data_27960 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR backbone and sidechain assignments of apo-pyoverdine PvdI, a siderophore from Pseudomonas aeruginosa ; _BMRB_accession_number 27960 _BMRB_flat_file_name bmr27960.str _Entry_type original _Submission_date 2019-06-25 _Accession_date 2019-06-25 _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 Wang Xu . . 2 Kleerekoper Quinn . . 3 Lai Shujuan . . 4 Kirienko Natalia . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 63 "13C chemical shifts" 41 "15N chemical shifts" 12 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2020-09-24 update BMRB 'update entry citation' 2020-09-17 original author 'original release' stop_ _Original_release_date 2019-06-25 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Identification and validation of a novel anti-virulent that binds to pyoverdine and inhibits its function ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 32962519 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Wang Xu . . 2 Kleerekoper Quinn . . 3 Revtovicha Alexey V. . 4 Kang Donghoon . . 5 Kirienko Natalia V. . stop_ _Journal_abbreviation Virulence _Journal_volume 11 _Journal_issue 1 _Journal_ISSN 2150-5608 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 1293 _Page_last 1309 _Year 2020 _Details . loop_ _Keyword 'P. aeruginosa' pyoverdine 'virulence inhibition' stop_ save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name pyoverdine _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'apo Pvd1' $pyoverdine stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_pyoverdine _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common pyoverdine _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 10 _Mol_residue_sequence ; XXSRSXKXTT ; loop_ _Residue_seq_code _Residue_label 1 SUC 2 CHR 3 DSN 4 ARG 5 DSN 6 FOH 7 LYS 8 FOH 9 THR 10 THR stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_DSN _Saveframe_category polymer_residue _Mol_type 'D-PEPTIDE LINKING' _Name_common D-SERINE _BMRB_code DSN _PDB_code DSN _Standard_residue_derivative . _Molecular_mass 105.093 _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 . ? C C C . 0 . ? O O O . 0 . ? OXT OXT O . 0 . ? CB CB C . 0 . ? OG OG O . 0 . ? H H H . 0 . ? H2 H2 H . 0 . ? HA HA H . 0 . ? HXT HXT H . 0 . ? HB2 HB2 H . 0 . ? HB3 HB3 H . 0 . ? HG HG 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 C ? ? SING CA CB ? ? SING CA HA ? ? DOUB C O ? ? SING C OXT ? ? SING OXT HXT ? ? SING CB OG ? ? SING CB HB2 ? ? SING CB HB3 ? ? SING OG HG ? ? 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 $pyoverdine 'Pseudomonas aeruginosa' 287 Bacteria . Pseudomonas aeruginosa PAO1 stop_ save_ ######################### # Experimental source # ######################### save_experimental_source _Saveframe_category experimental_source loop_ _Mol_label _Production_method _Host_organism_name_common _Genus _Species _Strain _Vector_type _Vector_name $pyoverdine 'purified from the natural source' . Pseudomonas aeruginosa PAO1 none N/A 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 $pyoverdine 1.2 mM '[U-100% 13C; U-100% 15N]' DSS 20 uM 'natural abundance' D2O 10 % '[U-99% 2H]' 'potassium phosphate' 25 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_NMRDraw _Saveframe_category software _Name NMRDraw _Version . loop_ _Vendor _Address _Electronic_address 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' . . stop_ loop_ _Task 'data analysis' processing stop_ _Details . save_ save_NMRPipe _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_NMRView _Saveframe_category software _Name NMRView _Version . loop_ _Vendor _Address _Electronic_address 'Johnson, One Moon Scientific' . . stop_ loop_ _Task 'data analysis' stop_ _Details . save_ save_TOPSPIN _Saveframe_category software _Name TOPSPIN _Version . loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task collection 'data analysis' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AMX _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-15N_HSQC_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N HSQC' _Sample_label $sample_1 save_ save_2D_1H-13C_HSQC_aliphatic_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC aliphatic' _Sample_label $sample_1 save_ save_3D_HNCO_3 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HNCO' _Sample_label $sample_1 save_ save_3D_HNCA_4 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HNCA' _Sample_label $sample_1 save_ save_3D_HNCACB_5 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HNCACB' _Sample_label $sample_1 save_ save_3D_HN(CO)CA_6 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HN(CO)CA' _Sample_label $sample_1 save_ save_3D_CBCA(CO)NH_7 _Saveframe_category NMR_applied_experiment _Experiment_name '3D CBCA(CO)NH' _Sample_label $sample_1 save_ save_3D_1H-15N_TOCSY_8 _Saveframe_category NMR_applied_experiment _Experiment_name '3D 1H-15N TOCSY' _Sample_label $sample_1 save_ save_3D_CCH-TOCSY_9 _Saveframe_category NMR_applied_experiment _Experiment_name '3D CCH-TOCSY' _Sample_label $sample_1 save_ save_3D_HNHA_10 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HNHA' _Sample_label $sample_1 save_ save_3D_1H-15N_NOESY_11 _Saveframe_category NMR_applied_experiment _Experiment_name '3D 1H-15N NOESY' _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 'ionic strength' 30 . mM pH 5.8 0.1 pH pressure 1 . atm temperature 278 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_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 na indirect . . . 0.25144953 DSS H 1 'methyl protons' ppm 0 internal direct . . . 1 DSS N 15 'methyl protons' ppm 0 na indirect . . . 0.101329 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_chem_shift_list_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-15N HSQC' '2D 1H-13C HSQC aliphatic' '3D HNCO' '3D HNCA' '3D HNCACB' '3D HN(CO)CA' '3D CBCA(CO)NH' '3D 1H-15N TOCSY' '3D CCH-TOCSY' '3D HNHA' '3D 1H-15N NOESY' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'apo Pvd1' _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 SUC H H 9.84 0.01 1 2 1 1 SUC HA1 H 2.60 0.05 2 3 1 1 SUC HA2 H 2.60 0.05 2 4 1 1 SUC HB1 H 2.68 0.05 2 5 1 1 SUC HB2 H 2.68 0.05 2 6 1 1 SUC C C 180.66 0.10 1 7 1 1 SUC CA C 35.66 0.30 1 8 1 1 SUC CB C 34.86 0.30 1 9 1 1 SUC N N 120.59 0.10 1 10 2 2 CHR H H 8.70 0.01 1 11 2 2 CHR H121 H 2.44 0.05 2 12 2 2 CHR H122 H 2.67 0.05 2 13 2 2 CHR H131 H 3.37 0.05 2 14 2 2 CHR H132 H 3.68 0.05 2 15 2 2 CHR H11 H 5.76 0.01 1 16 2 2 CHR C13 C 37.76 0.30 1 17 2 2 CHR C12 C 24.70 0.30 1 18 2 2 CHR C11 C 59.40 0.30 1 19 2 2 CHR N N 92.43 0.10 1 20 3 3 DSN H H 9.96 0.01 1 21 3 3 DSN HA H 4.34 0.05 1 22 3 3 DSN HB2 H 3.64 0.05 2 23 3 3 DSN HB3 H 3.68 0.05 2 24 3 3 DSN C C 176.15 0.10 1 25 3 3 DSN CA C 60.96 0.30 1 26 3 3 DSN CB C 63.66 0.30 1 27 3 3 DSN N N 118.97 0.08 1 28 4 4 ARG H H 8.67 0.01 1 29 4 4 ARG HA H 4.50 0.05 1 30 4 4 ARG HB2 H 1.94 0.05 2 31 4 4 ARG HB3 H 1.94 0.05 2 32 4 4 ARG HG2 H 0.93 0.05 2 33 4 4 ARG HG3 H 1.18 0.05 2 34 4 4 ARG HD2 H 2.29 0.05 2 35 4 4 ARG HD3 H 2.77 0.05 2 36 4 4 ARG HE H 6.62 0.05 1 37 4 4 ARG C C 176.40 0.10 1 38 4 4 ARG CA C 56.06 0.30 1 39 4 4 ARG CB C 30.36 0.30 1 40 4 4 ARG CG C 27.23 0.30 1 41 4 4 ARG CD C 43.40 0.30 1 42 4 4 ARG N N 121.30 0.10 1 43 4 4 ARG NE N 84.79 0.10 1 44 5 5 DSN H H 8.46 0.01 1 45 5 5 DSN HA H 4.29 0.05 1 46 5 5 DSN HB2 H 3.75 0.05 2 47 5 5 DSN HB3 H 3.82 0.05 2 48 5 5 DSN C C 174.93 0.10 1 49 5 5 DSN CA C 61.01 0.30 1 50 5 5 DSN CB C 63.62 0.30 1 51 5 5 DSN N N 116.25 0.10 1 52 6 6 FOH H H 8.41 0.01 1 53 6 6 FOH HA H 4.50 0.05 1 54 6 6 FOH HB2 H 1.73 0.05 2 55 6 6 FOH HB3 H 1.81 0.05 2 56 6 6 FOH HG2 H 1.54 0.05 2 57 6 6 FOH HG3 H 1.77 0.05 2 58 6 6 FOH HD2 H 3.60 0.05 2 59 6 6 FOH HD3 H 3.60 0.05 2 60 6 6 FOH C C 175.99 0.10 1 61 6 6 FOH CA C 56.17 0.30 1 62 6 6 FOH CB C 30.59 0.30 1 63 6 6 FOH CG C 25.27 0.30 1 64 6 6 FOH CD C 52.50 0.30 1 65 6 6 FOH N N 121.66 0.10 1 66 7 7 LYS H H 8.41 0.01 1 67 7 7 LYS HA H 4.28 0.05 1 68 7 7 LYS HB2 H 1.76 0.05 2 69 7 7 LYS HB3 H 1.76 0.05 2 70 7 7 LYS HG2 H 1.17 0.05 2 71 7 7 LYS HG3 H 1.30 0.05 2 72 7 7 LYS HD2 H 1.51 0.05 2 73 7 7 LYS HD3 H 1.51 0.05 2 74 7 7 LYS HE2 H 3.12 0.05 2 75 7 7 LYS HE3 H 3.37 0.05 2 76 7 7 LYS HZ H 8.07 0.01 1 77 7 7 LYS C C 176.62 0.10 1 78 7 7 LYS CA C 56.47 0.30 1 79 7 7 LYS CB C 33.42 0.30 1 80 7 7 LYS CG C 24.33 0.30 1 81 7 7 LYS CD C 30.19 0.30 1 82 7 7 LYS CE C 42.21 0.30 1 83 7 7 LYS N N 123.96 0.10 1 84 7 7 LYS NZ N 121.93 0.10 1 85 8 8 FOH H H 8.79 0.01 1 86 8 8 FOH HA H 4.30 0.05 2 87 8 8 FOH HB2 H 1.82 0.05 2 88 8 8 FOH HB3 H 1.90 0.05 2 89 8 8 FOH HG2 H 1.76 0.05 2 90 8 8 FOH HG3 H 1.86 0.05 2 91 8 8 FOH HD2 H 3.60 0.05 2 92 8 8 FOH HD3 H 3.60 0.05 2 93 8 8 FOH C C 177.56 0.10 1 94 8 8 FOH CA C 57.39 0.30 1 95 8 8 FOH CB C 30.40 0.30 1 96 8 8 FOH CG C 25.04 0.30 1 97 8 8 FOH CD C 48.90 0.30 1 98 8 8 FOH N N 124.79 0.10 1 99 9 9 THR H H 8.33 0.01 1 100 9 9 THR HA H 4.19 0.05 1 101 9 9 THR HB H 4.44 0.05 1 102 9 9 THR HG2 H 1.22 0.05 1 103 9 9 THR C C 175.15 0.10 1 104 9 9 THR CA C 61.94 0.30 1 105 9 9 THR CB C 69.44 0.30 1 106 9 9 THR CG2 C 22.09 0.30 1 107 9 9 THR N N 112.04 0.10 1 108 10 10 THR H H 8.53 0.01 1 109 10 10 THR HA H 4.09 0.05 1 110 10 10 THR HB H 4.37 0.05 1 111 10 10 THR HG2 H 1.22 0.05 1 112 10 10 THR C C 174.64 0.10 1 113 10 10 THR CA C 62.60 0.30 1 114 10 10 THR CB C 69.06 0.30 1 115 10 10 THR CG2 C 22.09 0.30 1 116 10 10 THR N N 114.64 0.10 1 stop_ save_