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- PDB-6ux5: Structure of acrorhagin I from the sea anemone Actinia equina -

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Basic information

Entry
Database: PDB / ID: 6ux5
TitleStructure of acrorhagin I from the sea anemone Actinia equina
ComponentsU-actitoxin-Aeq5a
KeywordsTOXIN
Function / homologynematocyst / toxin activity / extracellular region / U-actitoxin-Aeq5a
Function and homology information
Biological speciesActinia equina (sea anemone)
MethodSOLUTION NMR / simulated annealing
AuthorsKrishnarjuna, B. / Sunanda, P. / Norton, R.S.
CitationJournal: J.Struct.Biol. / Year: 2020
Title: A disulfide-stabilised helical hairpin fold in acrorhagin I: An emerging structural motif in peptide toxins.
Authors: Krishnarjuna, B. / Sunanda, P. / Villegas-Moreno, J. / Csoti, A. / A V Morales, R. / Wai, D.C.C. / Panyi, G. / Prentis, P. / Norton, R.S.
History
DepositionNov 6, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: U-actitoxin-Aeq5a


Theoretical massNumber of molelcules
Total (without water)5,6721
Polymers5,6721
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide U-actitoxin-Aeq5a / U-AITX-Aeq5a / Acrorhagin I / Acrorhagin-1


Mass: 5672.312 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinia equina (sea anemone) / Tissue: acrorhagi / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q3C258

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D DQF-COSY
121isotropic12D 1H-1H TOCSY
131isotropic12D 1H-1H NOESY
141isotropic12D 1H-13C HSQC
151isotropic12D 1H-15N HSQC
161isotropic13D HNCO
1141isotropic13D HNCA
1131isotropic13D CBCA(CO)NH
1121isotropic13D HN(CA)CB
1111isotropic13D HBHA(CO)NH
1101isotropic13D 1H-15N NOESY
191isotropic13D 1H-13C NOESY
181isotropic13D 1H-13C NOESY aliphatic
1151isotropic13D (H)CCH-COSY

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Sample preparation

DetailsType: solution / Contents: 0.5 mM 13C and 15N acrorhagin I, 95% H2O/5% D2O
Details: 0.5 mM peptide in 20 mM sodium phosphate buffer (pH 6) containing 0.01% sodium azide and 5% D2O
Label: acro1 / Solvent system: 95% H2O/5% D2O
SampleConc.: 0.5 mM / Component: acrorhagin I / Isotopic labeling: 13C and 15N
Sample conditionsIonic strength: 20 mM / Label: acro1 / pH: 6 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospinprocessing
CcpNmr AnalysisCCPNdata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 4
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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