data_30714 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution NMR structure of Prochlorosin 2.1 produced by Prochlorococcus MIT 9313 ; _BMRB_accession_number 30714 _BMRB_flat_file_name bmr30714.str _Entry_type original _Submission_date 2020-01-16 _Accession_date 2020-01-16 _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" 132 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2020-07-05 original BMRB . stop_ _Original_release_date 2020-01-21 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 ? 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 . _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 2.1' _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 2762.152 _Mol_thiol_state 'not reported' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 28 _Mol_residue_sequence ; CCIXGESPGXAPXNDYKCXK GRGPGGCY ; loop_ _Residue_seq_code _Residue_label 1 CYS 2 CYS 3 ILE 4 DBB 5 GLY 6 GLU 7 SER 8 PRO 9 GLY 10 DAL 11 ALA 12 PRO 13 DBB 14 ASN 15 ASP 16 TYR 17 LYS 18 CYS 19 DBB 20 LYS 21 GLY 22 ARG 23 GLY 24 PRO 25 GLY 26 GLY 27 CYS 28 TYR 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_ #################### # 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 '2 mM Prochlorosin 2.1, 90% H2O/10% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 2 mM 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details '3 mM Prochlorosin 2.1, 100% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 3 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name NMRPipe _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' 'peak picking' stop_ _Details . save_ save_software_3 _Saveframe_category software _Name 'X-PLOR NIH' _Version 2.51 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 0.1 pH pressure 1 0 atm temperature 296 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 296 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 CYS HA H 4.492 0.001 1 2 1 1 CYS HB2 H 3.155 0.008 2 3 1 1 CYS HB3 H 3.248 0.023 2 4 2 2 CYS H H 8.959 0.003 1 5 2 2 CYS HA H 4.798 0.005 1 6 2 2 CYS HB2 H 2.918 0.005 2 7 2 2 CYS HB3 H 3.020 0.001 2 8 3 3 ILE H H 9.097 0.470 1 9 3 3 ILE HA H 3.843 0.327 1 10 3 3 ILE HB H 2.302 0.322 1 11 3 3 ILE HG12 H 1.160 0.004 2 12 3 3 ILE HG13 H 1.535 0.005 2 13 3 3 ILE HG2 H 0.996 0.002 1 14 3 3 ILE HD1 H 0.882 0.003 1 15 4 4 DBB H H 7.844 0.010 1 16 4 4 DBB HA H 4.333 0.002 1 17 5 5 GLY H H 8.456 0.002 1 18 5 5 GLY HA2 H 3.934 0.004 2 19 5 5 GLY HA3 H 4.291 0.009 2 20 6 6 GLU H H 8.669 0.004 1 21 6 6 GLU HA H 4.563 0.018 1 22 6 6 GLU HB2 H 1.911 0.004 2 23 6 6 GLU HB3 H 1.911 0.004 2 24 6 6 GLU HG2 H 2.296 0.006 2 25 6 6 GLU HG3 H 2.474 0.007 2 26 7 7 SER H H 8.050 0.010 1 27 7 7 SER HA H 4.773 0.005 1 28 7 7 SER HB2 H 3.919 0.008 2 29 7 7 SER HB3 H 3.946 0.003 2 30 8 8 PRO HA H 4.465 0.008 1 31 8 8 PRO HB3 H 2.319 0.004 2 32 8 8 PRO HG2 H 2.000 0.006 2 33 8 8 PRO HG3 H 2.064 0.004 2 34 8 8 PRO HD2 H 3.798 0.001 2 35 8 8 PRO HD3 H 3.892 0.001 2 36 9 9 GLY H H 8.439 0.006 1 37 9 9 GLY HA2 H 3.955 0.005 2 38 9 9 GLY HA3 H 3.955 0.005 2 39 10 10 DAL H H 7.905 0.006 1 40 10 10 DAL HA H 4.543 0.008 1 41 10 10 DAL HB1 H 3.080 0.006 2 42 10 10 DAL HB2 H 2.983 0.006 2 43 11 11 ALA H H 8.523 0.003 1 44 11 11 ALA HA H 4.542 0.007 1 45 11 11 ALA HB H 1.347 0.003 1 46 12 12 PRO HA H 4.506 0.005 1 47 12 12 PRO HB2 H 1.892 0.006 2 48 12 12 PRO HB3 H 2.310 0.003 2 49 12 12 PRO HG2 H 2.012 0.007 2 50 12 12 PRO HG3 H 2.064 0.004 2 51 12 12 PRO HD2 H 3.619 0.005 2 52 12 12 PRO HD3 H 3.790 0.004 2 53 13 13 DBB H H 8.576 0.005 1 54 13 13 DBB HA H 4.732 0.014 1 55 14 14 ASN H H 8.411 0.005 1 56 14 14 ASN HA H 4.937 0.016 1 57 15 15 ASP H H 7.579 0.005 1 58 15 15 ASP HA H 4.849 0.006 1 59 16 16 TYR H H 8.558 0.002 1 60 16 16 TYR HA H 4.806 0.009 1 61 16 16 TYR HB2 H 2.855 0.010 2 62 16 16 TYR HB3 H 3.032 0.004 2 63 16 16 TYR HD1 H 7.102 0.008 3 64 16 16 TYR HD2 H 7.102 0.008 3 65 16 16 TYR HE1 H 6.829 0.009 3 66 16 16 TYR HE2 H 6.829 0.009 3 67 17 17 LYS H H 7.324 0.002 1 68 17 17 LYS HA H 4.402 1.232 1 69 17 17 LYS HB2 H 1.672 0.005 2 70 17 17 LYS HB3 H 1.770 0.006 2 71 17 17 LYS HG2 H 0.904 0.010 2 72 17 17 LYS HG3 H 0.995 0.001 2 73 17 17 LYS HD2 H 1.567 0.008 2 74 17 17 LYS HD3 H 1.567 0.008 2 75 17 17 LYS HE2 H 2.948 0.003 2 76 17 17 LYS HE3 H 2.948 0.003 2 77 17 17 LYS HZ H 7.535 0.001 1 78 18 18 CYS H H 7.959 0.004 1 79 18 18 CYS HA H 4.684 0.014 1 80 19 19 DBB H H 7.704 0.004 1 81 19 19 DBB HA H 4.504 0.007 1 82 20 20 LYS H H 7.727 0.004 1 83 20 20 LYS HA H 4.564 0.001 1 84 20 20 LYS HB2 H 1.508 0.007 2 85 20 20 LYS HB3 H 1.915 0.005 2 86 20 20 LYS HG2 H 1.300 0.004 2 87 20 20 LYS HG3 H 1.469 0.006 2 88 20 20 LYS HD2 H 1.725 0.005 2 89 20 20 LYS HD3 H 1.725 0.005 2 90 20 20 LYS HE2 H 3.020 0.004 2 91 20 20 LYS HE3 H 3.020 0.004 2 92 20 20 LYS HZ H 7.517 0.002 1 93 21 21 GLY H H 8.247 0.001 1 94 21 21 GLY HA2 H 3.853 0.009 2 95 21 21 GLY HA3 H 4.150 0.011 2 96 22 22 ARG H H 8.285 0.009 1 97 22 22 ARG HA H 4.647 0.001 1 98 22 22 ARG HB2 H 1.686 0.004 2 99 22 22 ARG HB3 H 1.865 0.003 2 100 22 22 ARG HG2 H 1.546 0.003 2 101 22 22 ARG HG3 H 1.602 0.004 2 102 22 22 ARG HD2 H 3.165 0.004 2 103 22 22 ARG HD3 H 3.165 0.004 2 104 22 22 ARG HH11 H 7.166 0.002 2 105 22 22 ARG HH12 H 7.166 0.002 2 106 23 23 GLY H H 8.264 0.005 1 107 23 23 GLY HA2 H 3.932 0.009 2 108 23 23 GLY HA3 H 4.181 0.010 2 109 24 24 PRO HA H 4.369 0.008 1 110 24 24 PRO HB2 H 1.957 0.010 2 111 24 24 PRO HB3 H 2.288 0.003 2 112 24 24 PRO HG2 H 1.997 0.005 2 113 24 24 PRO HG3 H 2.087 0.005 2 114 24 24 PRO HD2 H 3.607 0.003 2 115 25 25 GLY H H 8.675 0.004 1 116 25 25 GLY HA2 H 3.907 0.012 2 117 25 25 GLY HA3 H 4.095 0.008 2 118 26 26 GLY H H 8.298 0.004 1 119 26 26 GLY HA2 H 3.628 0.003 2 120 26 26 GLY HA3 H 4.305 0.006 2 121 27 27 CYS H H 7.873 0.003 1 122 27 27 CYS HA H 4.382 0.006 1 123 27 27 CYS HB2 H 2.506 0.005 2 124 27 27 CYS HB3 H 2.750 0.006 2 125 28 28 TYR H H 8.148 0.003 1 126 28 28 TYR HA H 4.588 0.011 1 127 28 28 TYR HB2 H 2.860 0.006 2 128 28 28 TYR HB3 H 3.174 0.006 2 129 28 28 TYR HD1 H 7.086 0.005 3 130 28 28 TYR HD2 H 7.086 0.005 3 131 28 28 TYR HE1 H 6.846 0.009 3 132 28 28 TYR HE2 H 6.846 0.009 3 stop_ save_