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- PDB-1nt6: F1-Gramicidin C In Sodium Dodecyl Sulfate Micelles (NMR) -

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Basic information

Entry
Database: PDB / ID: 1nt6
TitleF1-Gramicidin C In Sodium Dodecyl Sulfate Micelles (NMR)
ComponentsGRAMICIDIN CGramicidin
KeywordsANTIBIOTIC / GRAMICIDIN / ANTIFUNGAL / ANTIBACTERIAL / SDS MICELLES / MEMBRANE ION CHANNEL / LINEAR GRAMICIDIN
Function / homologymutant GRAMICIDIN C / :
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. / Fletcher, T.G. / Hinton, J.F.
CitationJournal: Biochemistry / Year: 2003
Title: The Structure, Cation Binding, Transport, and Conductance of Gly15-Gramicidin a Incorporated Into Sds Micelles and Pc/Pg Vesicles.
Authors: Sham, S.S. / Shobana, S. / Townsley, L.E. / Jordan, J.B. / Fernandez, J.Q. / Andersen, O.S. / Greathouse, D.V. / Hinton, J.F.
History
DepositionJan 28, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 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 / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GRAMICIDIN C
B: GRAMICIDIN C


Theoretical massNumber of molelcules
Total (without water)3,8152
Polymers3,8152
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-5 kcal/mol
Surface area2730 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
Representativeminimized average structure

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Components

#1: Protein/peptide GRAMICIDIN C / Gramicidin / Gramicidin


Type: PolypeptidePeptide / Class: Antibiotic / Mass: 1907.301 Da / Num. of mol.: 2 / Source method: obtained synthetically
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: (synth.) BREVIBACILLUS BREVIS (bacteria) / References: NOR: NOR00245, mutant GRAMICIDIN C
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 C 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 40MSEC MIXING TIME WAS USED IN THE NOESY EXPERIMENT FROM WHICH DISTANCE CONSTRAINTS WERE OBTAINED.

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Sample preparation

DetailsContents: 5MM F1-GRAMICIDIN C, 250MM DEUTERATED SODIUM DODECYL SULFATE, 80% 100MM PHOSPHATE BUFFER PH 6.5, 10% D2O, 10% DEUTERATED TFE
Sample conditionspH: 6.5 / 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 602 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 602 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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