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- PDB-2l3i: Oxki4a, spider derived antimicrobial peptide -

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Basic information

Entry
Database: PDB / ID: 2l3i
TitleOxki4a, spider derived antimicrobial peptide
ComponentsAOXKI4A, antimicrobial peptide in spider venom
KeywordsANTIMICROBIAL PROTEIN / antimicrobial peptide
Function / homologyhemolysis in another organism / other organism cell membrane / : / toxin activity / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / extracellular region / membrane / Oxyopinin-4a
Function and homology information
Biological speciesOxyopes takobius (spider)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsfewest violations, model 1
AuthorsVassilevski, A.A. / Dubovskii, P.V. / Samsonova, O.V. / Egorova, N.S. / Kozlov, S.A. / Feofanov, A.V. / Arseniev, A.S. / Grishin, E.V.
CitationJournal: Febs J. / Year: 2011
Title: Novel lynx spider toxin shares common molecular architecture with defense peptides from frog skin.
Authors: Dubovskii, P.V. / Vassilevski, A.A. / Samsonova, O.V. / Egorova, N.S. / Kozlov, S.A. / Feofanov, A.V. / Arseniev, A.S. / Grishin, E.V.
History
DepositionSep 14, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 14, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2011Group: Database references
Revision 1.2Mar 7, 2012Group: Database references
Revision 1.3May 15, 2019Group: Data collection / Source and taxonomy / Category: pdbx_entity_src_syn / pdbx_nmr_software
Item: _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AOXKI4A, antimicrobial peptide in spider venom


Theoretical massNumber of molelcules
Total (without water)3,6251
Polymers3,6251
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide AOXKI4A, antimicrobial peptide in spider venom


Mass: 3624.531 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Oxyopes takobius (spider) / References: UniProt: F8J4S0*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D 1H-1H NOESY
1322D 1H-1H TOCSY
1422D 1H-1H NOESY
1522D DQF-COSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM peptide, 60 mM dodecylphosphocholine-d38, 95% H2O/5% D2O95% H2O/5% D2O
21 mM peptide, 60 mM dodecylphosphocholine-d38, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
1 mMOxki4a-11
60 mMdodecylphosphocholine-d38-21
1 mMOxki4a-32
60 mMdodecylphosphocholine-d38-42
Sample conditionsIonic strength: 0 / pH: 4.0 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: Avance / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XEASYBartels C., Xia T., Billeter M., Guntert P., Wuthrich K.chemical shift assignment
XwinNMRBruker Biospincollection
CYANA2Guntert, Mumenthaler and Wuthrichstructure solution
CYANA2Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 20

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