data_19190 ####################### # 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 19190 _BMRB_flat_file_name bmr19190.str _Entry_type original _Submission_date 2013-04-24 _Accession_date 2013-04-24 _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" 99 "13C chemical shifts" 29 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2013-10-17 original author . stop_ _Original_release_date 2013-10-17 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 . _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first . _Page_last . _Year 2013 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name LptD _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label LptD $LptD 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_LptD _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common LptD _Molecular_mass 1717.131 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 14 _Mol_residue_sequence TWLXXXRWXXAKXP loop_ _Residue_seq_code _Residue_label 1 THR 2 TRP 3 LEU 4 DAB 5 ORN 6 DLY 7 ARG 8 TRP 9 ORN 10 DAB 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_DAB _Saveframe_category polymer_residue _Mol_type 'L-PEPTIDE LINKING' _Name_common '2,4-DIAMINOBUTYRIC ACID' _BMRB_code DAB _PDB_code DAB _Standard_residue_derivative . _Molecular_mass 118.134 _Mol_paramagnetic no _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 . ? ND ND N . 0 . ? OXT OXT O . 0 . ? H H H . 0 . ? H2 H2 H . 0 . ? HA HA H . 0 . ? HB2 HB2 H . 0 . ? HB3 HB3 H . 0 . ? HG2 HG2 H . 0 . ? HG3 HG3 H . 0 . ? HD1 HD1 H . 0 . ? HD2 HD2 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 C ? ? SING CA CB ? ? SING CA HA ? ? DOUB C O ? ? SING C OXT ? ? SING CB CG ? ? SING CB HB2 ? ? SING CB HB3 ? ? SING CG ND ? ? SING CG HG2 ? ? SING CG HG3 ? ? SING ND HD1 ? ? SING ND HD2 ? ? SING OXT HXT ? ? stop_ save_ save_chem_comp_ORN _Saveframe_category polymer_residue _Mol_type 'L-PEPTIDE LINKING' _Name_common L-ornithine _BMRB_code ORN _PDB_code ORN _Standard_residue_derivative . _Molecular_mass 132.161 _Mol_paramagnetic no _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 . ? NE NE N . 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 . ? HB2 HB2 H . 0 . ? HB3 HB3 H . 0 . ? HG2 HG2 H . 0 . ? HG3 HG3 H . 0 . ? HD2 HD2 H . 0 . ? HD3 HD3 H . 0 . ? HE1 HE1 H . 0 . ? HE2 HE2 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 CG ? ? SING CB HB2 ? ? SING CB HB3 ? ? SING CG CD ? ? SING CG HG2 ? ? SING CG HG3 ? ? SING CD NE ? ? SING CD HD2 ? ? SING CD HD3 ? ? SING NE HE1 ? ? SING NE HE2 ? ? DOUB C O ? ? SING C OXT ? ? SING OXT HXT ? ? stop_ save_ save_chem_comp_DLY _Saveframe_category polymer_residue _Mol_type 'D-PEPTIDE LINKING' _Name_common D-LYSINE _BMRB_code DLY _PDB_code DLY _Standard_residue_derivative . _Molecular_mass 146.188 _Mol_paramagnetic no _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 . ? CD CD C . 0 . ? CE CE C . 0 . ? NZ NZ N . 0 . ? OXT OXT O . 0 . ? H H H . 0 . ? H2 H2 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 . ? HE2 HE2 H . 0 . ? HE3 HE3 H . 0 . ? HZ1 HZ1 H . 0 . ? HZ2 HZ2 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 C ? ? SING CA CB ? ? SING CA HA ? ? DOUB C O ? ? SING C OXT ? ? SING CB CG ? ? SING CB HB2 ? ? SING CB HB3 ? ? SING CG CD ? ? SING CG HG2 ? ? SING CG HG3 ? ? SING CD CE ? ? SING CD HD2 ? ? SING CD HD3 ? ? SING CE NZ ? ? SING CE HE2 ? ? SING CE HE3 ? ? SING NZ HZ1 ? ? SING NZ HZ2 ? ? SING OXT HXT ? ? stop_ save_ 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 no _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 $LptD . . . . . . 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 $LptD '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 $LptD 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 $LptD 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' 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_2D_1H-13C_HMBC_8 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HMBC' _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 'ionic strength' 0 . M pH 2.3 . 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 carbon' 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' '2D 1H-13C HMBC' 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 LptD _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 4.421 0.000 1 2 1 1 THR HB H 4.162 0.000 1 3 1 1 THR HG2 H 1.183 0.000 1 4 1 1 THR H H 7.723 0.000 1 5 1 1 THR CA C 61.690 0.000 1 6 1 1 THR CB C 70.540 0.000 1 7 2 2 TRP H H 8.537 0.000 1 8 2 2 TRP HA H 4.751 0.000 1 9 2 2 TRP HB2 H 3.036 0.000 2 10 2 2 TRP HB3 H 3.036 0.000 2 11 2 2 TRP HD1 H 7.222 0.002 1 12 2 2 TRP HE1 H 10.157 0.002 1 13 2 2 TRP HE3 H 7.304 0.001 1 14 2 2 TRP HZ2 H 7.492 0.002 1 15 2 2 TRP HZ3 H 7.005 0.000 1 16 2 2 TRP HH2 H 7.229 0.000 1 17 2 2 TRP CA C 57.320 0.000 1 18 2 2 TRP CB C 30.760 0.000 1 19 3 3 LEU H H 8.646 0.000 1 20 3 3 LEU HA H 4.552 0.000 1 21 3 3 LEU HB2 H 1.643 0.000 2 22 3 3 LEU HB3 H 1.643 0.000 2 23 3 3 LEU HG H 1.526 0.000 1 24 3 3 LEU HD1 H 0.889 0.000 2 25 3 3 LEU HD2 H 0.905 0.000 2 26 3 3 LEU CA C 54.660 0.000 1 27 3 3 LEU CB C 43.410 0.000 1 28 4 4 DAB CA C 53.670 0.000 1 29 4 4 DAB CB C 32.850 0.000 1 30 4 4 DAB HA H 4.794 0.000 1 31 4 4 DAB HB2 H 2.043 0.000 2 32 4 4 DAB HB3 H 2.126 0.001 2 33 4 4 DAB HG2 H 2.825 0.000 1 34 4 4 DAB HG3 H 2.937 0.000 1 35 4 4 DAB H H 8.629 0.000 1 36 5 5 ORN CA C 55.790 0.000 1 37 5 5 ORN CB C 31.730 0.000 1 38 5 5 ORN HA H 4.479 0.000 1 39 5 5 ORN HB2 H 1.785 0.004 2 40 5 5 ORN HB3 H 1.890 0.000 2 41 5 5 ORN HG2 H 1.643 0.000 1 42 5 5 ORN HG3 H 1.711 0.000 1 43 5 5 ORN H H 8.392 0.001 1 44 5 5 ORN CD C 2.950 0.000 1 45 6 6 DLY CA C 57.880 0.000 1 46 6 6 DLY CB C 32.430 0.000 1 47 6 6 DLY HA H 4.256 0.002 1 48 6 6 DLY HG2 H 1.354 0.001 1 49 6 6 DLY HG3 H 1.481 0.001 1 50 6 6 DLY H H 8.862 0.000 1 51 6 6 DLY HB2 H 1.765 0.001 1 52 6 6 DLY HB3 H 1.765 0.001 1 53 6 6 DLY HD2 H 1.689 0.001 1 54 6 6 DLY HD3 H 1.689 0.001 1 55 7 7 ARG H H 8.801 0.000 1 56 7 7 ARG HA H 4.203 0.000 1 57 7 7 ARG HB2 H 1.575 0.002 2 58 7 7 ARG HB3 H 1.699 0.002 2 59 7 7 ARG HG2 H 1.295 0.002 1 60 7 7 ARG HG3 H 1.352 0.002 1 61 7 7 ARG HD2 H 3.043 0.000 1 62 7 7 ARG HD3 H 3.043 0.000 1 63 7 7 ARG HE H 7.055 0.000 1 64 7 7 ARG CA C 56.710 0.000 1 65 7 7 ARG CB C 30.320 0.000 1 66 8 8 TRP H H 8.163 0.001 1 67 8 8 TRP HA H 4.726 0.000 1 68 8 8 TRP HB2 H 3.266 0.002 2 69 8 8 TRP HB3 H 3.447 0.000 2 70 8 8 TRP HD1 H 7.329 0.000 1 71 8 8 TRP HE1 H 10.132 0.001 1 72 8 8 TRP HE3 H 7.543 0.001 1 73 8 8 TRP HZ2 H 7.479 0.000 1 74 8 8 TRP HZ3 H 7.027 0.000 1 75 8 8 TRP HH2 H 7.197 0.000 1 76 8 8 TRP CA C 57.350 0.000 1 77 8 8 TRP CB C 30.110 0.000 1 78 9 9 ORN CA C 55.320 0.000 1 79 9 9 ORN CB C 32.430 0.000 1 80 9 9 ORN HA H 4.892 0.000 1 81 9 9 ORN HB2 H 1.698 0.000 2 82 9 9 ORN HB3 H 1.808 0.001 2 83 9 9 ORN HD2 H 2.559 0.000 1 84 9 9 ORN HD3 H 2.702 0.000 1 85 9 9 ORN HG2 H 1.582 0.008 1 86 9 9 ORN HG3 H 1.608 0.010 1 87 9 9 ORN H H 8.220 0.000 1 88 10 10 DAB CA C 53.580 0.000 1 89 10 10 DAB CB C 33.700 0.000 1 90 10 10 DAB HA H 4.450 0.000 1 91 10 10 DAB HB2 H 1.834 0.001 2 92 10 10 DAB HB3 H 2.018 0.007 2 93 10 10 DAB HG2 H 2.818 0.000 1 94 10 10 DAB HG3 H 2.973 0.000 1 95 10 10 DAB H H 8.468 0.000 1 96 11 11 ALA H H 8.567 0.000 1 97 11 11 ALA HA H 3.978 0.000 1 98 11 11 ALA HB H 0.891 0.002 1 99 11 11 ALA CA C 52.700 0.000 1 100 11 11 ALA CB C 19.340 0.000 1 101 12 12 LYS H H 8.220 0.000 1 102 12 12 LYS HA H 4.607 0.000 1 103 12 12 LYS HB2 H 1.476 0.002 2 104 12 12 LYS HB3 H 1.698 0.002 2 105 12 12 LYS HG2 H 1.252 0.000 1 106 12 12 LYS HG3 H 1.350 0.001 1 107 12 12 LYS HD2 H 1.626 0.000 1 108 12 12 LYS HD3 H 1.626 0.000 1 109 12 12 LYS CA C 53.630 0.000 1 110 12 12 LYS CB C 33.420 0.000 1 111 13 13 DPR CA C 61.740 0.000 1 112 13 13 DPR CB C 30.670 0.000 1 113 13 13 DPR HA H 4.688 0.002 1 114 13 13 DPR HB2 H 1.849 0.000 2 115 13 13 DPR HB3 H 2.252 0.001 2 116 13 13 DPR HD2 H 3.389 0.000 1 117 13 13 DPR HD3 H 3.683 0.001 1 118 13 13 DPR HG2 H 1.948 0.000 1 119 13 13 DPR HG3 H 2.039 0.000 1 120 14 14 PRO HA H 4.437 0.000 1 121 14 14 PRO HB2 H 2.026 0.000 2 122 14 14 PRO HB3 H 2.130 0.000 2 123 14 14 PRO HG2 H 1.900 0.000 1 124 14 14 PRO HG3 H 2.026 0.000 1 125 14 14 PRO HD2 H 3.662 0.003 1 126 14 14 PRO HD3 H 3.916 0.000 1 127 14 14 PRO CA C 63.830 0.000 1 128 14 14 PRO CB C 32.270 0.000 1 stop_ save_