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- PDB-1aj1: NMR STRUCTURE OF THE LANTIBIOTIC ACTAGARDINE -

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Basic information

Entry
Database: PDB / ID: 1aj1
TitleNMR STRUCTURE OF THE LANTIBIOTIC ACTAGARDINE
ComponentsLANTIBIOTIC ACTAGARDINE
KeywordsANTIBIOTIC / LANTIBIOTIC / ANTIMICROBIAL / BACTERIOCIN / THIOESTER / TRANSMEMBRANE PORE
Function / homologykilling of cells of another organism / defense response to bacterium / signaling receptor binding / ACTAGARDINE / Lantibiotic actagardine
Function and homology information
Biological speciesActinoplanes liguriensis (bacteria)
MethodSOLUTION NMR / DISTANCE GEOMETRY, ITERATIVE RELAXATION MATRIX REFINEMENT, RESTRAINED MOLECULAR DYNAMICS
AuthorsZimmermann, N. / Jung, G.
Citation
Journal: Eur.J.Biochem. / Year: 1997
Title: The three-dimensional solution structure of the lantibiotic murein-biosynthesis-inhibitor actagardine determined by NMR.
Authors: Zimmermann, N. / Jung, G.
#1: Journal: Eur.J.Biochem. / Year: 1995
Title: The Tetracyclic Lantibiotic Actagardine. 1H-NMR and 13C-NMR Assignments and Revised Primary Structure
Authors: Zimmermann, N. / Metzger, J.W. / Jung, G.
History
DepositionMay 14, 1997Processing site: BNL
Revision 1.0Oct 15, 1997Provider: 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 1.5Dec 11, 2019Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Source and taxonomy / Structure summary
Category: citation / entity_name_com ...citation / entity_name_com / entity_src_nat / pdbx_database_status / struct_conn / struct_ref / struct_ref_seq
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity_src_nat.pdbx_beg_seq_num / _entity_src_nat.pdbx_end_seq_num / _entity_src_nat.pdbx_ncbi_taxonomy_id / _entity_src_nat.pdbx_organism_scientific / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession
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 / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code_can / _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
Revision 2.1Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LANTIBIOTIC ACTAGARDINE


Theoretical massNumber of molelcules
Total (without water)1,8821
Polymers1,8821
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)15 / 100LEAST RESTRAINT VIOLATIONS, BEST RELAXATION MATRIX R- FACTORS
Representative

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Components

#1: Protein/peptide LANTIBIOTIC ACTAGARDINE


Type: Oligopeptide / Class: Lantibiotic / Mass: 1882.296 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: ACTAGARDINE IS A TRICYCLIC PEPTIDE. POST TRANSLATIONAL MATURATION OF LANTIBIOTICS INVOLVES THE ENZYMIC CONVERSION OF THR AND SER INTO DEHYDRATED AMINO ACIDS AND THE FORMATION OF THIOETHER ...Details: ACTAGARDINE IS A TRICYCLIC PEPTIDE. POST TRANSLATIONAL MATURATION OF LANTIBIOTICS INVOLVES THE ENZYMIC CONVERSION OF THR AND SER INTO DEHYDRATED AMINO ACIDS AND THE FORMATION OF THIOETHER BONDS WITH CYSTEINE. THE THIOETHER BONDS WITH CYSTEINE RESULT IN THREE RING STRUCTURES. THIS IS FOLLOWED BY MEMBRANE TRANSLOCATION AND CLEAVAGE OF THE MODIFIED PRECURSOR.
Source: (natural) Actinoplanes liguriensis (bacteria) / References: ACTAGARDINE, UniProt: P56650*PLUS
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: NOESY

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Sample preparation

Sample conditionspH: 3 / Temperature: 296 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AMX2 600 / Manufacturer: Bruker / Model: AMX2 600 / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
IRMABOELENS,BONVINrefinement
BRUKER UXNMR UXNMRstructure solution
BIOSYM FELIX 2.3structure solution
BIOSYM NMRCHITECT NMRCHITECTstructure solution
RefinementMethod: DISTANCE GEOMETRY, ITERATIVE RELAXATION MATRIX REFINEMENT, RESTRAINED MOLECULAR DYNAMICS
Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATIONS, BEST RELAXATION MATRIX R- FACTORS
Conformers calculated total number: 100 / Conformers submitted total number: 15

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