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- PDB-1r9u: Refined structure of peptaibol zervamicin IIB in methanol solutio... -

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Entry
Database: PDB / ID: 1r9u
TitleRefined structure of peptaibol zervamicin IIB in methanol solution from trans-hydrogen bond J couplings
ComponentsZERVAMICIN IIB
KeywordsANTIBIOTIC / ZREVAMICIN / BIFURCATED HYDROGEN BOND / PEPTAIBOL / ANTIBACTERIAL / ANTIFUNGAL / BENT HELIX
Function / homologyZervamicin IIB / :
Function and homology information
Biological speciesEMERICELLOPSIS SALMOSYNNEMATA (fungus)
MethodSOLUTION NMR / SIMULATED ANNEALING, TORSION ANGLE DYNAMICS, ENERGY MINIMISATION
AuthorsShenkarev, Z.O. / Balashova, T.A. / Yakimenko, Z.A. / Ovchinnikova, T.V. / Arseniev, A.S.
Citation
Journal: J.Pept.Sci. / Year: 2003
Title: Biosynthetic Uniform 13C,15N-Labelling of Zervamicin Iib. Complete 13C and 15N NMR Assignment.
Authors: Ovchinnikova, T.V. / Shenkarev, Z.O. / Yakimenko, Z.A. / Svishcheva, N.V. / Tagaev, A.A. / Skladnev, D.A. / Arseniev, A.S.
#1: Journal: FEBS Lett. / Year: 2000
Title: NMR Structure of the Channel-Former Zervamicin Iib in Isotropic Solvents
Authors: Balashova, T.A. / Shenkarev, Z.O. / Tagaev, A.A. / Ovchinnikova, T.V. / Raap, J. / Arseniev, A.S.
History
DepositionOct 31, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2004Provider: 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 1.5Oct 10, 2018Group: Data collection / Database references ...Data collection / Database references / Experimental preparation / Other / Structure summary
Category: cell / chem_comp ...cell / chem_comp / citation / citation_author / diffrn / diffrn_radiation / diffrn_radiation_wavelength / pdbx_nmr_exptl_sample_conditions / pdbx_nmr_representative
Item: _chem_comp.pdbx_synonyms / _pdbx_nmr_exptl_sample_conditions.pressure_units / _pdbx_nmr_representative.selection_criteria
Revision 1.6Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_entry_details.has_protein_modification / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag

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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 software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)24 / 1000STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS, STRUCTURES WITH THE LOWEST ENERGY,TARGET FUNCTION
RepresentativeModel #1lowest energy

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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)
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: LONG RANGE 2D-HNCO
NMR detailsText: THIS STRUCTURE IS A REFINED STRUCTURE OF PREVIOUS DEPOSITION (1DLZ) ON THE BASIS OF HYDROGEN BOND RESTRAINTS, DETERMINED EXPERIMENTALY. INCLUDING RESTRAINTS FOR OBSERVED BIFURCATED HYDROGEN BOND.

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Sample preparation

DetailsContents: 4MM U-15N-13C ZRV-IIB, METHANOL (CD3OH) PH 6.2
Sample conditionsIonic strength: 0 / pH: 6.2 / Pressure: 1 atm / Temperature: 305 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 500 MHz

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Processing

NMR software
NameDeveloperClassification
FANTOM 4.0VON FREYBERGrefinement
XWINNMR 2.6structure solution
XEASY Xstructure solution
DYANA 1.5structure solution
RefinementMethod: SIMULATED ANNEALING, TORSION ANGLE DYNAMICS, ENERGY MINIMISATION
Software ordinal: 1
Details: STRUCTURE WAS REFINED USING ADDITIONAL 22/22 (UPPER/LOWER) RESTRAINTS FOR HYDROGEN BONDS. REFINEMENT WAS DONE IN ECEPP/2 FORCE FIELD USING IMPLICIT SOLVENT MODEL
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS, STRUCTURES WITH THE LOWEST ENERGY,TARGET FUNCTION
Conformers calculated total number: 1000 / Conformers submitted total number: 24

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