data_5581 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR solution structure of type-B lantibiotics mersacidin in MeOH/H2O mixture ; _BMRB_accession_number 5581 _BMRB_flat_file_name bmr5581.str _Entry_type original _Submission_date 2002-11-06 _Accession_date 2002-11-06 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details . loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Hsu Shang-Te D. . 2 Breukink Eefjan . . 3 Bierbaum Gabriele . . 4 Sahl Hans-Georg . . 5 'de Kruijff' Ben . . 6 Kaptein Rob . . 7 'van Nuland' Nico A.J. . 8 Bonvin Alexandre M.J.J. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 82 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2008-07-17 update BMRB 'Updating non-standard residue' stop_ loop_ _Related_BMRB_accession_number _Relationship 5580 'free form lantibiotics mersacidin bound to lipid II in DPC micelles.' 5582 'free form lantibiotics mersacidin in DPC micelles.' stop_ _Original_release_date 2002-11-06 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; NMR Study of Mersacidin and Lipid II Interaction in Dodecylphosphocholine Micelles: Conformational Changes are a Key to Antimicrobial Activity ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code 22566040 _PubMed_ID 12562773 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Hsu Shang-Te D. . 2 Breukink Eefjan . . 3 Bierbaum Gabriele . . 4 Sahl Hans-Georg . . 5 'de Kruijff' Ben . . 6 Kaptein Rob . . 7 'van Nuland' Nico A.J. . 8 Bonvin Alexandre M.J.J. . stop_ _Journal_abbreviation 'J. Biol. Chem.' _Journal_volume 278 _Journal_issue 15 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 13110 _Page_last 13117 _Year 2003 _Details . loop_ _Keyword Lantibiotics peptidoglycan stop_ save_ ####################################### # Cited references within the entry # ####################################### save_X-ray_structure _Saveframe_category citation _Citation_full ; Schneider TR, Karcher J, Pohl E, Lubini P, Sheldrick GM. Ab initio structure determination of the lantibiotic mersacidin. Acta Crystallogr D Biol Crystallogr. 2000 Jun;56 (Pt 6):705-13. ; _Citation_title ; Ab initio structure determination of the lantibiotic mersacidin. ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 10818347 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Schneider 'T. R.' R. . 2 Karcher J. . . 3 Pohl E. . . 4 Lubini P. . . 5 Sheldrick 'G. M.' M. . stop_ _Journal_abbreviation 'Acta Crystallogr. D Biol. Crystallogr.' _Journal_name_full 'Acta crystallographica. Section D, Biological crystallography' _Journal_volume 56 _Journal_issue 'Pt 6' _Journal_CSD . _Book_title . _Book_chapter_title . _Book_volume . _Book_series . _Book_publisher . _Book_publisher_city . _Book_ISBN . _Conference_title . _Conference_site . _Conference_state_province . _Conference_country . _Conference_start_date . _Conference_end_date . _Conference_abstract_number . _Thesis_institution . _Thesis_institution_city . _Thesis_institution_country . _Page_first 705 _Page_last 713 _Year 2000 _Details ; The crystal structure of mersacidin, a potential novel antibiotic against methicillin- and vancomycin-resistant Staphylococcus aureus strains, has been determined by ab initio methods. Despite all crystals being merohedrally twinned, an accurate structural model with an R value of 13.4% has been obtained at atomic resolution. With six molecules in the asymmetric unit and no atom heavier than sulfur, the structure corresponds to a protein of 120 amino acids and is the largest approximately equal-atom unknown structure solved by direct methods. In the crystal, the molecule assumes a compact fold different from that found by NMR in solution. Comparison of the NCS-related molecules reveals regions of variable flexibility. The region highly homologous to the related antibiotic actagardine is very rigid and possibly defines an essential building block of this class of new antibacterial substances. ; save_ save_NMR_structure _Saveframe_category citation _Citation_full ; Prasch T, Naumann T, Markert RL, Sattler M, Schubert W, Schaal S, Bauch M, Kogler H, Griesinger C. Constitution and solution conformation of the antibiotic mersacidin determined by NMR and molecular dynamics. Eur J Biochem. 1997 Mar 1;244(2):501-12. ; _Citation_title ; Constitution and solution conformation of the antibiotic mersacidin determined by NMR and molecular dynamics. ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 9119018 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Prasch T. . . 2 Naumann T. . . 3 Markert 'R. L.' L. . 4 Sattler M. . . 5 Schubert W. . . 6 Schaal S. . . 7 Bauch M. . . 8 Kogler H. . . 9 Griesinger C. . . stop_ _Journal_abbreviation 'Eur. J. Biochem.' _Journal_name_full 'European journal of biochemistry / FEBS' _Journal_volume 244 _Journal_issue 2 _Journal_CSD . _Book_title . _Book_chapter_title . _Book_volume . _Book_series . _Book_publisher . _Book_publisher_city . _Book_ISBN . _Conference_title . _Conference_site . _Conference_state_province . _Conference_country . _Conference_start_date . _Conference_end_date . _Conference_abstract_number . _Thesis_institution . _Thesis_institution_city . _Thesis_institution_country . _Page_first 501 _Page_last 512 _Year 1997 _Details ; The solution structure of the tetracyclic lantibiotic mersacidin in methanol (CD3OH) has been determined by NMR followed by distance bound driven dynamics and subsequent restrained molecular dynamics simulations combined with an iterative relaxation matrix approach and alternatively by a simulated annealing protocol. The molecular dynamics simulations were performed with the AMBER program system and with the INSIGHT program package. The distance bound driven dynamics calculation was conducted using a modified version of the DISGEO II program. The interproton distance restraints were derived from jump symmetrized rotating-frame Overhauser enhancement and exchange (JS-ROESY) spectra, which yield optimum sensitivity for medium-sized molecules like mersacidin. The connectivities via the sulfide bridges were unambiguously confirmed by heteronuclear NMR techniques (heteronuclear single quantum coherence and heteronuclear multiple bond correlation methods). Due to the tetracyclic structure, mersacidin exhibits a rather rigid globular shape, which neither belongs to the duramycin nor to the nisin structure type lantibiotics. The resulting structures for the simulated annealing protocol of restrained and subsequent free molecular dynamics were compared and found to be very similar. ; save_ ################################## # Molecular system description # ################################## save_system_Mersacidin _Saveframe_category molecular_system _Mol_system_name 'Type B lantibiotic mersacidin' _Abbreviation_common Mersacidin _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'lantibiotic Mersacidin' $Mersacidin stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state monomer _System_paramagnetic no _System_thiol_state 'all other bound' _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_Mersacidin _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common 'Type B lantibiotics mersacidin' _Abbreviation_common Mersacidin _Molecular_mass . _Mol_thiol_state 'all other bound' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 20 _Mol_residue_sequence ; CXFXLPGGGGVCXLXXECIX ; loop_ _Residue_seq_code _Residue_label 1 CYS 2 ABA 3 PHE 4 ABA 5 LEU 6 PRO 7 GLY 8 GLY 9 GLY 10 GLY 11 VAL 12 CYS 13 ABA 14 LEU 15 ABA 16 DHA 17 GLU 18 CYS 19 ILE 20 DHL stop_ _Sequence_homology_query_date 2005-11-24 _Sequence_homology_query_revised_last_date 2005-11-22 loop_ _Database_name _Database_accession_code _Database_entry_mol_name _Sequence_query_to_submitted_percentage _Sequence_subject_length _Sequence_identity _Sequence_positive _Sequence_homology_expectation_value BMRB 5580 'Type B lantibiotics mersacidin' 100.00 20 100 100 0.54 BMRB 5581 'Type B lantibiotics mersacidin' 100.00 20 100 100 0.54 BMRB 5582 'Type B lantibiotics mersacidin' 100.00 20 100 100 0.54 PDB 1MQX 'A Chain A, Nmr Solution Structure Of Type-BLantibiotics Mersacidin In MeohH2O MIXTURE' 100.00 20 100 100 0.54 PDB 1MQY 'A Chain A, Nmr Solution Structure Of Type-BLantibiotics Mersacidin In Dpc Micelles' 100.00 20 100 100 0.54 PDB 1MQZ 'A Chain A, Nmr Solution Structure Of Type-BLantibiotics Mersacidin Bound To Lipid Ii In DpcMicelles' 100.00 20 100 100 0.54 PDB 1QOW 'A Chain A, Mersacidin From Bacillus' 100.00 20 100 100 0.54 stop_ save_ ###################### # Polymer residues # ###################### save_chem_comp_ABA _Saveframe_category polymer_residue _Mol_type 'L-peptide linking' _Name_common 'ALPHA-AMINOBUTYRIC ACID' _BMRB_code . _PDB_code ABA _Standard_residue_derivative . _Molecular_mass 103.120 _Mol_paramagnetic . _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Mon Jul 25 12:48:05 2011 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons N N N . 0 . ? CA CA C . 0 . ? C C C . 0 . ? O O O . 0 . ? CB CB C . 0 . ? CG CG C . 0 . ? OXT OXT O . 0 . ? H H H . 0 . ? HN2 HN2 H . 0 . ? HA HA H . 0 . ? HB3 HB3 H . 0 . ? HB2 HB2 H . 0 . ? HG1 HG1 H . 0 . ? HG3 HG3 H . 0 . ? HG2 HG2 H . 0 . ? HXT HXT H . 0 . ? stop_ loop_ _Bond_order _Bond_atom_one_atom_name _Bond_atom_two_atom_name _PDB_bond_atom_one_atom_name _PDB_bond_atom_two_atom_name SING N CA ? ? SING N H ? ? SING N HN2 ? ? SING CA C ? ? SING CA CB ? ? SING CA HA ? ? DOUB C O ? ? SING C OXT ? ? SING CB CG ? ? SING CB HB3 ? ? SING CB HB2 ? ? SING CG HG1 ? ? SING CG HG3 ? ? SING CG HG2 ? ? SING OXT HXT ? ? stop_ save_ save_chem_comp_DHA _Saveframe_category polymer_residue _Mol_type 'PEPTIDE LINKING' _Name_common '2-AMINO-ACRYLIC ACID' _BMRB_code . _PDB_code DHA _Standard_residue_derivative . _Molecular_mass 87.077 _Mol_paramagnetic . _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Mon Jul 25 12:49:16 2011 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons N N N . 0 . ? CA CA C . 0 . ? CB CB C . 0 . ? C C C . 0 . ? O O O . 0 . ? OXT OXT O . 0 . ? H H H . 0 . ? H2 H2 H . 0 . ? HB1 HB1 H . 0 . ? HB2 HB2 H . 0 . ? HXT HXT H . 0 . ? stop_ loop_ _Bond_order _Bond_atom_one_atom_name _Bond_atom_two_atom_name _PDB_bond_atom_one_atom_name _PDB_bond_atom_two_atom_name SING N CA ? ? SING N H ? ? SING N H2 ? ? DOUB CA CB ? ? SING CA C ? ? SING CB HB1 ? ? SING CB HB2 ? ? DOUB C O ? ? SING C OXT ? ? SING OXT HXT ? ? stop_ save_ save_chem_comp_DHL _Saveframe_category polymer_residue _Mol_type 'L-PEPTIDE LINKING' _Name_common 2-AMINO-ETHANETHIOL _BMRB_code DHL _PDB_code DHL _Standard_residue_derivative . _Molecular_mass 77.149 _Mol_paramagnetic . _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons N N N . 0 . ? CA CA C . 0 . ? CB CB C . 0 . ? SG SG S . 0 . ? HN1 HN1 H . 0 . ? HN2 HN2 H . 0 . ? HA2 HA2 H . 0 . ? HA3 HA3 H . 0 . ? HB2 HB2 H . 0 . ? HB3 HB3 H . 0 . ? HS HS H . 0 . ? stop_ loop_ _Bond_order _Bond_atom_one_atom_name _Bond_atom_two_atom_name _PDB_bond_atom_one_atom_name _PDB_bond_atom_two_atom_name SING N CA ? ? SING N HN1 ? ? SING N HN2 ? ? SING CA CB ? ? SING CA HA2 ? ? SING CA HA3 ? ? SING CB SG ? ? SING CB HB2 ? ? SING CB HB3 ? ? SING SG HS ? ? stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species _Strain $Mersacidin 'Bacillus sp.' 1409 Eubacteria . Bacillus 'Bacillus sp.' 'HIL Y-85,54728' stop_ save_ ######################### # Experimental source # ######################### save_experimental_source _Saveframe_category experimental_source loop_ _Mol_label _Production_method _Host_organism_name_common _Genus _Species _Strain _Vector_name $Mersacidin 'purified from the natural source' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $Mersacidin 2 mM . MeOH 37 % [U-2H] stop_ save_ ############################ # Computer software used # ############################ save_XWINNMR _Saveframe_category software _Name xwinnmr _Version . loop_ _Task collection stop_ _Details . save_ save_NMRPipe _Saveframe_category software _Name NMRPipe _Version . loop_ _Task processing stop_ _Details . save_ save_CNS _Saveframe_category software _Name CNS _Version 1.1 loop_ _Task 'structure solution' stop_ _Details . save_ save_ARIA _Saveframe_category software _Name ARIA _Version 1.1 loop_ _Task 'structure solution' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DRX _Field_strength 750 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _Sample_label $sample_1 save_ save_2D_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D TOCSY' _Sample_label $sample_1 save_ save_DQF-COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name DQF-COSY _Sample_label $sample_1 save_ ####################### # Sample conditions # ####################### save_sample_cond_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 6.0 0.2 n/a pressure 1 . atm temperature 293 0.5 K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference _Saveframe_category chemical_shift_reference _Details . loop_ _Mol_common_name _Atom_type _Atom_isotope_number _Atom_group _Chem_shift_units _Chem_shift_value _Reference_method _Reference_type _External_reference_sample_geometry _External_reference_location _External_reference_axis _Indirect_shift_ratio DSS H 1 'methyl protons' ppm 0.0 internal direct . . . 1.0 stop_ save_ ################################### # Assigned chemical shift lists # ################################### ################################################################### # Chemical Shift Ambiguity Index Value Definitions # # # # The values other than 1 are used for those atoms with different # # chemical shifts that cannot be assigned to stereospecific atoms # # or to specific residues or chains. # # # # Index Value Definition # # # # 1 Unique (including isolated methyl protons, # # geminal atoms, and geminal methyl # # groups with identical chemical shifts) # # (e.g. ILE HD11, HD12, HD13 protons) # # 2 Ambiguity of geminal atoms or geminal methyl # # proton groups (e.g. ASP HB2 and HB3 # # protons, LEU CD1 and CD2 carbons, or # # LEU HD11, HD12, HD13 and HD21, HD22, # # HD23 methyl protons) # # 3 Aromatic atoms on opposite sides of # # symmetrical rings (e.g. TYR HE1 and HE2 # # protons) # # 4 Intraresidue ambiguities (e.g. LYS HG and # # HD protons or TRP HZ2 and HZ3 protons) # # 5 Interresidue ambiguities (LYS 12 vs. LYS 27) # # 6 Intermolecular ambiguities (e.g. ASP 31 CA # # in monomer 1 and ASP 31 CA in monomer 2 # # of an asymmetrical homodimer, duplex # # DNA assignments, or other assignments # # that may apply to atoms in one or more # # molecule in the molecular assembly) # # 9 Ambiguous, specific ambiguity not defined # # # ################################################################### save_chemical_shift_set_1 _Saveframe_category assigned_chemical_shifts _Details ; Two distinct conformations were obtained for the glycine-rich ring (residues 5-11) and models 1-9 and models 10-17 belong to those clusters, respectively. ; loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_cond_1 _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name 'lantibiotic Mersacidin' _Text_data_format . _Text_data . loop_ _Atom_shift_assign_ID _Residue_author_seq_code _Residue_seq_code _Residue_label _Atom_name _Atom_type _Chem_shift_value _Chem_shift_value_error _Chem_shift_ambiguity_code 1 . 1 CYS HB3 H 2.599 0.025 2 2 . 1 CYS HB2 H 3.056 0.025 2 3 . 2 ABA H H 8.005 0.025 1 4 . 2 ABA HA H 4.160 0.025 1 5 . 2 ABA HB H 3.433 0.025 1 6 . 2 ABA HG1 H 1.480 0.025 1 7 . 3 PHE H H 8.575 0.025 1 8 . 3 PHE HA H 5.002 0.025 1 9 . 3 PHE HB3 H 2.967 0.025 2 10 . 3 PHE HB2 H 3.150 0.025 2 11 . 3 PHE HD1 H 7.255 0.025 1 12 . 3 PHE HE1 H 7.303 0.025 1 13 . 3 PHE HE2 H 7.303 0.025 1 14 . 3 PHE HD2 H 7.255 0.025 1 15 . 4 ABA H H 8.205 0.025 1 16 . 4 ABA HA H 4.981 0.025 1 17 . 4 ABA HB H 3.425 0.025 1 18 . 4 ABA HG1 H 0.557 0.025 1 19 . 5 LEU H H 8.209 0.025 1 20 . 5 LEU HA H 4.605 0.025 1 21 . 5 LEU HB3 H 1.995 0.025 1 22 . 5 LEU HB2 H 1.995 0.025 1 23 . 6 PRO HA H 4.348 0.025 1 24 . 6 PRO HB3 H 2.164 0.025 1 25 . 6 PRO HB2 H 2.164 0.025 1 26 . 6 PRO HG3 H 1.788 0.025 2 27 . 6 PRO HG2 H 1.911 0.025 2 28 . 6 PRO HD3 H 3.661 0.025 1 29 . 6 PRO HD2 H 3.661 0.025 1 30 . 7 GLY H H 8.847 0.025 1 31 . 7 GLY HA3 H 3.940 0.025 2 32 . 7 GLY HA2 H 3.990 0.025 2 33 . 8 GLY H H 8.738 0.025 1 34 . 8 GLY HA3 H 3.857 0.025 2 35 . 8 GLY HA2 H 3.983 0.025 2 36 . 9 GLY H H 8.280 0.025 1 37 . 9 GLY HA3 H 3.861 0.025 2 38 . 9 GLY HA2 H 4.091 0.025 2 39 . 10 GLY H H 8.037 0.025 1 40 . 10 GLY HA3 H 3.999 0.025 1 41 . 10 GLY HA2 H 3.999 0.025 1 42 . 11 VAL H H 8.390 0.025 1 43 . 11 VAL HA H 4.129 0.025 1 44 . 11 VAL HB H 2.031 0.025 1 45 . 11 VAL HG2 H 0.898 0.025 2 46 . 11 VAL HG1 H 0.921 0.025 2 47 . 12 CYS H H 8.771 0.025 1 48 . 12 CYS HA H 4.188 0.025 1 49 . 12 CYS HB3 H 2.794 0.025 2 50 . 12 CYS HB2 H 2.870 0.025 2 51 . 13 ABA H H 8.467 0.025 1 52 . 13 ABA HA H 4.720 0.025 1 53 . 13 ABA HB H 3.904 0.025 1 54 . 13 ABA HG1 H 1.331 0.025 1 55 . 14 LEU H H 8.091 0.025 1 56 . 14 LEU HA H 4.970 0.025 1 57 . 14 LEU HB3 H 1.471 0.025 2 58 . 14 LEU HB2 H 1.716 0.025 2 59 . 15 ABA H H 8.653 0.025 1 60 . 15 ABA HA H 4.931 0.025 1 61 . 15 ABA HB H 3.254 0.025 1 62 . 15 ABA HG1 H 1.381 0.025 1 63 . 16 DHA HB2 H 5.641 0.025 2 64 . 16 DHA HB3 H 5.306 0.025 2 65 . 17 GLU H H 8.824 0.025 1 66 . 17 GLU HA H 4.245 0.025 1 67 . 17 GLU HB3 H 1.963 0.025 2 68 . 17 GLU HB2 H 2.315 0.025 2 69 . 17 GLU HG3 H 2.227 0.025 1 70 . 17 GLU HG2 H 2.227 0.025 1 71 . 18 CYS H H 8.334 0.025 1 72 . 18 CYS HA H 4.792 0.025 1 73 . 18 CYS HB3 H 2.992 0.025 2 74 . 18 CYS HB2 H 3.201 0.025 2 75 . 19 ILE H H 8.037 0.025 1 76 . 19 ILE HA H 3.911 0.025 1 77 . 19 ILE HB H 2.112 0.025 1 78 . 19 ILE HD1 H 0.903 0.025 1 79 . 19 ILE HG2 H 0.904 0.025 1 80 . 20 DHL H H 8.288 0.025 1 81 . 20 DHL HA H 6.802 0.025 1 82 . 20 DHL HB2 H 5.516 0.025 1 stop_ save_