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- PDB-1dlz: SOLUTION STRUCTURE OF THE CHANNEL-FORMER ZERVAMICIN IIB (PEPTAIBO... -

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Entry
Database: PDB / ID: 1dlz
TitleSOLUTION STRUCTURE OF THE CHANNEL-FORMER ZERVAMICIN IIB (PEPTAIBOL ANTIBIOTIC)
ComponentsZERVAMICIN IIB
KeywordsANTIBIOTIC / ZREVAMICIN / PEPTAIBOL / ANTIBACTERIAL / ANTIFUNGAL / BENT HELIX
Function / homologyZervamicin IIB / :
Function and homology information
Biological speciesEMERICELLOPSIS SALMOSYNNEMATA (fungus)
MethodSOLUTION NMR / simulated annealing
AuthorsBalashova, T.A. / Shenkarev, Z.O. / Tagaev, A.A. / Ovchinnikova, T.V. / Raap, J. / Arseniev, A.S.
CitationJournal: 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
DepositionDec 13, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2000Provider: 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 1.5Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_nmr_exptl_sample_conditions / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _pdbx_nmr_exptl_sample_conditions.pressure_units / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
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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)20 / 100BEST 20 OUT OF 100 WITH CA BACKBONE RMSD NO LESS THAN 0.05 ANGSTROMS
Representative

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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) / 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 experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121DQF-COSY
1312D TOCSY
NMR detailsText: NOESY SPECTRUM 200MS, WE DETERMINED N15HB CONSTANT FROM NOESY SPECTRA (N15 ENRICHED SAMPLE)

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Sample preparation

Details
Solution-IDContents
110MM ZERVAMICIN IIB
23MM ZERVAMICIN IIB, UNIFORM LABELING WITH 15N
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
105.81 atm303 K
205.81 atm303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian UNITY / Manufacturer: Varian / Model: UNITY / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
DISCOVER 3.1INSIGHT II/95refinement
DYANA 1.5structure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: 335 NOESY PEAKS, 129 UPPER CONSTRAINTS, 19 ADDITIONAL LOWER CONSTRAINTS, 48 ADDITIONAL CONSTRAINTS FOR HYDROGEN BONDS, 12 ANGLE CONSTRAINTS
NMR ensembleConformer selection criteria: BEST 20 OUT OF 100 WITH CA BACKBONE RMSD NO LESS THAN 0.05 ANGSTROMS
Conformers calculated total number: 100 / Conformers submitted total number: 20

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