data_19192 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution Structure of a Beta-Hairpin Peptidomimetic antibiotic that target LptD in Pseudomonas sp. ; _BMRB_accession_number 19192 _BMRB_flat_file_name bmr19192.str _Entry_type original _Submission_date 2013-04-25 _Accession_date 2013-04-25 _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 Moehle Kerstin . . 2 Schmidt Jasmin . . 3 Robinson 'John A.' . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 103 "13C chemical shifts" 28 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2013-10-17 update BMRB 'update entry citation' 2013-08-16 original author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 19190 'Beta-Hairpin Peptidomimetic antibiotic that target LptD in Pseudomonas sp.' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Structural studies of -hairpin peptidomimetic antibiotics that target LptD in Pseudomonas sp.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 23932450 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Schmidt Jasmin . . 2 Patora-Komisarska Krystyna . . 3 Moehle Kerstin . . 4 Obrecht Daniel . . 5 Robinson John A. . stop_ _Journal_abbreviation 'Bioorg. Med. Chem.' _Journal_name_full 'Bioorganic & medicinal chemistry' _Journal_volume 21 _Journal_issue 18 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 5806 _Page_last 5810 _Year 2013 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'beta-Hairpin Peptidomimetic Antibiotics' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'beta-Hairpin Peptidomimetic Antibiotics' $entity 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_entity _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common entity _Molecular_mass 1830.313 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 14 _Mol_residue_sequence TWLKKRRWKKAKXP loop_ _Residue_seq_code _Residue_label 1 THR 2 TRP 3 LEU 4 LYS 5 LYS 6 ARG 7 ARG 8 TRP 9 LYS 10 LYS 11 ALA 12 LYS 13 DPR 14 PRO stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_DPR _Saveframe_category polymer_residue _Mol_type 'D-PEPTIDE LINKING' _Name_common D-PROLINE _BMRB_code DPR _PDB_code DPR _Standard_residue_derivative . _Molecular_mass 115.130 _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 . ? CD CD C . 0 . ? C C C . 0 . ? O O O . 0 . ? OXT OXT O . 0 . ? H H H . 0 . ? HA HA H . 0 . ? HB2 HB2 H . 0 . ? HB3 HB3 H . 0 . ? HG2 HG2 H . 0 . ? HG3 HG3 H . 0 . ? HD2 HD2 H . 0 . ? HD3 HD3 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 CD ? ? SING N H ? ? SING CA CB ? ? SING CA C ? ? SING CA HA ? ? SING CB CG ? ? SING CB HB2 ? ? SING CB HB3 ? ? SING CG CD ? ? SING CG HG2 ? ? SING CG HG3 ? ? SING CD HD2 ? ? SING CD HD3 ? ? 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 . . . . . . 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 _Details $entity 'chemical synthesis' . . . . . 'The peptidomimetic was synthesized using a mixed solid/solution phase procedure and purified by reversed phase HPLC.' 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 $entity 5 mM 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity 5 mM 'natural abundance' D2O 100 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_TOPSPIN _Saveframe_category software _Name TOPSPIN _Version 2.0 loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task processing stop_ _Details . save_ save_XEASY _Saveframe_category software _Name XEASY _Version 1.53 loop_ _Vendor _Address _Electronic_address 'Bartels et al.' . . stop_ loop_ _Task 'chemical shift assignment' 'peak picking' stop_ _Details . save_ save_DYANA _Saveframe_category software _Name DYANA _Version 1.5 loop_ _Vendor _Address _Electronic_address 'Guntert, Braun and Wuthrich' . . stop_ loop_ _Task 'structure solution' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_DQF-COSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _Sample_label $sample_1 save_ save_2D_1H-1H_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ save_2D_DQF-COSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _Sample_label $sample_2 save_ save_2D_1H-1H_TOCSY_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_2 save_ save_2D_1H-1H_NOESY_6 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_2 save_ save_2D_1H-13C_HSQC_7 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $sample_2 save_ save_NMR_spectrometer_expt _Saveframe_category NMR_applied_experiment _Experiment_name . _BMRB_pulse_sequence_accession_number . _Details . 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' 0 . M pH 5 . pH pressure 1 . atm temperature 298 . 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 TSP C 13 'methyl carbons' ppm 0 internal direct . . . 1 TSP H 1 'methyl protons' ppm 0 internal direct . . . 1 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 DQF-COSY' '2D 1H-1H TOCSY' '2D 1H-1H NOESY' '2D 1H-13C HSQC' stop_ loop_ _Sample_label $sample_1 $sample_2 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'beta-Hairpin Peptidomimetic Antibiotics' _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 THR HA H 4.292 0.000 . 2 1 1 THR HB H 4.209 0.000 . 3 1 1 THR HG2 H 1.193 0.000 . 4 1 1 THR H H 7.930 0.002 . 5 1 1 THR CA C 62.360 0.000 . 6 1 1 THR CB C 69.950 0.000 . 7 2 2 TRP H H 8.187 0.004 . 8 2 2 TRP HA H 4.695 0.000 . 9 2 2 TRP HB2 H 3.098 0.000 . 10 2 2 TRP HB3 H 3.235 0.000 . 11 2 2 TRP HD1 H 7.215 0.002 . 12 2 2 TRP HE1 H 10.128 0.000 . 13 2 2 TRP HE3 H 7.472 0.001 . 14 2 2 TRP HZ2 H 7.497 0.002 . 15 2 2 TRP HZ3 H 7.102 0.005 . 16 2 2 TRP HH2 H 7.227 0.005 . 17 2 2 TRP CA C 57.250 0.000 . 18 2 2 TRP CB C 30.220 0.000 . 19 3 3 LEU H H 8.058 0.000 . 20 3 3 LEU HA H 4.293 0.000 . 21 3 3 LEU HB2 H 1.491 0.000 . 22 3 3 LEU HB3 H 1.491 0.000 . 23 3 3 LEU HG H 1.392 0.000 . 24 3 3 LEU HD1 H 0.828 0.000 . 25 3 3 LEU HD2 H 0.876 0.000 . 26 3 3 LEU CA C 56.300 0.000 . 27 3 3 LEU CB C 42.470 0.000 . 28 4 4 LYS H H 8.175 0.000 . 29 4 4 LYS HA H 4.275 0.000 . 30 4 4 LYS HE2 H 2.879 0.000 . 31 4 4 LYS HE3 H 2.879 0.000 . 32 4 4 LYS HZ H 7.503 0.000 . 33 4 4 LYS CA C 57.000 0.000 . 34 4 4 LYS CB C 32.750 0.000 . 35 5 5 LYS H H 8.173 0.000 . 36 5 5 LYS HA H 4.285 0.000 . 37 5 5 LYS HB2 H 1.686 0.000 . 38 5 5 LYS HB3 H 1.827 0.000 . 39 5 5 LYS HE2 H 2.888 0.000 . 40 5 5 LYS HE3 H 2.888 0.000 . 41 5 5 LYS HZ H 7.506 0.000 . 42 5 5 LYS CA C 56.200 0.000 . 43 5 5 LYS CB C 33.040 0.000 . 44 6 6 ARG H H 8.140 0.000 . 45 6 6 ARG HA H 4.111 0.002 . 46 6 6 ARG HB2 H 1.722 0.000 . 47 6 6 ARG HB3 H 1.722 0.000 . 48 6 6 ARG HG2 H 1.487 0.000 . 49 6 6 ARG HG3 H 1.545 0.000 . 50 6 6 ARG CA C 56.850 0.000 . 51 6 6 ARG CB C 30.000 0.000 . 52 7 7 ARG H H 8.191 0.002 . 53 7 7 ARG HA H 4.166 0.000 . 54 7 7 ARG HB2 H 1.672 0.003 . 55 7 7 ARG HB3 H 1.734 0.000 . 56 7 7 ARG HG2 H 1.365 0.000 . 57 7 7 ARG HG3 H 1.393 0.000 . 58 7 7 ARG CA C 56.670 0.000 . 59 7 7 ARG CB C 30.000 0.000 . 60 8 8 TRP H H 7.917 0.003 . 61 8 8 TRP HB2 H 3.236 0.000 . 62 8 8 TRP HB3 H 3.362 0.000 . 63 8 8 TRP HD1 H 7.257 0.000 . 64 8 8 TRP HE1 H 10.233 0.002 . 65 8 8 TRP HE3 H 7.605 0.001 . 66 8 8 TRP HZ2 H 7.510 0.002 . 67 8 8 TRP HZ3 H 7.126 0.000 . 68 8 8 TRP HH2 H 7.242 0.000 . 69 8 8 TRP CA C 56.840 0.000 . 70 8 8 TRP CB C 30.190 0.000 . 71 9 9 LYS H H 8.291 0.000 . 72 9 9 LYS HA H 4.460 0.000 . 73 9 9 LYS HB2 H 1.687 0.000 . 74 9 9 LYS HB3 H 1.783 0.000 . 75 9 9 LYS HG2 H 1.311 0.000 . 76 9 9 LYS HG3 H 1.311 0.000 . 77 9 9 LYS HD2 H 1.481 0.000 . 78 9 9 LYS HD3 H 1.532 0.000 . 79 9 9 LYS HE2 H 2.786 0.004 . 80 9 9 LYS HE3 H 2.786 0.004 . 81 9 9 LYS HZ H 7.406 0.000 . 82 9 9 LYS CA C 56.770 0.000 . 83 9 9 LYS CB C 33.800 0.000 . 84 10 10 LYS H H 8.059 0.000 . 85 10 10 LYS HA H 4.285 0.000 . 86 10 10 LYS HB2 H 1.510 0.000 . 87 10 10 LYS HB3 H 1.731 0.000 . 88 10 10 LYS HG2 H 1.346 0.000 . 89 10 10 LYS HG3 H 1.346 0.000 . 90 10 10 LYS HD2 H 1.652 0.000 . 91 10 10 LYS HD3 H 1.652 0.000 . 92 10 10 LYS HE2 H 2.957 0.000 . 93 10 10 LYS HE3 H 2.957 0.000 . 94 10 10 LYS HZ H 7.538 0.000 . 95 10 10 LYS CA C 56.200 0.000 . 96 10 10 LYS CB C 34.010 0.000 . 97 11 11 ALA H H 8.169 0.000 . 98 11 11 ALA HA H 4.115 0.000 . 99 11 11 ALA HB H 1.185 0.001 . 100 11 11 ALA CA C 52.520 0.000 . 101 11 11 ALA CB C 19.750 0.000 . 102 12 12 LYS H H 8.184 0.000 . 103 12 12 LYS HA H 4.699 0.000 . 104 12 12 LYS HB2 H 1.593 0.000 . 105 12 12 LYS HB3 H 1.735 0.008 . 106 12 12 LYS HG2 H 1.302 0.000 . 107 12 12 LYS HG3 H 1.356 0.000 . 108 12 12 LYS HD2 H 1.580 0.000 . 109 12 12 LYS HD3 H 1.580 0.000 . 110 12 12 LYS HE2 H 2.878 0.000 . 111 12 12 LYS HE3 H 2.878 0.000 . 112 12 12 LYS CA C 53.630 0.000 . 113 12 12 LYS CB C 33.470 0.000 . 114 13 13 DPR CA C 61.800 0.000 . 115 13 13 DPR CB C 30.830 0.000 . 116 13 13 DPR HA H 4.728 0.001 . 117 13 13 DPR HB2 H 1.924 0.000 . 118 13 13 DPR HB3 H 2.302 0.000 . 119 13 13 DPR HD2 H 3.538 0.000 . 120 13 13 DPR HD3 H 3.689 0.001 . 121 13 13 DPR HG2 H 2.000 0.000 . 122 13 13 DPR HG3 H 2.071 0.000 . 123 14 14 PRO HA H 4.419 0.000 . 124 14 14 PRO HB2 H 1.915 0.005 . 125 14 14 PRO HB3 H 2.155 0.006 . 126 14 14 PRO HG2 H 1.958 0.003 . 127 14 14 PRO HG3 H 2.043 0.002 . 128 14 14 PRO HD2 H 3.690 0.002 . 129 14 14 PRO HD3 H 3.905 0.001 . 130 14 14 PRO CA C 63.850 0.000 . 131 14 14 PRO CB C 32.110 0.000 . stop_ save_