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- PDB-1s4a: NMR Structure of a D,L alternating decamer of norleucine: double ... -

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Basic information

Entry
Database: PDB / ID: 1s4a
TitleNMR Structure of a D,L alternating decamer of norleucine: double antiparallel beta-helix
ComponentsHCO-(D-Nle-L-Nle)3-D-MeNle-L-Nle-D-Nle-L-Nle-OMe
KeywordsDE NOVO PROTEIN / D / L-alternating / norleucine / Beta-helix / Gramicidin
Function / homologyHCO-(D-NLE-L-NLE)3-D-MENLE-L-NLE-D-NLE-L-NLE-OME
Function and homology information
MethodSOLUTION NMR / molecular dynamics
AuthorsNavarro, E. / Fenude, E. / Celda, B.
CitationJournal: Biopolymers / Year: 2004
Title: Conformational and structural analysis of the equilibrium between single- and double-strand beta-helix of a D,L-alternating oligonorleucine.
Authors: Navarro, E. / Fenude, E. / Celda, B.
History
DepositionJan 15, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 19, 2012Group: Structure summary
Revision 1.4Dec 12, 2012Group: Other
Revision 1.5Feb 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HCO-(D-Nle-L-Nle)3-D-MeNle-L-Nle-D-Nle-L-Nle-OMe
B: HCO-(D-Nle-L-Nle)3-D-MeNle-L-Nle-D-Nle-L-Nle-OMe


Theoretical massNumber of molelcules
Total (without water)2,4112
Polymers2,4112
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)5 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide HCO-(D-Nle-L-Nle)3-D-MeNle-L-Nle-D-Nle-L-Nle-OMe


Type: Polypeptide / Class: Antibiotic / Mass: 1205.655 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: The peptide was chemimcally synthesized.
References: HCO-(D-NLE-L-NLE)3-D-MENLE-L-NLE-D-NLE-L-NLE-OME

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D TOCSY
121ROESY
131HSQC
NMR detailsText: This structure was determined using standard 2D homonuclear techniques

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Sample preparation

DetailsContents: HXMe 5mM / Solvent system: d-chloroform
Sample conditionsPressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Discover2.9.7BIOSYMstructure solution
XwinNMRBrukercollection
Discover2.9.7BIOSYMrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
Details: This structures are based on a total of 130 distance restraints, where 80 are between backbone protons.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 5

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