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- PDB-1ih9: NMR Structure of Zervamicin IIB (peptaibol antibiotic) Bound to D... -

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Entry
Database: PDB / ID: 1ih9
TitleNMR Structure of Zervamicin IIB (peptaibol antibiotic) Bound to DPC Micelles
ComponentsZERVAMICIN IIB
KeywordsANTIBIOTIC / ZREVAMICIN / PEPTAIBOL ANTIBACTERIAL / ANTIFUNGAL / ANTIBIOTIC BENT HELIX
Function / homologyZervamicin IIB / :
Function and homology information
Biological speciesEMERICELLOPSIS SALMOSYNNEMATA (fungus)
MethodSOLUTION NMR / SIMULATED ANNELING. ENERGY MINIMISATION.
AuthorsShenkarev, Z.O. / Balasheva, T.A. / Efremov, R.G. / Yakimenko, Z.A. / Ovchinnikova, T.V. / Raap, J. / Arseniev, A.S.
CitationJournal: Biophys.J. / Year: 2002
Title: Spatial Structure of Zervamicin Iib Bound to Dpc Micelles: Implications for Voltage-Gating.
Authors: Shenkarev, Z.O. / Balashova, T.A. / Efremov, R.G. / Yakimenko, Z.A. / Ovchinnikova, T.V. / Raap, J. / Arseniev, A.S.
History
DepositionApr 19, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2002Provider: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ZERVAMICIN IIB


Theoretical massNumber of molelcules
Total (without water)1,8231
Polymers1,8231
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1

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Components

#1: Protein/peptide ZERVAMICIN IIB


Type: Peptaibol / Class: Antibiotic / Mass: 1823.183 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: ZERVAMICIN IS A HEXADECAMERIC HELICAL PEPTIDE. THE N-TERM IS ACETYLATED (RESIDUE 0)
Source: (natural) EMERICELLOPSIS SALMOSYNNEMATA (fungus) / Strain: 336 IMI 58330 / References: NOR: NOR01092, Zervamicin IIB
Compound detailsZERVAMICIN IIB IS LINEAR PEPTIDE, A MEMBER OF THE PEPTAIBOL FAMILY OF MEMBRANE CHANNEL FORMING ...ZERVAMICIN IIB IS LINEAR PEPTIDE, A MEMBER OF THE PEPTAIBOL FAMILY OF MEMBRANE CHANNEL FORMING PEPTIDES. HERE, ZERVAMICIN IS REPRESENTED BY THE SEQUENCE (SEQRES)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121DQF-COSY
131TOCSY
NMR detailsText: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D HOMONUCLEAR TECHNIQUES.

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Sample preparation

Details
Solution-IDContents
11.8 MM ZRV-IIB
270MM D-DPC
390% H2O, 10% D2O
Sample conditionsIonic strength: 0 / pH: 6.8 / Pressure: 1ATM ATM / Temperature: 303 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: 600 MHz

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Processing

NMR software
NameDeveloperClassification
DISCOVER 1.2BIOSYM TECHNOLOGIESrefinement
VNMR 5.3structure solution
XEASY 2.1structure solution
DYANA 1.5structure solution
RefinementMethod: SIMULATED ANNELING. ENERGY MINIMISATION. / Software ordinal: 1
Details: 536 NOESY PEAKS, 174 UPPER CONSTRAINTS 29 ADDITIONAL LOWER CONSTRAINTS 60 ADDITIONAL CONSTRAINTS FOR HYDROGEN BONDS 11 ANGLE CONSTRAINTS
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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