
4 mg/mLrecifinnatural abundance2
Sample conditionsIonic strength: 0 mM / Label: conditions_1 / pH: 4.85 / Pressure: ambient atm / Temperature: 298 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.5Bruker Biospincollection
TopSpin3.5Bruker Biospinprocessing
CcpNmr Analysis2.4.1CCPNchemical shift assignment
XEASYBartels et al.data analysis
CYANA3.97Guntert, Mumenthaler and Wuthrichstructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 6
Details: Structures calculated with erosion angle dynamics then refined and minimized in explicit water using Cartesian dynamics
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry
Conformers calculated total number: 50 / Conformers submitted total number: 20

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