data_25916 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Novel antimicrobial peptide PaDBS1R1 designed from the ribosomal protein L39E from Pyrobaculum aerophilum using bioinformatics ; _BMRB_accession_number 25916 _BMRB_flat_file_name bmr25916.str _Entry_type original _Submission_date 2015-12-03 _Accession_date 2015-12-03 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details 'Active against gram-positive and negative bacteria' loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Irazazabal Luz S.F. . 2 Porto William F. . 3 Alves Eliane S.F. . 4 Matos Carolina O. . 5 Hancock Robert E.W. . 6 Haney Evan . . 7 Ribeiro Suzana M. . 8 Liao Luciano M. . 9 Ladram Ali S.F. . 10 Franco Octavio L. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 101 "13C chemical shifts" 75 "15N chemical shifts" 18 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2016-12-01 original BMRB . stop_ _Original_release_date 2016-02-17 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Novel antimicrobial peptide PaDBS1R1 designed from the ribosomal protein L39E from Pyrobaculum aerophilum using bioinformatics ; _Citation_status 'in preparation' _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 Alves Eliane S.F. . 2 Matos Carolina O. . 3 Liao Luciano M. . stop_ _Journal_abbreviation 'Not known' _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 . _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name PaDBS1R1 _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label entity $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 2112.733 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 19 _Mol_residue_sequence ; PKILNKILGKILRLAAAFK ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 PRO 2 2 LYS 3 3 ILE 4 4 LEU 5 5 ASN 6 6 LYS 7 7 ILE 8 8 LEU 9 9 GLY 10 10 LYS 11 11 ILE 12 12 LEU 13 13 ARG 14 14 LEU 15 15 ALA 16 16 ALA 17 17 ALA 18 18 PHE 19 19 LYS stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . 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 $entity 'obtained from a vendor' . . . . . 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 TSP 5 % 'natural abundance' D2O 10 % 'natural abundance' H2O 90 % 'natural abundance' SDS 100 mM 'natural abundance' 'sodium phosphate' 30 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_X-PLOR_NIH _Saveframe_category software _Name X-PLOR_NIH _Version 2.28 loop_ _Vendor _Address _Electronic_address 'Schwieters, Kuszewski, Tjandra and Clore' . . stop_ loop_ _Task refinement 'structure solution' stop_ _Details . save_ save_NMRDraw _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_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_TALOS _Saveframe_category software _Name TALOS _Version . loop_ _Vendor _Address _Electronic_address 'Cornilescu, Delaglio and Bax' . . stop_ loop_ _Task 'data analysis' 'geometry optimization' stop_ _Details . save_ save_QUEEN _Saveframe_category software _Name QUEEN _Version . loop_ _Vendor _Address _Electronic_address 'Nabuurs, Spronk, Krieger, Maassen, Vriend and Vuister' . . stop_ loop_ _Task 'data analysis' stop_ _Details . save_ save_ProcheckNMR _Saveframe_category software _Name ProcheckNMR _Version . loop_ _Vendor _Address _Electronic_address 'Laskowski and MacArthur' . . stop_ loop_ _Task 'data analysis' stop_ _Details . save_ save_Molmol _Saveframe_category software _Name Molmol _Version . loop_ _Vendor _Address _Electronic_address 'Koradi, Billeter and Wuthrich' . . stop_ loop_ _Task 'data analysis' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 500 _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-13C_HSQC_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $sample_1 save_ save_2D_1H-15N_sfHMQC_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N sfHMQC' _Sample_label $sample_1 save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details 'temperature controller setting: 298 K.' loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 7 . 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 DSS C 13 'methyl protons' ppm 0 internal direct . . . . DSS H 1 'methyl protons' ppm 0 internal direct . . . 1.0 formamide N 15 'methyl protons' ppm 0 external indirect . . . . 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 '2H isotope effect for all 1H.' loop_ _Experiment_label '2D 1H-1H TOCSY' '2D 1H-1H NOESY' '2D 1H-13C HSQC' '2D 1H-15N sfHMQC' 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 entity _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 PRO HA H 4.5140 0.0000 1 2 1 1 PRO HB2 H 2.0840 0.0000 2 3 1 1 PRO HG2 H 2.1020 0.0000 2 4 1 1 PRO HD2 H 2.5550 0.0000 1 5 1 1 PRO CA C 58.9110 0.0000 1 6 1 1 PRO CB C 31.4470 0.0000 1 7 1 1 PRO CG C 26.5660 0.0000 1 8 1 1 PRO CD C 49.4190 0.0000 1 9 2 2 LYS H H 7.4410 0.0000 1 10 2 2 LYS HA H 4.3300 0.0000 1 11 2 2 LYS HB2 H 1.9010 0.0000 2 12 2 2 LYS HG2 H 1.4430 0.0000 2 13 2 2 LYS HD2 H 1.7350 0.0000 2 14 2 2 LYS HE2 H 3.0090 0.0000 2 15 2 2 LYS CA C 57.0840 0.0000 1 16 2 2 LYS CB C 32.2340 0.0000 1 17 2 2 LYS CG C 24.9750 0.0000 1 18 2 2 LYS CD C 30.1270 0.0000 1 19 2 2 LYS CE C 42.2830 0.0000 1 20 2 2 LYS N N 119.6820 0.0000 1 21 3 3 ILE H H 8.4240 0.0000 1 22 3 3 ILE HA H 3.8410 0.0000 1 23 3 3 ILE HB H 2.1200 0.0000 1 24 3 3 ILE HG12 H 1.2500 0.0000 2 25 3 3 ILE HG2 H 0.8990 0.0000 1 26 3 3 ILE HD1 H 0.9480 0.0000 1 27 3 3 ILE CA C 57.9480 0.0000 1 28 3 3 ILE CB C 37.4700 0.0000 1 29 3 3 ILE CG1 C 26.7160 0.0000 1 30 3 3 ILE CD1 C 13.2160 0.0000 1 31 3 3 ILE N N 119.9420 0.0000 1 32 4 4 LEU H H 8.0110 0.0000 1 33 4 4 LEU HA H 4.0060 0.0000 1 34 4 4 LEU HB2 H 1.7590 0.0000 2 35 4 4 LEU HG H 1.5930 0.0000 1 36 4 4 LEU HD1 H 0.9500 0.0000 2 37 4 4 LEU HD2 H 0.8900 0.0000 2 38 4 4 LEU CA C 58.3490 0.0000 1 39 4 4 LEU CB C 41.4970 0.0000 1 40 4 4 LEU CG C 26.6110 0.0000 1 41 4 4 LEU CD1 C 24.7120 0.0000 2 42 4 4 LEU CD2 C 24.8430 0.0000 2 43 4 4 LEU N N 119.8070 0.0000 1 44 5 5 ASN H H 8.0550 0.0000 1 45 5 5 ASN HA H 4.3280 0.0000 1 46 5 5 ASN HB2 H 2.7300 0.0000 2 47 5 5 ASN HD21 H 7.5360 0.0000 2 48 5 5 ASN HD22 H 6.8560 0.0000 2 49 5 5 ASN CA C 58.5050 0.0000 1 50 5 5 ASN CB C 39.0220 0.0000 1 51 5 5 ASN N N 119.7460 0.0000 1 52 5 5 ASN ND2 N 111.6070 0.0000 1 53 6 6 LYS H H 7.8130 0.0000 1 54 6 6 LYS HA H 4.1480 0.0000 1 55 6 6 LYS HB2 H 2.0710 0.0000 2 56 6 6 LYS HG2 H 1.6450 0.0000 2 57 6 6 LYS HD2 H 1.5090 0.0000 2 58 6 6 LYS HE2 H 3.0000 0.0000 2 59 6 6 LYS CA C 59.3090 0.0000 1 60 6 6 LYS CB C 32.0910 0.0000 1 61 6 6 LYS CG C 25.1070 0.0000 1 62 6 6 LYS CD C 31.5000 0.0000 1 63 6 6 LYS CE C 42.2830 0.0000 1 64 6 6 LYS N N 119.8580 0.0000 1 65 7 7 ILE H H 8.0940 0.0000 1 66 7 7 ILE HA H 3.7350 0.0000 1 67 7 7 ILE HB H 2.0100 0.0000 1 68 7 7 ILE HG12 H 1.8600 0.0000 1 69 7 7 ILE HG2 H 0.8560 0.0000 1 70 7 7 ILE HD1 H 0.8980 0.0000 1 71 7 7 ILE CB C 38.2800 0.0000 1 72 7 7 ILE CG1 C 26.7690 0.0000 1 73 7 7 ILE CG2 C 17.7990 0.0000 1 74 7 7 ILE CD1 C 14.0900 0.0000 1 75 7 7 ILE N N 119.5950 0.0000 1 76 8 8 LEU H H 8.5600 0.0000 1 77 8 8 LEU HA H 4.0290 0.0000 1 78 8 8 LEU HB2 H 1.7500 0.0000 2 79 8 8 LEU HG H 1.7100 0.0000 1 80 8 8 LEU HD1 H 0.9700 0.0000 2 81 8 8 LEU HD2 H 0.9200 0.0000 2 82 8 8 LEU CA C 58.2600 0.0000 1 83 8 8 LEU CB C 41.5710 0.0000 1 84 8 8 LEU CG C 27.0470 0.0000 1 85 8 8 LEU CD1 C 24.9320 0.0000 2 86 8 8 LEU CD2 C 24.2140 0.0000 2 87 8 8 LEU N N 119.9700 0.0000 1 88 9 9 GLY H H 8.0960 0.0000 1 89 9 9 GLY HA2 H 3.9500 0.0000 2 90 9 9 GLY CA C 49.0700 0.0000 1 91 10 10 LYS H H 7.5700 0.0000 1 92 10 10 LYS HA H 4.1990 0.0000 1 93 10 10 LYS HB2 H 2.0890 0.0000 2 94 10 10 LYS HG2 H 1.5110 0.0000 2 95 10 10 LYS HE2 H 3.0040 0.0000 2 96 10 10 LYS CA C 58.5910 0.0000 1 97 10 10 LYS CB C 32.0900 0.0000 1 98 10 10 LYS CG C 25.0230 0.0000 1 99 10 10 LYS CE C 42.2830 0.0000 1 100 10 10 LYS N N 121.0520 0.0000 1 101 11 11 ILE H H 8.1290 0.0000 1 102 11 11 ILE HA H 3.7040 0.0000 1 103 11 11 ILE HB H 2.1050 0.0000 1 104 11 11 ILE HG12 H 1.1440 0.0000 1 105 11 11 ILE HG2 H 0.8290 0.0000 1 106 11 11 ILE HD1 H 0.9170 0.0000 1 107 11 11 ILE CB C 37.4860 0.0000 1 108 11 11 ILE CG1 C 31.6600 0.0000 1 109 11 11 ILE CG2 C 17.7440 0.0000 1 110 11 11 ILE CD1 C 13.6990 0.0000 1 111 11 11 ILE N N 119.5760 0.0000 1 112 12 12 LEU H H 8.5100 0.0000 1 113 12 12 LEU HA H 4.0620 0.0000 1 114 12 12 LEU HB2 H 1.8800 0.0000 2 115 12 12 LEU HG H 1.5100 0.0000 1 116 12 12 LEU HD1 H 0.9100 0.0000 2 117 12 12 LEU HD2 H 0.8900 0.0000 2 118 12 12 LEU CA C 58.5370 0.0000 1 119 12 12 LEU CB C 41.5280 0.0000 1 120 12 12 LEU CG C 27.3930 0.0000 1 121 12 12 LEU CD1 C 24.3000 0.0000 2 122 12 12 LEU CD2 C 24.2630 0.0000 2 123 12 12 LEU N N 119.6810 0.0000 1 124 13 13 ARG H H 7.6810 0.0000 1 125 13 13 ARG HA H 4.1190 0.0000 1 126 13 13 ARG HB2 H 1.9800 0.0000 2 127 13 13 ARG HG2 H 1.6800 0.0000 2 128 13 13 ARG HD2 H 3.2350 0.0000 2 129 13 13 ARG HE H 7.1970 0.0000 1 130 13 13 ARG HH21 H 7.2100 0.0000 1 131 13 13 ARG HH22 H 7.1840 0.0000 1 132 13 13 ARG CA C 58.0920 0.0000 1 133 13 13 ARG CB C 30.5860 0.0000 1 134 13 13 ARG CG C 28.8980 0.0000 1 135 13 13 ARG CD C 43.6700 0.0000 1 136 13 13 ARG N N 119.5110 0.0000 1 137 14 14 LEU H H 7.9910 0.0000 1 138 14 14 LEU HA H 4.1850 0.0000 1 139 14 14 LEU HB2 H 1.9100 0.0000 2 140 14 14 LEU HG H 1.7190 0.0000 1 141 14 14 LEU HD1 H 0.9710 0.0000 2 142 14 14 LEU HD2 H 0.9140 0.0000 2 143 14 14 LEU CA C 57.9750 0.0000 1 144 14 14 LEU CB C 42.2080 0.0000 1 145 14 14 LEU CG C 26.2460 0.0000 1 146 14 14 LEU CD1 C 25.1620 0.0000 2 147 14 14 LEU CD2 C 24.8400 0.0000 2 148 14 14 LEU N N 121.3880 0.0000 1 149 15 15 ALA H H 8.4650 0.0000 1 150 15 15 ALA HA H 4.0590 0.0000 1 151 15 15 ALA HB H 1.4900 0.0000 1 152 15 15 ALA CA C 54.9110 0.0000 1 153 15 15 ALA CB C 18.5450 0.0000 1 154 15 15 ALA N N 120.2890 0.0000 1 155 16 16 ALA H H 7.7340 0.0000 1 156 16 16 ALA HA H 4.1330 0.0000 1 157 16 16 ALA HB H 1.5180 0.0000 1 158 16 16 ALA CA C 54.2310 0.0000 1 159 16 16 ALA CB C 18.6840 0.0000 1 160 16 16 ALA N N 117.9630 0.0000 1 161 17 17 ALA H H 7.6160 0.0000 1 162 17 17 ALA HA H 4.1960 0.0000 1 163 17 17 ALA HB H 1.3160 0.0000 1 164 17 17 ALA CA C 53.7010 0.0000 1 165 17 17 ALA CB C 18.8200 0.0000 1 166 17 17 ALA N N 119.6180 0.0000 1 167 18 18 PHE H H 7.7100 0.0000 1 168 18 18 PHE HA H 4.5400 0.0000 1 169 18 18 PHE HB2 H 2.9400 0.0000 2 170 18 18 PHE HD1 H 7.3690 0.0000 3 171 18 18 PHE HD2 H 7.3690 0.0000 3 172 18 18 PHE HE1 H 7.2670 0.0000 3 173 18 18 PHE HE2 H 7.2670 0.0000 3 174 18 18 PHE HZ H 7.2000 0.0000 1 175 18 18 PHE CA C 58.5100 0.0000 1 176 18 18 PHE CB C 37.9210 0.0000 1 177 18 18 PHE CD1 C 132.2410 0.0000 3 178 18 18 PHE CD2 C 132.0570 0.0000 3 179 18 18 PHE CE1 C 131.1770 0.0000 3 180 18 18 PHE CE2 C 131.3610 0.0000 3 181 18 18 PHE CZ C 129.6220 0.0000 1 182 18 18 PHE N N 116.8410 0.0000 1 183 19 19 LYS H H 7.4470 0.0000 1 184 19 19 LYS HA H 4.1560 0.0000 1 185 19 19 LYS HB2 H 1.8600 0.0000 2 186 19 19 LYS HG2 H 1.4400 0.0000 2 187 19 19 LYS HD2 H 1.6940 0.0000 2 188 19 19 LYS HE2 H 3.0020 0.0000 2 189 19 19 LYS CA C 59.1890 0.0000 1 190 19 19 LYS CB C 33.5440 0.0000 1 191 19 19 LYS CG C 24.9190 0.0000 1 192 19 19 LYS CD C 28.9510 0.0000 1 193 19 19 LYS CE C 42.2830 0.0000 1 194 19 19 LYS N N 125.3880 0.0000 1 stop_ save_