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- PDB-1nru: Gramicidin A in Dodecyl Phosphocholine Micelles in the Presence o... -

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Basic information

Entry
Database: PDB / ID: 1nru
TitleGramicidin A in Dodecyl Phosphocholine Micelles in the Presence of Excess Na+ (NMR)
ComponentsGRAMICIDIN A
KeywordsANTIBIOTIC / GRAMICIDIN / ANTIFUNGAL / ANTIBACTERIAL / DPC MICELLES / MEMBRANE ION CHANNEL / LINEAR GRAMICIDIN
Function / homologyGRAMICIDIN A / :
Function and homology information
Biological speciesBREVIBACILLUS BREVIS (bacteria)
MethodSOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING, RELAXATION MATRIX CALCULATION, MINIMIZATION
Model type detailsminimized average
AuthorsTownsley, L.E. / Hinton, J.F.
CitationJournal: Phd Thesis / Year: 2000
Title: The Three-Dimensional Structure of Gramicidin Analogs in Micellar Environments Determined Using Two-Dimensional Nuclear Magnetic Resonance Spectroscopic Techniques
Authors: Townsley, L.E.
History
DepositionJan 25, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2003Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 27, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary
Revision 1.4Dec 12, 2012Group: Other
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GRAMICIDIN A
B: GRAMICIDIN A


Theoretical massNumber of molelcules
Total (without water)3,7652
Polymers3,7652
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
Representativeminimized average structure

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Components

#1: Protein/peptide GRAMICIDIN A / VALYL GRAMICIDIN


Type: Polypeptide / Class: Antibiotic / Mass: 1882.294 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: GRAMICIDIN A IS A HEXADECAMERIC HELICAL PEPTIDE WITH ALTERNATING D,L CHARACTERISTICS. THE N-TERM IS FORMYLATED (RESIDUE 0). THE C-TERM IS CAPPED WITH ETHANOLAMINE (RESIDUE 16).
Source: (natural) BREVIBACILLUS BREVIS (bacteria) / References: NOR: NOR00243, GRAMICIDIN A
Compound detailsGRAMICIDIN IS A HETEROGENEOUS MIXTURE OF SEVERAL COMPOUNDS INCLUDING GRAMICIDIN A, B AND C WHICH ...GRAMICIDIN IS A HETEROGENEOUS MIXTURE OF SEVERAL COMPOUNDS INCLUDING GRAMICIDIN A, B AND C WHICH ARE OBTAINED FROM BACILLUS BREVIS AND CALLED COLLECTIVELY GRAMICIDIN D HERE, GRAMICIDIN A IS REPRESENTED BY THE SEQUENCE (SEQRES)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D NOESY
NMR detailsText: A 55MSEC MIXING TIME WAS USED IN THE NOESY EXPERIMENT FROM WHICH DISTANCE CONSTRAINTS WERE OBTAINED.

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Sample preparation

Details
Solution-IDContents
11.67MM GRAMICIDIN A
2~20MM DODECYL PHOSPHOCHOLINE
3~20MM NACL
490% PH 4.0 POTASSIUM BIPHTHALATE BUFFER, 10% D2O
Sample conditionspH: 4.0 / Pressure: AMBIENT / Temperature: 328 K

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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 VXRS / Manufacturer: Varian / Model: VXRS / Field strength: 500 MHz

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Processing

NMR software
NameDeveloperClassification
DISCOVER 97.2BIOSYM/MSIrefinement
VNMR 3.2structure solution
FELIX 95.0structure solution
DSPACE 4.0structure solution
RefinementMethod: DISTANCE GEOMETRY, SIMULATED ANNEALING, RELAXATION MATRIX CALCULATION, MINIMIZATION
Software ordinal: 1
Details: THE STRUCTURE WAS MODELED USING 712 DISTANCE CONSTRAINTS AND 13 HYDROGEN BOND CONSTRAINTS PER MONOMER, INCLUDING CONSTRAINTS BETWEEN THE MONOMERS. THE C2 SYMMETRY CONSTRAINT DOUBLES THIS ...Details: THE STRUCTURE WAS MODELED USING 712 DISTANCE CONSTRAINTS AND 13 HYDROGEN BOND CONSTRAINTS PER MONOMER, INCLUDING CONSTRAINTS BETWEEN THE MONOMERS. THE C2 SYMMETRY CONSTRAINT DOUBLES THIS NUMBER OF CONSTRAINTS FOR THE DIMER. 100 STRUCTURES WERE GENERATED USING DSPACE, OF WHICH THE 10 WITH THE FEWEST VIOLATIONS FROM THE DISTANCE CONSTRAINTS WERE CHOSEN FOR THE AVERAGE STRUCTURE. THIS AVERAGE STRUCTURE WAS FURTHER REFINED BY CONSTRAINED MINIMIZATION WITH DISCOVER USING THE ALL-ATOM AMBER FORCE FIELD AND A DIELECTRIC CONSTANT OF 2.0 TO EMULATE THAT OF THE MICELLE INTERIOR.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformers submitted total number: 1

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