data_30165 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; [3]catenane from MccJ25 G12R/I13C/G21C lasso peptide ; _BMRB_accession_number 30165 _BMRB_flat_file_name bmr30165.str _Entry_type original _Submission_date 2016-08-30 _Accession_date 2016-08-30 _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 Link A. J. . 2 Allen C. D. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 4 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 206 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2016-11-28 original BMRB . stop_ _Original_release_date 2016-11-28 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Self-assembly of catenanes from lasso peptides ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 27768305 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Link A. J. . 2 Allen C. D. . stop_ _Journal_abbreviation 'J. Am. Chem. Soc.' _Journal_volume 138 _Journal_issue 43 _Journal_CSD 0353 _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 14214 _Page_last 14217 _Year 2016 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'Microcin J25' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'entity_1, chain 1' $entity_1 'entity_2, chain 1' $entity_2 'entity_1, chain 2' $entity_1 'entity_2, chain 2' $entity_2 stop_ _System_molecular_weight . _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_entity_1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common 'Microcin J25' _Molecular_mass 1290.427 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 12 _Mol_residue_sequence ; GGAGHVPEYFVR ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 GLY 2 2 GLY 3 3 ALA 4 4 GLY 5 5 HIS 6 6 VAL 7 7 PRO 8 8 GLU 9 9 TYR 10 10 PHE 11 11 VAL 12 12 ARG stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ save_entity_2 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common 'Microcin J25' _Molecular_mass 990.154 _Mol_thiol_state 'all disulfide bound' _Details . _Residue_count 9 _Mol_residue_sequence ; CGTPISFYC ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 13 CYS 2 14 GLY 3 15 THR 4 16 PRO 5 17 ILE 6 18 SER 7 19 PHE 8 20 TYR 9 21 CYS stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species _Gene_mnemonic $entity_1 enterobacteria 562 Bacteria . Escherichia coli mcjA $entity_2 enterobacteria 562 Bacteria . Escherichia coli mcjA 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 $entity_1 'recombinant technology' . Escherichia coli . . $entity_2 'recombinant technology' . Escherichia coli . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details '3.7 mg/mL [3]catenane from MccJ25 RCC lasso peptide, 95% H2O/5% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 3.7 mg/mL 'natural abundance' H2O 95 % 'natural abundance' D2O 5 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name CYANA _Version 2.1 loop_ _Vendor _Address _Electronic_address 'Guntert, Mumenthaler and Wuthrich' . . stop_ loop_ _Task 'structure calculation' stop_ _Details . save_ save_software_2 _Saveframe_category software _Name GROMACS _Version 5.1.1 loop_ _Vendor _Address _Electronic_address 'Abraham, Hess, van der Spoel, Lindahl' . . stop_ loop_ _Task refinement stop_ _Details . save_ save_software_3 _Saveframe_category software _Name MestReNova _Version 9.0.1 loop_ _Vendor _Address _Electronic_address 'Mestrelab Research S.L.' . . stop_ loop_ _Task 'data analysis' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AvanceIII _Field_strength 800 _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_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pressure 1 . atm temperature 295 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chem_shift_reference_1 _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 'Deuterium Oxide' H 2 protons ppm 4.8 internal indirect . . . 6.5143996113 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_assigned_chemical_shifts_1_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D NOESY' '2D TOCSY' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chem_shift_reference_1 _Mol_system_component_name 'entity_1, chain 1' _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 1 GLY H H 7.781 0.04 1 2 1 1 GLY HA2 H 4.060 0.04 2 3 1 1 GLY HA3 H 3.385 0.04 2 4 2 2 GLY H H 8.842 0.04 1 5 2 2 GLY HA2 H 4.123 0.04 2 6 2 2 GLY HA3 H 3.727 0.04 2 7 3 3 ALA H H 8.442 0.04 1 8 3 3 ALA HA H 4.589 0.04 1 9 3 3 ALA HB H 1.209 0.04 1 10 4 4 GLY H H 7.858 0.04 1 11 4 4 GLY HA2 H 3.940 0.04 2 12 4 4 GLY HA3 H 3.410 0.04 2 13 5 5 HIS HA H 4.306 0.04 1 14 5 5 HIS HB2 H 3.119 0.04 2 15 5 5 HIS HB3 H 2.980 0.04 2 16 5 5 HIS HD2 H 7.180 0.04 1 17 6 6 VAL H H 8.820 0.04 1 18 6 6 VAL HA H 4.614 0.04 1 19 6 6 VAL HB H 1.843 0.04 1 20 6 6 VAL HG1 H 0.762 0.04 2 21 6 6 VAL HG2 H 0.996 0.04 2 22 7 7 PRO HA H 4.014 0.04 1 23 7 7 PRO HB2 H 1.801 0.04 2 24 7 7 PRO HB3 H 2.001 0.04 2 25 7 7 PRO HG2 H 1.415 0.04 1 26 7 7 PRO HG3 H 1.415 0.04 1 27 7 7 PRO HD2 H 3.722 0.04 2 28 7 7 PRO HD3 H 3.208 0.04 2 29 8 8 GLU HB2 H 1.357 0.04 2 30 8 8 GLU HB3 H 1.288 0.04 2 31 8 8 GLU HG2 H 1.607 0.04 2 32 8 8 GLU HG3 H 1.503 0.04 2 33 9 9 TYR HA H 4.435 0.04 1 34 9 9 TYR HB2 H 2.755 0.04 2 35 9 9 TYR HB3 H 2.576 0.04 2 36 9 9 TYR HD1 H 6.797 0.04 3 37 9 9 TYR HD2 H 6.797 0.04 3 38 9 9 TYR HE1 H 6.521 0.04 3 39 9 9 TYR HE2 H 6.521 0.04 3 40 10 10 PHE H H 8.025 0.04 1 41 10 10 PHE HA H 4.505 0.04 1 42 10 10 PHE HB2 H 2.779 0.04 2 43 10 10 PHE HB3 H 2.650 0.04 2 44 10 10 PHE HD1 H 6.880 0.04 3 45 10 10 PHE HD2 H 6.880 0.04 3 46 10 10 PHE HE1 H 7.002 0.04 3 47 10 10 PHE HE2 H 7.002 0.04 3 48 11 11 VAL H H 8.005 0.04 1 49 11 11 VAL HA H 3.873 0.04 1 50 11 11 VAL HB H 1.780 0.04 1 51 11 11 VAL HG1 H 0.726 0.04 1 52 11 11 VAL HG2 H 0.726 0.04 1 53 12 12 ARG H H 7.914 0.04 1 54 12 12 ARG HA H 4.025 0.04 1 55 12 12 ARG HB2 H 1.675 0.04 2 56 12 12 ARG HB3 H 1.552 0.04 2 57 12 12 ARG HG2 H 1.424 0.04 1 58 12 12 ARG HG3 H 1.424 0.04 1 59 12 12 ARG HD2 H 2.984 0.04 1 60 12 12 ARG HD3 H 2.984 0.04 1 61 12 12 ARG HE H 7.037 0.04 1 stop_ save_ save_assigned_chemical_shifts_1_2 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D NOESY' '2D TOCSY' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chem_shift_reference_1 _Mol_system_component_name 'entity_2, chain 1' _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 13 1 CYS HA H 4.149 0.04 1 2 13 1 CYS HB2 H 3.212 0.04 2 3 13 1 CYS HB3 H 2.968 0.04 2 4 14 2 GLY H H 8.668 0.04 1 5 14 2 GLY HA2 H 4.048 0.04 2 6 14 2 GLY HA3 H 3.881 0.04 2 7 15 3 THR H H 8.223 0.04 1 8 15 3 THR HA H 4.503 0.04 1 9 15 3 THR HB H 3.976 0.04 1 10 15 3 THR HG2 H 1.111 0.04 1 11 16 4 PRO HA H 4.254 0.04 1 12 16 4 PRO HB2 H 1.838 0.04 2 13 16 4 PRO HB3 H 1.708 0.04 2 14 16 4 PRO HG2 H 1.582 0.04 2 15 16 4 PRO HG3 H 1.582 0.04 2 16 16 4 PRO HD2 H 3.745 0.04 2 17 16 4 PRO HD3 H 3.580 0.04 2 18 17 5 ILE H H 8.054 0.04 1 19 17 5 ILE HA H 4.060 0.04 1 20 17 5 ILE HB H 1.678 0.04 1 21 17 5 ILE HG13 H 1.211 0.04 2 22 17 5 ILE HG2 H 0.661 0.04 1 23 17 5 ILE HD1 H 0.661 0.04 1 24 18 6 SER HA H 4.253 0.04 1 25 18 6 SER HB2 H 3.744 0.04 2 26 18 6 SER HB3 H 3.660 0.04 2 27 19 7 PHE H H 8.636 0.04 1 28 19 7 PHE HA H 5.150 0.04 1 29 19 7 PHE HB2 H 2.486 0.04 2 30 19 7 PHE HB3 H 2.330 0.04 2 31 19 7 PHE HD1 H 6.692 0.04 3 32 19 7 PHE HD2 H 6.692 0.04 3 33 19 7 PHE HE1 H 7.016 0.04 3 34 19 7 PHE HE2 H 7.016 0.04 3 35 20 8 TYR H H 9.398 0.04 1 36 20 8 TYR HA H 4.556 0.04 1 37 20 8 TYR HB2 H 2.912 0.04 1 38 20 8 TYR HB3 H 2.912 0.04 1 39 20 8 TYR HD1 H 6.948 0.04 3 40 20 8 TYR HD2 H 6.948 0.04 3 41 20 8 TYR HE1 H 6.690 0.04 3 42 20 8 TYR HE2 H 6.690 0.04 3 stop_ save_ save_assigned_chemical_shifts_1_3 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D NOESY' '2D TOCSY' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chem_shift_reference_1 _Mol_system_component_name 'entity_1, chain 2' _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 22 1 GLY H H 7.781 0.04 1 2 22 1 GLY HA2 H 4.060 0.04 2 3 22 1 GLY HA3 H 3.385 0.04 2 4 23 2 GLY H H 8.842 0.04 1 5 23 2 GLY HA2 H 4.123 0.04 2 6 23 2 GLY HA3 H 3.727 0.04 2 7 24 3 ALA H H 8.442 0.04 1 8 24 3 ALA HA H 4.589 0.04 1 9 24 3 ALA HB H 1.209 0.04 1 10 25 4 GLY H H 7.858 0.04 1 11 25 4 GLY HA2 H 3.940 0.04 2 12 25 4 GLY HA3 H 3.410 0.04 2 13 26 5 HIS HA H 4.306 0.04 1 14 26 5 HIS HB2 H 3.119 0.04 2 15 26 5 HIS HB3 H 2.980 0.04 2 16 26 5 HIS HD2 H 7.180 0.04 1 17 27 6 VAL H H 8.820 0.04 1 18 27 6 VAL HA H 4.614 0.04 1 19 27 6 VAL HB H 1.843 0.04 1 20 27 6 VAL HG1 H 0.762 0.04 2 21 27 6 VAL HG2 H 0.996 0.04 2 22 28 7 PRO HA H 4.014 0.04 1 23 28 7 PRO HB2 H 1.801 0.04 2 24 28 7 PRO HB3 H 2.001 0.04 2 25 28 7 PRO HG2 H 1.415 0.04 1 26 28 7 PRO HG3 H 1.415 0.04 1 27 28 7 PRO HD2 H 3.722 0.04 2 28 28 7 PRO HD3 H 3.208 0.04 2 29 29 8 GLU HB2 H 1.357 0.04 2 30 29 8 GLU HB3 H 1.288 0.04 2 31 29 8 GLU HG2 H 1.607 0.04 2 32 29 8 GLU HG3 H 1.503 0.04 2 33 30 9 TYR HA H 4.435 0.04 1 34 30 9 TYR HB2 H 2.755 0.04 2 35 30 9 TYR HB3 H 2.576 0.04 2 36 30 9 TYR HD1 H 6.797 0.04 3 37 30 9 TYR HD2 H 6.797 0.04 3 38 30 9 TYR HE1 H 6.521 0.04 3 39 30 9 TYR HE2 H 6.521 0.04 3 40 31 10 PHE H H 8.025 0.04 1 41 31 10 PHE HA H 4.505 0.04 1 42 31 10 PHE HB2 H 2.779 0.04 2 43 31 10 PHE HB3 H 2.650 0.04 2 44 31 10 PHE HD1 H 6.880 0.04 3 45 31 10 PHE HD2 H 6.880 0.04 3 46 31 10 PHE HE1 H 7.002 0.04 3 47 31 10 PHE HE2 H 7.002 0.04 3 48 32 11 VAL H H 8.005 0.04 1 49 32 11 VAL HA H 3.873 0.04 1 50 32 11 VAL HB H 1.780 0.04 1 51 32 11 VAL HG1 H 0.726 0.04 1 52 32 11 VAL HG2 H 0.726 0.04 1 53 33 12 ARG H H 7.914 0.04 1 54 33 12 ARG HA H 4.025 0.04 1 55 33 12 ARG HB2 H 1.675 0.04 2 56 33 12 ARG HB3 H 1.552 0.04 2 57 33 12 ARG HG2 H 1.424 0.04 1 58 33 12 ARG HG3 H 1.424 0.04 1 59 33 12 ARG HD2 H 2.984 0.04 1 60 33 12 ARG HD3 H 2.984 0.04 1 61 33 12 ARG HE H 7.037 0.04 1 stop_ save_ save_assigned_chemical_shifts_1_4 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D NOESY' '2D TOCSY' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chem_shift_reference_1 _Mol_system_component_name 'entity_2, chain 2' _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 34 1 CYS HA H 4.149 0.04 1 2 34 1 CYS HB2 H 3.212 0.04 2 3 34 1 CYS HB3 H 2.968 0.04 2 4 35 2 GLY H H 8.668 0.04 1 5 35 2 GLY HA2 H 4.048 0.04 2 6 35 2 GLY HA3 H 3.881 0.04 2 7 36 3 THR H H 8.223 0.04 1 8 36 3 THR HA H 4.503 0.04 1 9 36 3 THR HB H 3.976 0.04 1 10 36 3 THR HG2 H 1.111 0.04 1 11 37 4 PRO HA H 4.254 0.04 1 12 37 4 PRO HB2 H 1.838 0.04 2 13 37 4 PRO HB3 H 1.708 0.04 2 14 37 4 PRO HG2 H 1.582 0.04 2 15 37 4 PRO HG3 H 1.582 0.04 2 16 37 4 PRO HD2 H 3.745 0.04 2 17 37 4 PRO HD3 H 3.580 0.04 2 18 38 5 ILE H H 8.054 0.04 1 19 38 5 ILE HA H 4.060 0.04 1 20 38 5 ILE HB H 1.678 0.04 1 21 38 5 ILE HG13 H 1.211 0.04 2 22 38 5 ILE HG2 H 0.661 0.04 1 23 38 5 ILE HD1 H 0.661 0.04 1 24 39 6 SER HA H 4.253 0.04 1 25 39 6 SER HB2 H 3.744 0.04 2 26 39 6 SER HB3 H 3.660 0.04 2 27 40 7 PHE H H 8.636 0.04 1 28 40 7 PHE HA H 5.150 0.04 1 29 40 7 PHE HB2 H 2.486 0.04 2 30 40 7 PHE HB3 H 2.330 0.04 2 31 40 7 PHE HD1 H 6.692 0.04 3 32 40 7 PHE HD2 H 6.692 0.04 3 33 40 7 PHE HE1 H 7.016 0.04 3 34 40 7 PHE HE2 H 7.016 0.04 3 35 41 8 TYR H H 9.398 0.04 1 36 41 8 TYR HA H 4.556 0.04 1 37 41 8 TYR HB2 H 2.912 0.04 1 38 41 8 TYR HB3 H 2.912 0.04 1 39 41 8 TYR HD1 H 6.948 0.04 3 40 41 8 TYR HD2 H 6.948 0.04 3 41 41 8 TYR HE1 H 6.690 0.04 3 42 41 8 TYR HE2 H 6.690 0.04 3 stop_ save_