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- PDB-1zy6: Membrane-bound dimer structure of Protegrin-1 (PG-1), a beta-Hair... -

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Basic information

Entry
Database: PDB / ID: 1zy6
TitleMembrane-bound dimer structure of Protegrin-1 (PG-1), a beta-Hairpin Antimicrobial Peptide in Lipid Bilayers from Rotational-Echo Double-Resonance Solid-State NMR
ComponentsProtegrin 1
KeywordsANTIBIOTIC / beta-hairpin / solid state NMR
Function / homology
Function and homology information


lipopolysaccharide binding / antimicrobial humoral immune response mediated by antimicrobial peptide / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / innate immune response / extracellular space
Similarity search - Function
Cathelicidin / Cathelicidins signature 1. / Cathelicidin, conserved site / Cathelicidins signature 2. / Cathelicidin-like / Cystatin superfamily
Similarity search - Domain/homology
MethodSOLID-STATE NMR / Distance geometry; Simulated annealing
AuthorsWu, X. / Mani, R. / Tang, M. / Buffy, J.J. / Waring, A.J. / Sherman, M.A. / Hong, M.
CitationJournal: Biochemistry / Year: 2006
Title: Membrane-Bound Dimer Structure of a beta-Hairpin Antimicrobial Peptide from Rotational-Echo Double-Resonance Solid-State NMR.
Authors: Mani, R. / Tang, M. / Wu, X. / Buffy, J.J. / Waring, A.J. / Sherman, M.A. / Hong, M.
History
DepositionJun 9, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2006Provider: 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 ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protegrin 1
B: Protegrin 1


Theoretical massNumber of molelcules
Total (without water)4,3292
Polymers4,3292
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)1 / 100least violations
Representative

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Components

#1: Protein/peptide Protegrin 1 / PG-1 / Neutrophil peptide 1


Mass: 2164.679 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: BIOLOGICAL SEQUENCE WITH AMIDATED C-TERMINUS / References: UniProt: P32194

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111rotational-echo double resonance (REDOR) NMR technique, which measures distances between heteronuclear spins
122rotational-echo double resonance (REDOR) NMR technique, which measures distances between heteronuclear spins
NMR detailsText: Solid State NMR was performed at 400.49 MHz for 1H, 376.8 MHz for 19F, 100.72 MHz for 13C, and 40.58 MHz for 15N. The 15N{13C} and 13C{1H} REDOR experiments were carried out on a 1H/13C/15N ...Text: Solid State NMR was performed at 400.49 MHz for 1H, 376.8 MHz for 19F, 100.72 MHz for 13C, and 40.58 MHz for 15N. The 15N{13C} and 13C{1H} REDOR experiments were carried out on a 1H/13C/15N triple resonance MAS probe. Spinning speeds were regulated to 3 Hz using a pneumatic control unit. 13C and 15N chemical shifts were referenced externally to the 13C signal of alpha-Gly at 176.4 ppm on the TMS scale and the 15N signal of N-acetyl-valine at 122 ppm, respectively. The 13C{19F} REDOR experiments, where the nucleus in the bracket is the unobserved dephasing spin, was conducted on a 4-mm magic-angle spinning (MAS) probe equipped with a Bruker HFX unit, which allows simultaneous tuning of 1H and 19F on the 1H channel.

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Sample preparation

Details
Solution-IDContentsSolvent system
11:1 molar mixture of [13C-Cys15] PG-1 and [15N-Cys15] PG-1POPC bilayers at a peptide-lipid molar ratio of 1:20
2[4-19F-Phe12, 13C-Val16] PG-1POPC bilayers at a peptide-lipid molar ratio of 1:12.5
Sample conditionsPressure: ambient / Temperature: 233 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DSX 400 / Manufacturer: Bruker / Model: DSX 400 / Field strength: 400 MHz

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Processing

NMR software
NameVersionDeveloperClassification
SIMPSONBak, Rasmussen, Nielsenstructure solution
MODELLER6.1Sali, Blundellrefinement
RefinementMethod: Distance geometry; Simulated annealing / Software ordinal: 1
Details: Two-spin REDOR curves were simulated using a Fortran program. Three-spin REDOR curves for the C -F experiment were simulated using the SIMPSON program. The input distances and angles in the ...Details: Two-spin REDOR curves were simulated using a Fortran program. Three-spin REDOR curves for the C -F experiment were simulated using the SIMPSON program. The input distances and angles in the three-spin simulation were obtained from model building. The simulations assumed delta-function pulses for all pi pulses. Models that were potentially consistent with all the experimentally measured distances were created using MODELLER. In addition to the REDOR-based restraints, the input file included a restraint to preserve the intramolecular hydrogen bond ladder of each monomer, and a restraint to maintain monomer symmetry.
NMR ensembleConformer selection criteria: least violations / Conformers calculated total number: 100 / Conformers submitted total number: 1

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