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- PDB-1xc0: Twenty Lowest Energy Structures of Pa4 by Solution NMR -

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Basic information

Entry
Database: PDB / ID: 1xc0
TitleTwenty Lowest Energy Structures of Pa4 by Solution NMR
ComponentsPardaxin P-4
KeywordsSIGNALING PROTEIN / Bend-helix-bend-helix motif
Function / homologyPardaxin / Pardaxin / other organism cell membrane / monoatomic ion transport / toxin activity / extracellular region / membrane / Pardaxin P-4
Function and homology information
MethodSOLUTION NMR / extended structure; random simulated annealing; molecular dynamics
AuthorsPorcelli, F. / Buck, B. / Lee, D.-K. / Hallock, K.J. / Ramamoorthy, A. / Veglia, G.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Structure and orientation of pardaxin determined by NMR experiments in model membranes
Authors: Porcelli, F. / Buck, B. / Lee, D.-K. / Hallock, K.J. / Ramamoorthy, A. / Veglia, G.
History
DepositionAug 31, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pardaxin P-4


Theoretical massNumber of molelcules
Total (without water)3,3261
Polymers3,3261
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 350structures with the lowest energy
Representative

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Components

#1: Protein/peptide Pardaxin P-4 / Pa4


Mass: 3325.851 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Pardaxins naturally occur in sole fish of genus Pardachirus. Pa4 was synthesized using standard 9-fluorenylmethoxycarbonyl-based solid-pahse methods with an ABI 431A peptide synthesizer. ...Details: Pardaxins naturally occur in sole fish of genus Pardachirus. Pa4 was synthesized using standard 9-fluorenylmethoxycarbonyl-based solid-pahse methods with an ABI 431A peptide synthesizer. Crude peptide was purified by reversed-phase HPLC
References: UniProt: P81861

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D TOCSY
1212D NOESY

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Sample preparation

DetailsContents: ~1.5 mg of lyophilized Pa4 in 20 mM PBS (pH 6.5),300 mM d31-DPC and 10% D2O. Sample pH was adjusted to ~4.5 with NaOH.
Solvent system: 90% water and 10% D2O
Sample conditionspH: 4.5 / Temperature: 303 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1variancollection
NMRPipe2006Delaglioprocessing
Sparky3.11Goddarddata analysis
X-PLOR3.851Brungerstructure solution
X-PLOR3.851Brungerrefinement
RefinementMethod: extended structure; random simulated annealing; molecular dynamics
Software ordinal: 1 / Details: 335 NOEs; 13 H-bonds
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 350 / Conformers submitted total number: 20

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