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- PDB-1mqz: NMR solution structure of type-B lantibiotics mersacidin bound to... -

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Basic information

Entry
Database: PDB / ID: 1mqz
TitleNMR solution structure of type-B lantibiotics mersacidin bound to lipid II in DPC micelles
ComponentsLANTIBIOTIC MERSACIDIN
KeywordsANTIBIOTIC / ANTIMICROBIAL / LANTIBIOTICS / BACTERIOCIN / PEPTIDOGLYCAN / METHICILLIN RESISTANCE / THIOESTER
Function / homologyType 2 lantibiotic, leader peptide domain / killing of cells of another organism / defense response to bacterium / signaling receptor binding / Mersacidin / Lantibiotic mersacidin
Function and homology information
Biological speciesBACILLUS SP. HIL-Y85/54728 (bacteria)
MethodSOLUTION NMR / SIMULATED ANNEALING TORSION, ANGLE DYNAMICS
AuthorsHsu, S.-T. / Breukink, E. / Bierbaum, G. / Sahl, H.-G. / de Kruijff, B. / Kaptein, R. / van Nuland, N.A. / Bonvin, A.M.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: NMR Study of Mersacidin and Lipid II Interaction in Dodecylphosphocholine Micelles. Conformational Changes are a Key to Antimicrobial Activity
Authors: Hsu, S.-T. / Breukink, E. / Bierbaum, G. / Sahl, H.-G. / De Kruijff, B. / Kaptein, R. / Van Nuland, N.A. / Bonvin, A.M.
History
DepositionSep 17, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2003Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2009Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Jul 27, 2011Group: Other
Revision 1.4Dec 12, 2012Group: Other
Revision 1.5Aug 8, 2018Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation
Category: pdbx_database_related / pdbx_nmr_ensemble ...pdbx_database_related / pdbx_nmr_ensemble / pdbx_nmr_sample_details / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_nmr_ensemble.conformer_selection_criteria / _pdbx_nmr_ensemble.conformers_calculated_total_number ..._pdbx_nmr_ensemble.conformer_selection_criteria / _pdbx_nmr_ensemble.conformers_calculated_total_number / _pdbx_nmr_sample_details.contents / _pdbx_nmr_sample_details.label / _pdbx_nmr_sample_details.solvent_system / _pdbx_nmr_sample_details.type / _pdbx_nmr_software.classification / _pdbx_nmr_software.name / _pdbx_nmr_software.version / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LANTIBIOTIC MERSACIDIN


Theoretical massNumber of molelcules
Total (without water)1,8341
Polymers1,8341
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area210 Å2
ΔGint-2 kcal/mol
Surface area1560 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)17 / 50structures with the lowest energy
Representative

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Components

#1: Protein/peptide LANTIBIOTIC MERSACIDIN / TYPE-B LANTIBIOTICS MERSACIDIN


Type: Oligopeptide / Class: Antibiotic / Mass: 1834.256 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: MERSACIDIN IS A TETRACYCLIC PEPTIDE. POST TRANSLATIONAL MATURATION OF LANTIBIOTICS INVOLVES THE ENZYMIC CONVERSION OF THR, AND SER INTO DEHYDRATED AA AND THE FORMATION OF THIOETHER BONDS ...Details: MERSACIDIN IS A TETRACYCLIC PEPTIDE. POST TRANSLATIONAL MATURATION OF LANTIBIOTICS INVOLVES THE ENZYMIC CONVERSION OF THR, AND SER INTO DEHYDRATED AA AND THE FORMATION OF THIOETHER BONDS WITH CYSTEINE. THE CARBOXY-TERMINAL BETA-METHYLLANTHIONINE UNDERGOES DECARBOXYLATION. THIOETHER BONDS WITH CYSTEINE RESULT IN FOUR RINGS. THIS IS FOLLOWED BY MEMBRANE TRANSLOCATION AND CLEAVAGE OF THE MODIFIED PRECURSOR.
Source: (natural) BACILLUS SP. HIL-Y85/54728 (bacteria) / Strain: HIL Y-85, 54728 / References: UniProt: P43683, Mersacidin
Compound detailsMERSACIDIN IS A GLOBULAR TYPE B LANTIBIOTIC. THE LANTIBIOTICS ARE CHARACTERIZED BY THIOETHER AMINO ...MERSACIDIN IS A GLOBULAR TYPE B LANTIBIOTIC. THE LANTIBIOTICS ARE CHARACTERIZED BY THIOETHER AMINO ACIDS LANTHIONINE AND/OR METHYLLANTHIONINE. HERE, MERSACIDIN 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
1212D TOCSY
131DQF-COSY

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Sample preparation

DetailsType: micelle
Contents: 2 mM mersacidin in 10 mM sodium phosphate buffer at pH 6.0, 2mM unlabeled lipid II, 100mM perdeuterated DPC, 37% methanol/63% H2O
Label: sample_1 / Solvent system: 37% methanol/63% H2O
Sample conditionspH: 6.0 / Pressure: 1 atm / Temperature: 293 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 spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYPLUSVarianUNITYPLUS5001
Bruker DRXBrukerDRX6002
Bruker DRXBrukerDRX7503

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Processing

NMR software
NameVersionClassification
ARIA1.1refinement
XWINNMRcollection
NMRPIPEprocessing
CNS1.1structure calculation
ARIA1.1structure calculation
RefinementMethod: SIMULATED ANNEALING TORSION, ANGLE DYNAMICS / Software ordinal: 1 / Details: OPLS WATER REFINEMENT
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 17

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