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Basic information

Entry
Database: PDB / ID: 1x7k
TitlePV5 nmr solution structure
ComponentsPolyphemusin I
KeywordsANTIMICROBIAL PROTEIN / PV5 / POLYPHEMUSIN VARIANT / BETA HAIRPIN / DISULFIDE BRIDGE / ANTIMICROBIAL PEPTIDE
Function / homologydefense response to bacterium / extracellular region / Polyphemusin-1
Function and homology information
MethodSOLUTION NMR / DISTANCE GEOMETRY WITH SIMULATED ANNEALING
AuthorsPowers, J.P. / Tan, A. / Ramamoorthy, A. / Hancock, R.E.
CitationJournal: Biochemistry / Year: 2005
Title: Solution structure and interaction of the antimicrobial polyphemusins with lipid membranes
Authors: Powers, J.P. / Tan, A. / Ramamoorthy, A. / Hancock, R.E.
History
DepositionAug 14, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2005Provider: 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: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polyphemusin I


Theoretical massNumber of molelcules
Total (without water)2,6231
Polymers2,6231
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)16 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Polyphemusin I / PV5


Mass: 2623.210 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED USING FMOC SOLID STATE SYNTHESIS. THE SEQUENCE OF THE PEPTIDE IS NATURALLY FOUND IN Limulus polyphemus (Atlantic horseshoe crab).
References: UniProt: P14215
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
131DQF-COSY
NMR detailsText: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D HOMONUCLEAR TECHNIQUES.

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Sample preparation

DetailsContents: 2 MM PV5
Sample conditionsIonic strength: NO SALT / pH: 3.8 / Pressure: AMBIENT / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian UNITY / Manufacturer: Varian / Model: UNITY / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XPLOR-NIH2.9.0SCHWIETERS,KUSZEWSKI,TJANDRA,CLORErefinement
NMRView5.0.3data analysis
RefinementMethod: DISTANCE GEOMETRY WITH SIMULATED ANNEALING / Software ordinal: 1
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: 16

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