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- PDB-2igz: NMR structure of the sterol-dependent antifungal antibiotic bacil... -

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Basic information

Entry
Database: PDB / ID: 2igz
TitleNMR structure of the sterol-dependent antifungal antibiotic bacillomycin Lc
ComponentsBACILLOMYCIN L-3
KeywordsANTIBIOTIC / ITURINS / ANTIFUNGAL / CYCLOPEPTIDE / LIPOPEPTIDE / SURFACTANT BACILLOMYCIN
Function / homologyBacillomycin Lc / :
Function and homology information
Biological speciesBACILLUS SUBTILIS (bacteria)
MethodSOLUTION NMR / DISTANCE GEOMETRY SIMULATED ANNEALING
AuthorsVolpon, L. / Tsan, P. / Besson, F. / Lancelin, J.M.
Citation
Journal: Spectrochim Acta a Mol.Biomol.Spectrosc. / Year: 2007
Title: NMR Structure Determination of a Synthetic Analogue of Bacillomycin Lc Reveals the Strategic Role of L-Asn1 in the Natural Iturinic Antibiotics.
Authors: Volpon, L. / Tsan, P. / Majer, Z. / Vass, E. / Hollosi, M. / Noguera, V. / Lancelin, J.M. / Besson, F.
#1: Journal: Eur.J.Biochem. / Year: 1999
Title: NMR Structure of Active and Inactive Forms of the Sterol-Dependent Antifungal Antibiotic Bacillomycin L
Authors: Volpon, L. / Besson, F. / Lancelin, J.M.
History
DepositionSep 25, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2006Provider: 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 30, 2024Group: 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_software / 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_software.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BACILLOMYCIN L-3


Theoretical massNumber of molelcules
Total (without water)1,0531
Polymers1,0531
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)19 / 50STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS, STRUCTURES WITH THE LOWEST ENERGY
RepresentativeModel #1

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Components

#1: Protein/peptide BACILLOMYCIN L-3


Type: Polypeptide / Class: Antibiotic / Mass: 1053.165 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: BACILLOMYCIN LC IS A CYCLIC HEPTA-LIPOPETIDE WITH 7 AMINO-ACIDS OF CONFIGURATION LDDLLDL AND ONE D-BETA-AMINO CARBOXYLIC ACID. THE FATTY ACID IS LINKED VIA A PEPTID BOND TO BOTH RESIDUES 2 AND 8.
Source: (synth.) BACILLUS SUBTILIS (bacteria) / References: NOR: NOR00781, Bacillomycin Lc
Compound detailsBACILLOMYCIN LC IS A CYCLIC HEPTA-LIPOPETIDE. HERE, BACILLOMYCIN 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
111DQF-COSY
1212D-TOCSY (HOHAHA)
1312D NOESY
1412D-ROESY
1511H-13C HSQC
NMR detailsText: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D HOMONUCLEAR TECHNIQUES

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Sample preparation

DetailsContents: 3MM BACILLOMYCIN LC IN 100% DMSO-D6
Sample conditionsPressure: AMBIENT / Temperature: 292 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: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

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Processing

NMR software
NameDeveloperClassification
CHARMM 22BROOKS,BRUCCOLERI,OLAFSON,STATES,SWAMINATHAN, KARPLUSrefinement
X-PLOR 3.851structure solution
XwinNMRstructure solution
GIFA 4.0structure solution
MOLMOLstructure solution
RefinementMethod: DISTANCE GEOMETRY SIMULATED ANNEALING / Software ordinal: 1
Details: THE STRUCTURES ARE BASED ON A TOTAL OF 74 RESTRAINTS, 71 ARE NOE-DERIVED DISTANCE CONSTRAINTS, 3 DIHEDRAL ANGLE RESTRAINTS. THE 19 STRUCTURES WERE DIVIDED INTO TWO FAMILIES OF SIMILAR ENERGY ...Details: THE STRUCTURES ARE BASED ON A TOTAL OF 74 RESTRAINTS, 71 ARE NOE-DERIVED DISTANCE CONSTRAINTS, 3 DIHEDRAL ANGLE RESTRAINTS. THE 19 STRUCTURES WERE DIVIDED INTO TWO FAMILIES OF SIMILAR ENERGY WHICH ESSENTIALLY DIFFER IN THE NUMBER AND TYPE OF TURNS. THE TWO FAMILIES ARE S1 (STRUCTURES 1-12) AND S2 (STRUCTURES 13-19).
NMR ensembleConformer selection criteria: STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS, STRUCTURES WITH THE LOWEST ENERGY
Conformers calculated total number: 50 / Conformers submitted total number: 19

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