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- PDB-1r9v: NMR Structure of a D,L-Alternating Dodecamer of Norleucine -

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Basic information

Entry
Database: PDB / ID: 1r9v
TitleNMR Structure of a D,L-Alternating Dodecamer of Norleucine
ComponentsBOC-(D-NLE-L-NLE)4-D-NLE(METHYL)-L-NLE-D-NLE-L-NLE METHYL ESTER
KeywordsDE NOVO PROTEIN / BETA HELIX / ION CHANNEL
Function / homologyBOC-(D-NLE-L-NLE)4-D-NLE(METHYL)-L-NLE-D-NLE-L-NLE METHYL ESTER
Function and homology information
MethodSOLUTION NMR / molecular dynamics
AuthorsNavarro, E. / Celda, B.
CitationJournal: Biopolymers / Year: 2001
Title: Solution NMR Structure of a D,L-Alternating Oligonorleucine as a Model of Beta-Helix
Authors: Navarro, E. / Tejero, R. / Fenude, E. / Celda, B.
History
DepositionOct 31, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 12, 2012Group: Other
Revision 1.4Feb 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software / 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 / _struct_conn.pdbx_leaving_atom_flag
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: BOC-(D-NLE-L-NLE)4-D-NLE(METHYL)-L-NLE-D-NLE-L-NLE METHYL ESTER


Theoretical massNumber of molelcules
Total (without water)1,5041
Polymers1,5041
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 / 25structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide BOC-(D-NLE-L-NLE)4-D-NLE(METHYL)-L-NLE-D-NLE-L-NLE METHYL ESTER


Type: Polypeptide / Class: Antibiotic / Mass: 1504.076 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: D,L-Alternating sequence as in Gramicidin A
References: BOC-(D-NLE-L-NLE)4-D-NLE(METHYL)-L-NLE-D-NLE-L-NLE METHYL ESTER

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DQF-COSY
1212D TOCSY
1312D ROESY

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Sample preparation

DetailsContents: 5.5 mM ; chloroform-d / Solvent system: chloroform-d
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: Varian UNITY / Manufacturer: Varian / Model: UNITY / Field strength: 400 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Discover2.9.7BIOSYMstructure solution
Discover2.9.7BIOSYMrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
Details: Structures based in 38 distance restraints deduced from NOE NMR data, 16 are backbone restraints.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 25 / Conformers submitted total number: 5

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