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- PDB-6my1: Solution structure of gomesin at 278 K -

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Basic information

Entry
Database: PDB / ID: 6my1
TitleSolution structure of gomesin at 278 K
Componentsgomesin
KeywordsTOXIN / Peptides / Beta hairpin motif
Function / homologydefense response to fungus / killing of cells of another organism / defense response to bacterium / innate immune response / extracellular region / Gomesin
Function and homology information
Biological speciesAcanthoscurria gomesiana (spider)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsChin, Y.K.-Y. / Deplazes, E.
CitationJournal: Proteins / Year: 2020
Title: The unusual conformation of cross-strand disulfide bonds is critical to the stability of beta-hairpin peptides.
Authors: Deplazes, E. / Chin, Y.K. / King, G.F. / Mancera, R.L.
History
DepositionOct 31, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 2.0Feb 5, 2020Group: Database references / Polymer sequence / Category: citation / citation_author / entity_poly
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID / _entity_poly.pdbx_seq_one_letter_code_can
Revision 2.1Jun 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: gomesin


Theoretical massNumber of molelcules
Total (without water)2,2801
Polymers2,2801
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy and best stereochemical properties as judged by Molprobity
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide gomesin


Mass: 2279.762 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Acanthoscurria gomesiana (spider) / References: UniProt: P82358*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC
131isotropic12D 1H-1H NOESY
141isotropic12D 1H-1H TOCSY

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Sample preparation

DetailsType: solution / Contents: 1.4 mM Gomesin, 5 % D2O, 95% H2O/5% D2O / Label: 1 / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.4 mMGomesinnatural abundance1
5 %D2Onatural abundance1
Sample conditionsIonic strength: 0 Not defined / Label: Condition1 / pH: 3.5 / Pressure: 1 atm / Temperature: 278 K

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NMR measurement

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

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CcpNMRCCPNchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichchemical shift assignment
CcpNMRCCPNpeak picking
TopSpinBruker Biospinprocessing
TopSpinBruker Biospincollection
TALOSCornilescu, Delaglio and Bax (TALOSn)geometry optimization
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy and best stereochemical properties as judged by Molprobity
Conformers calculated total number: 200 / Conformers submitted total number: 20

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