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- PDB-8v2v: Solution NMR structure of recifin A [Y6F] -

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Basic information

Entry
Database: PDB / ID: 8v2v
TitleSolution NMR structure of recifin A [Y6F]
ComponentsRecifin A
KeywordsTOXIN / CYSTINE-RICH PEPTIDE / PROTEIN KNOT / TYROSYL-DNA PHOSPHODIESTERASE I INHIBITOR / MARINE NATURAL PRODUCT
Function / homologyPYROGLUTAMIC ACID
Function and homology information
Biological speciesAxinella sp. 1 TF-2017 (invertebrata)
MethodSOLUTION NMR / simulated annealing
AuthorsPayne, C.D. / Schroeder, C.I. / Rosengren, K.J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Chem Sci / Year: 2024
Title: Picking the tyrosine-lock: chemical synthesis of the tyrosyl-DNA phosphodiesterase I inhibitor recifin A and analogues.
Authors: Smallwood, T.B. / Krumpe, L.R.H. / Payne, C.D. / Klein, V.G. / O'Keefe, B.R. / Clark, R.J. / Schroeder, C.I. / Rosengren, K.J.
History
DepositionNov 23, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Recifin A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,9262
Polymers4,7971
Non-polymers1291
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: all NMR data are consistent with a monomeric form.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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 A


Mass: 4797.343 Da / Num. of mol.: 1 / Mutation: Y6F / Source method: obtained synthetically / Source: (synth.) Axinella sp. 1 TF-2017 (invertebrata)
#2: Chemical ChemComp-PCA / PYROGLUTAMIC ACID


Type: L-peptide linking / Mass: 129.114 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H7NO3
Has ligand of interestN

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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-13C HSQC
141isotropic12D 1H-15N HSQC

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Sample preparation

DetailsType: solution / Contents: 1 mM recifin A [Y6F], 90% H2O/10% D2O / Label: Sample 1 / Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mM / Component: recifin A [Y6F] / Isotopic labeling: natural abundance
Sample conditionsIonic strength: 0 mM / Label: conditions_1 / pH: 4.9 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 900 MHz / Details: equipped with cryoprobe

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Processing

NMR software
NameVersionDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
CARAKeller and Wuthrichchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 5
Details: Preliminary structures were calculated using CYANA and final structures were calculated and water minimised using CNS.
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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