data_30713 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution NMR structure of Prochlorosin 2.10 produced by Prochlorococcus MIT 9313 ; _BMRB_accession_number 30713 _BMRB_flat_file_name bmr30713.str _Entry_type original _Submission_date 2020-01-13 _Accession_date 2020-01-13 _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 Bobeica S. C. . 2 'van der Donk' W. A. . 3 Zhu L. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 109 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2020-07-05 original BMRB . stop_ _Original_release_date 2020-01-15 save_ ############################# # Citation for this entry # ############################# save_citation_3 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Catalytic promiscuity in the biosynthesis of cyclic peptide secondary metabolites in planktonic marine cyanobacteria. ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 20479271 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Li B. . . 2 Sher D. . . 3 Kelly L. . . 4 Shi Y. . . 5 Huang K. . . 6 Knerr P. J. . 7 Joewono I. . . 8 Rusch D. . . 9 Chisholm S. W. . 10 'van der Donk' W. A. . stop_ _Journal_abbreviation 'Proc. Natl. Acad. Sci. U.S.A.' _Journal_volume 107 _Journal_issue 23 _Journal_ASTM PNASA6 _Journal_ISSN 1091-6490 _Journal_CSD 0040 _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 10430 _Page_last 10435 _Year 2010 _Details . save_ ####################################### # Cited references within the entry # ####################################### save_citation_1 _Saveframe_category citation _Citation_full . _Citation_title ; Evolutionary radiation of lanthipeptides in marine cyanobacteria. ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 28630351 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Cubillos-Ruiz A. . . 2 Berta-Thompson J. W. . 3 Becker J. W. . 4 'van der Donk' W. A. . 5 Chisholm S. W. . stop_ _Journal_abbreviation 'Proc. Natl. Acad. Sci. U.S.A.' _Journal_name_full . _Journal_volume 114 _Journal_issue 27 _Journal_CSD 0040 _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 E5424 _Page_last E5433 _Year 2017 _Details . save_ save_citation_2 _Saveframe_category citation _Citation_full . _Citation_title ; Structural characterization of four prochlorosins: a novel class of lantipeptides produced by planktonic marine cyanobacteria. ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID ? loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Tang W. . . 2 'van der Donk' W. A. . stop_ _Journal_abbreviation Biochemistry _Journal_name_full . _Journal_volume 51 _Journal_issue 21 _Journal_CSD 0033 _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 4271 _Page_last 4279 _Year 2012 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'Prochlorosin 2.10' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label entity_1 $entity_1 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 entity_1 _Molecular_mass 2026.474 _Mol_thiol_state 'not reported' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 21 _Mol_residue_sequence ; AGGXIPXLMXGCGWLXGLCV R ; loop_ _Residue_seq_code _Residue_label 1 ALA 2 GLY 3 GLY 4 DBU 5 ILE 6 PRO 7 DAL 8 LEU 9 MET 10 DBB 11 GLY 12 CYS 13 GLY 14 TRP 15 LEU 16 DBU 17 GLY 18 LEU 19 CYS 20 VAL 21 ARG stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_DAL _Saveframe_category polymer_residue _Mol_type 'D-PEPTIDE LINKING' _Name_common D-ALANINE _BMRB_code DAL _PDB_code DAL _Standard_residue_derivative . _Molecular_mass 89.093 _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 . ? C C C . 0 . ? O O O . 0 . ? OXT OXT O . 0 . ? H H H . 0 . ? H2 H2 H . 0 . ? HA HA H . 0 . ? HB1 HB1 H . 0 . ? HB2 HB2 H . 0 . ? HB3 HB3 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 ? ? SING CA CB ? ? SING CA C ? ? SING CA HA ? ? SING CB HB1 ? ? SING CB HB2 ? ? SING CB HB3 ? ? DOUB C O ? ? SING C OXT ? ? SING OXT HXT ? ? stop_ save_ save_chem_comp_DBB _Saveframe_category polymer_residue _Mol_type 'D-PEPTIDE LINKING' _Name_common 'D-ALPHA-AMINOBUTYRIC ACID' _BMRB_code DBB _PDB_code DBB _Standard_residue_derivative . _Molecular_mass 103.120 _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 . ? C C C . 0 . ? O O O . 0 . ? CB CB C . 0 . ? CG CG C . 0 . ? OXT OXT O . 0 . ? H H H . 0 . ? H1 H1 H . 0 . ? HA HA H . 0 . ? HB2 HB2 H . 0 . ? HB3 HB3 H . 0 . ? HG1 HG1 H . 0 . ? HG2 HG2 H . 0 . ? HG3 HG3 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 CA C ? ? SING CA CB ? ? DOUB C O ? ? SING CB CG ? ? SING C OXT ? ? SING N H ? ? SING N H1 ? ? SING CA HA ? ? SING CB HB2 ? ? SING CB HB3 ? ? SING CG HG1 ? ? SING CG HG2 ? ? SING CG HG3 ? ? SING OXT HXT ? ? stop_ save_ save_chem_comp_DBU _Saveframe_category polymer_residue _Mol_type 'PEPTIDE LINKING' _Name_common '(2Z)-2-AMINOBUT-2-ENOIC ACID' _BMRB_code DBU _PDB_code DBU _Standard_residue_derivative . _Molecular_mass 101.104 _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 . ? CG CG C . 0 . ? C C C . 0 . ? O O O . 0 . ? OXT OXT O . 0 . ? H H H . 0 . ? H2 H2 H . 0 . ? HB HB H . 0 . ? HG1 HG1 H . 0 . ? HG2 HG2 H . 0 . ? HG3 HG3 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 CG ? ? SING CB HB ? ? SING CG HG1 ? ? SING CG HG2 ? ? SING CG HG3 ? ? DOUB C O ? ? SING C OXT ? ? SING OXT HXT ? ? stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $entity_1 'Prochlorococcus marinus' 74547 Bacteria . Prochlorococcus marinus 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 . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details '4 mM Prochlorosin 2.10, 90% H2O/10% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 4 mM 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details '4 mM Prochlorosin 2.10, 100% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 4 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name NMRDraw _Version . loop_ _Vendor _Address _Electronic_address 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' . . stop_ loop_ _Task processing stop_ _Details . save_ save_software_2 _Saveframe_category software _Name Sparky _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' 'data analysis' 'peak picking' stop_ _Details . save_ save_software_3 _Saveframe_category software _Name 'X-PLOR NIH' _Version . loop_ _Vendor _Address _Electronic_address 'Schwieters, Kuszewski, Tjandra and Clore' . . stop_ loop_ _Task refinement 'structure calculation' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Agilent _Model VNMRs _Field_strength 750 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_TOCSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ save_2D_1H-1H_TOCSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_2 save_ save_2D_1H-1H_NOESY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_2 save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 6.0 0.1 pH pressure 1 0 atm temperature 313 0.1 K stop_ save_ save_sample_conditions_2 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 6 0.1 pH pressure 1 0 atm temperature 313 0.1 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 DSS C 13 'methyl protons' ppm 0.000 internal indirect . . . 0.25144953 DSS H 1 'methyl protons' ppm 0.000 internal direct . . . 1.0 DSS N 15 'methyl protons' ppm 0.000 internal indirect . . . 0.10132912 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 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H TOCSY' '2D 1H-1H NOESY' stop_ loop_ _Sample_label $sample_1 $sample_2 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chem_shift_reference_1 _Mol_system_component_name entity_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 ALA HA H 4.193 0.004 1 2 1 1 ALA HB H 1.580 0.006 1 3 2 2 GLY H H 8.594 0.009 1 4 2 2 GLY HA2 H 4.085 0.000 2 5 2 2 GLY HA3 H 4.063 0.014 2 6 3 3 GLY H H 8.332 0.001 1 7 3 3 GLY HA2 H 4.098 0.001 2 8 3 3 GLY HA3 H 4.098 0.001 2 9 4 4 DBU H H 9.247 0.007 1 10 4 4 DBU HB H 6.589 0.010 1 11 4 4 DBU HG1 H 1.768 0.006 1 12 4 4 DBU HG2 H 1.768 0.006 1 13 4 4 DBU HG3 H 1.768 0.006 1 14 5 5 ILE H H 7.663 0.003 1 15 5 5 ILE HA H 4.520 0.010 1 16 5 5 ILE HB H 1.936 0.012 1 17 5 5 ILE HG12 H 1.196 0.013 2 18 5 5 ILE HG13 H 1.552 0.009 2 19 5 5 ILE HG2 H 0.973 0.012 1 20 5 5 ILE HD1 H 0.890 0.015 1 21 6 6 PRO HA H 4.443 0.016 1 22 6 6 PRO HB2 H 2.006 0.009 2 23 6 6 PRO HB3 H 2.383 0.009 2 24 6 6 PRO HG2 H 2.043 0.016 2 25 6 6 PRO HG3 H 2.132 0.013 2 26 6 6 PRO HD2 H 3.756 0.020 2 27 6 6 PRO HD3 H 3.978 0.010 2 28 7 7 DAL H H 8.508 0.002 1 29 7 7 DAL HA H 4.342 0.001 1 30 7 7 DAL HB1 H 3.129 0.005 2 31 7 7 DAL HB2 H 3.073 0.016 2 32 8 8 LEU H H 7.727 0.003 1 33 8 8 LEU HA H 4.328 0.011 1 34 8 8 LEU HB2 H 1.697 0.013 2 35 8 8 LEU HB3 H 1.697 0.013 2 36 8 8 LEU HG H 1.656 0.007 1 37 8 8 LEU HD1 H 0.919 0.001 1 38 8 8 LEU HD2 H 0.886 0.002 1 39 9 9 MET H H 8.166 0.002 1 40 9 9 MET HA H 4.552 0.006 1 41 9 9 MET HB2 H 2.058 0.014 2 42 9 9 MET HB3 H 2.225 0.029 2 43 9 9 MET HG2 H 2.570 0.006 2 44 9 9 MET HG3 H 2.596 0.006 2 45 10 10 DBB H H 7.762 0.006 1 46 10 10 DBB HA H 4.732 0.007 1 47 10 10 DBB HB2 H 3.550 0.008 1 48 10 10 DBB HG1 H 1.272 0.001 1 49 10 10 DBB HG2 H 1.272 0.001 1 50 10 10 DBB HG3 H 1.272 0.001 1 51 11 11 GLY H H 8.369 0.002 1 52 11 11 GLY HA2 H 3.790 0.014 2 53 11 11 GLY HA3 H 4.157 0.015 2 54 12 12 CYS H H 7.840 0.002 1 55 12 12 CYS HA H 4.472 0.012 1 56 12 12 CYS HB2 H 2.700 0.013 2 57 12 12 CYS HB3 H 2.782 0.007 2 58 13 13 GLY H H 8.444 0.005 1 59 13 13 GLY HA2 H 3.817 0.008 2 60 13 13 GLY HA3 H 3.897 0.018 2 61 14 14 TRP H H 7.754 0.003 1 62 14 14 TRP HA H 4.730 0.037 1 63 14 14 TRP HB2 H 3.332 0.017 2 64 14 14 TRP HB3 H 3.401 0.011 2 65 14 14 TRP HD1 H 7.244 0.006 1 66 14 14 TRP HE1 H 9.757 0.938 1 67 14 14 TRP HE3 H 7.605 0.047 1 68 14 14 TRP HZ2 H 7.636 0.602 1 69 14 14 TRP HZ3 H 7.155 0.015 1 70 14 14 TRP HH2 H 7.217 0.016 1 71 15 15 LEU H H 7.859 0.011 1 72 15 15 LEU HA H 4.358 0.010 1 73 15 15 LEU HB2 H 1.527 0.014 2 74 15 15 LEU HB3 H 1.632 0.012 2 75 15 15 LEU HG H 1.261 0.021 1 76 15 15 LEU HD1 H 0.872 0.022 1 77 15 15 LEU HD2 H 0.786 0.018 1 78 16 16 DBU H H 8.885 0.000 1 79 16 16 DBU HB H 6.657 0.015 1 80 17 17 GLY H H 7.946 0.003 1 81 17 17 GLY HA2 H 3.832 0.017 2 82 17 17 GLY HA3 H 3.968 0.003 2 83 18 18 LEU H H 7.795 0.002 1 84 18 18 LEU HA H 4.344 0.009 1 85 18 18 LEU HB2 H 1.609 0.008 2 86 18 18 LEU HB3 H 1.714 0.004 2 87 18 18 LEU HD1 H 0.909 0.005 1 88 18 18 LEU HD2 H 0.868 0.006 1 89 19 19 CYS H H 8.034 0.003 1 90 19 19 CYS HA H 4.579 0.006 1 91 19 19 CYS HB2 H 2.752 0.014 2 92 19 19 CYS HB3 H 3.066 0.006 2 93 20 20 VAL H H 7.846 0.002 1 94 20 20 VAL HA H 4.153 0.008 1 95 20 20 VAL HB H 2.089 0.012 1 96 20 20 VAL HG1 H 0.941 0.013 1 97 20 20 VAL HG2 H 0.906 0.012 1 98 21 21 ARG H H 8.204 0.002 1 99 21 21 ARG HA H 4.375 0.009 1 100 21 21 ARG HB2 H 1.784 0.015 2 101 21 21 ARG HB3 H 1.928 0.011 2 102 21 21 ARG HG2 H 1.648 0.012 2 103 21 21 ARG HG3 H 1.648 0.012 2 104 21 21 ARG HD2 H 3.205 0.009 2 105 21 21 ARG HD3 H 3.205 0.009 2 106 21 21 ARG HH11 H 7.150 0.000 2 107 21 21 ARG HH12 H 7.150 0.000 2 108 21 21 ARG HH21 H 6.627 0.008 2 109 21 21 ARG HH22 H 6.627 0.008 2 stop_ save_