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- PDB-2mh5: Structure and NMR assignments of lantibiotic NAI-107 in DPC micelles -

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Basic information

Entry
Database: PDB / ID: 2mh5
TitleStructure and NMR assignments of lantibiotic NAI-107 in DPC micelles
ComponentsLantibiotic 107891
KeywordsANTIBIOTIC / lantibiotic
Function / homologycytolysis / defense response to bacterium / signaling receptor binding / Lantibiotic 107891 / dodecyl 2-(trimethylammonio)ethyl phosphate / Lantibiotic 107891
Function and homology information
Biological speciesMicrobispora (bacteria)
MethodSOLUTION NMR / molecular dynamics
Model detailsfewest violations, model1
AuthorsMunch, D. / Muller, A. / Schneider, T. / Kohl, B. / Wenzel, M. / Bandow, J. / Maffioli, S. / Sosio, M. / Donadio, S. / Wimmer, R. / Sahl, H.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: The Lantibiotic NAI-107 Binds to Bactoprenol-bound Cell Wall Precursors and Impairs Membrane Functions.
Authors: Munch, D. / Muller, A. / Schneider, T. / Kohl, B. / Wenzel, M. / Bandow, J.E. / Maffioli, S. / Sosio, M. / Donadio, S. / Wimmer, R. / Sahl, H.G.
History
DepositionNov 18, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2014Group: Database references
Revision 1.2May 14, 2014Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Jul 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Polymer sequence
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_poly / struct_conn
Item: _database_2.pdbx_DOI / _entity_poly.pdbx_seq_one_letter_code_can / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lantibiotic 107891
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,08866
Polymers2,2431
Non-polymers22,84565
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 80structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide Lantibiotic 107891


Type: Oligopeptide / Class: Antibiotic / Mass: 2243.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: NAI-107 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 ...Details: NAI-107 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) Microbispora (bacteria) / Strain: 107891 / References: UniProt: P85065, Lantibiotic 107891
#2: Chemical...
ChemComp-DPV / dodecyl 2-(trimethylammonio)ethyl phosphate / dodecylphosphocholine


Mass: 351.462 Da / Num. of mol.: 65 / Source method: obtained synthetically / Formula: C17H38NO4P
Compound detailsNAI-107 (LANTIBIOTIC 107891) IS A GLOBULAR TYPE B LANTIBIOTIC. THE LANTIBIOTICS ARE CHARACTERIZED ...NAI-107 (LANTIBIOTIC 107891) IS A GLOBULAR TYPE B LANTIBIOTIC. THE LANTIBIOTICS ARE CHARACTERIZED BY THIOETHER AMINO ACIDS LANTHIONINE AND/OR METHYLLANTHIONINE. HERE, NAI-107 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 1H-1H TOCSY
1212D 1H-1H NOESY
1312D 1H-13C HSQC aliphatic
1412D 1H-13C HSQC aromatic

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Sample preparation

DetailsContents: 3.5 mM entity_1, 150 mM [U-2H] dodecylphosphocholine-d38, 10 mM potassium phosphate, 0.02 mM 2,2,3,3-D TSP-d4, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
3.5 mMentity_1-11
150 mMdodecylphosphocholine-d38-2[U-2H]1
10 mMpotassium phosphate-31
0.02 mMTSP-d4-42,2,3,3-D1
Sample conditionspH: 6.2 / Pressure: ambient / Temperature: 310.1 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVIIIBrukerAVIII6001
Bruker AvanceBrukerAVANCE9002
Bruker DRXBrukerDRX6003

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.1Bruker Biospincollection
CARAKeller and Wuthrichchemical shift assignment
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
YASARAYasara Biosciencesrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
Details: Refinement was done in two steps: first in vacuo and then with explicit micelle/water system. The pseudo atoms labeled ANI are included in the constraint file. These define an alignment ...Details: Refinement was done in two steps: first in vacuo and then with explicit micelle/water system. The pseudo atoms labeled ANI are included in the constraint file. These define an alignment frame used in the structural interpretation of rdc data.
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 80 / Conformers submitted total number: 20

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