data_36146 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; mBjAMP1 structure ; _BMRB_accession_number 36146 _BMRB_flat_file_name bmr36146.str _Entry_type original _Submission_date 2017-12-28 _Accession_date 2018-06-27 _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 Nam J. Y. . 2 Lee C. W. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 122 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2019-06-21 update BMRB 'update entry citation' 2018-12-18 original author 'original release' stop_ _Original_release_date 2018-06-27 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Structural and functional assessment of mBjAMP1, an antimicrobial peptide from Branchiostoma japonicum, revealed a novel alpha-hairpinin-like scaffold with membrane permeable and DNA binding activity. ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 30475621 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Nam Jiyong Y. . 2 Yun Hyosuk . . 3 Rajasekaran Ganesan . . 4 Kumar 'S. Dinesh' . . 5 Kim 'Jae Il' . . 6 Min 'Hye Jung' . . 7 Shin 'Song Yub' . . 8 Lee 'Chul Won' W. . stop_ _Journal_abbreviation 'J. Med. Chem.' _Journal_name_full 'Journal of medicinal chemistry' _Journal_volume 61 _Journal_issue 24 _Journal_ISSN 0022-2623 _Journal_CSD 0353 _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 11101 _Page_last 11113 _Year 2018 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'mBjAMP1 peptide' _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 'mBjAMP1 peptide' _Molecular_mass 2490.979 _Mol_thiol_state 'all disulfide bound' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 21 _Mol_residue_sequence ; NLCASLRARHTIPQCRKFGR R ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 ASN 2 2 LEU 3 3 CYS 4 4 ALA 5 5 SER 6 6 LEU 7 7 ARG 8 8 ALA 9 9 ARG 10 10 HIS 11 11 THR 12 12 ILE 13 13 PRO 14 14 GLN 15 15 CYS 16 16 ARG 17 17 LYS 18 18 PHE 19 19 GLY 20 20 ARG 21 21 ARG 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_1 'Florida lancelet' 7739 Eukaryota Metazoa Branchiostoma floridae 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 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details '2 mM WT peptides, 10 mM pH 6.0 sodium phosphate, 50 mM pH 6.0 sodium chloride, 10 % pH 6.0 D2O, 90% H2O/10% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 2 mM 'natural abundance' 'sodium chloride' 50 mM 'natural abundance' 'sodium phosphate' 10 mM 'natural abundance' H2O 90 % 'natural abundace' D2O 10 % [U-2H] stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name CYANA _Version 2.1 loop_ _Vendor _Address _Electronic_address 'Guntert, Mumenthaler and Wuthrich' . . stop_ loop_ _Task 'structure calculation' stop_ _Details . save_ save_software_2 _Saveframe_category software _Name Molmol _Version . loop_ _Vendor _Address _Electronic_address 'Koradi, Billeter and Wuthrich' . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ save_software_3 _Saveframe_category software _Name NMRView _Version . loop_ _Vendor _Address _Electronic_address 'Johnson, One Moon Scientific' . . stop_ loop_ _Task 'peak picking' stop_ _Details . save_ save_software_4 _Saveframe_category software _Name 'X-PLOR NIH' _Version . loop_ _Vendor _Address _Electronic_address 'Schwieters, Kuszewski, Tjandra and Clore' . . stop_ loop_ _Task refinement stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 600 _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_DQF-COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _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' 50 . mM pH 6.0 . pH pressure 1 . atm temperature 298.0 . 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 H 1 'methyl protons' ppm 0.0 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_chemical_shifts_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H TOCSY' '2D 1H-1H NOESY' '2D DQF-COSY' stop_ loop_ _Sample_label $sample_1 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 3 3 CYS H H 8.1970 0.01 1 2 3 3 CYS HA H 4.6340 0.01 1 3 3 3 CYS HB2 H 3.1760 0.01 2 4 3 3 CYS HB3 H 2.5930 0.01 2 5 4 4 ALA H H 7.5860 0.01 1 6 4 4 ALA HA H 4.1500 0.01 1 7 4 4 ALA HB H 1.4200 0.01 1 8 5 5 SER H H 7.9020 0.01 1 9 5 5 SER HA H 4.4890 0.01 1 10 5 5 SER HB2 H 4.1020 0.01 2 11 5 5 SER HB3 H 3.9390 0.01 2 12 6 6 LEU H H 8.4780 0.01 1 13 6 6 LEU HA H 4.0560 0.01 1 14 6 6 LEU HB2 H 1.6810 0.01 2 15 6 6 LEU HB3 H 1.5870 0.01 2 16 6 6 LEU HG H 1.5900 0.01 1 17 6 6 LEU HD1 H 0.8630 0.01 2 18 6 6 LEU HD2 H 0.9150 0.01 2 19 7 7 ARG H H 8.3480 0.01 1 20 7 7 ARG HA H 4.1500 0.01 1 21 7 7 ARG HB2 H 1.8200 0.01 2 22 7 7 ARG HB3 H 1.8200 0.01 2 23 7 7 ARG HG2 H 1.6430 0.01 2 24 7 7 ARG HG3 H 1.5640 0.01 2 25 7 7 ARG HD2 H 3.1780 0.01 2 26 7 7 ARG HD3 H 3.1780 0.01 2 27 7 7 ARG HE H 7.2860 0.01 1 28 8 8 ALA H H 8.0030 0.01 1 29 8 8 ALA HA H 4.1050 0.01 1 30 8 8 ALA HB H 1.5300 0.01 1 31 9 9 ARG H H 7.9910 0.01 1 32 9 9 ARG HA H 3.8940 0.01 1 33 9 9 ARG HB2 H 1.8250 0.01 2 34 9 9 ARG HB3 H 1.8240 0.01 2 35 9 9 ARG HG2 H 1.7180 0.01 2 36 9 9 ARG HG3 H 1.5840 0.01 2 37 9 9 ARG HD2 H 3.1160 0.01 2 38 9 9 ARG HD3 H 3.1160 0.01 2 39 9 9 ARG HE H 7.0830 0.01 1 40 10 10 HIS H H 7.9010 0.01 1 41 10 10 HIS HA H 4.6950 0.01 1 42 10 10 HIS HB2 H 3.2880 0.01 2 43 10 10 HIS HB3 H 3.1780 0.01 2 44 11 11 THR H H 7.8260 0.01 1 45 11 11 THR HA H 4.4410 0.01 1 46 11 11 THR HB H 4.1800 0.01 1 47 11 11 THR HG2 H 1.1720 0.01 1 48 12 12 ILE H H 8.2300 0.01 1 49 12 12 ILE HA H 4.5950 0.01 1 50 12 12 ILE HB H 1.9440 0.01 1 51 12 12 ILE HG12 H 1.6120 0.01 2 52 12 12 ILE HG13 H 1.1760 0.01 2 53 12 12 ILE HG2 H 0.9420 0.01 1 54 12 12 ILE HD1 H 0.8520 0.01 1 55 13 13 PRO HA H 4.1200 0.01 1 56 13 13 PRO HB2 H 2.3690 0.01 2 57 13 13 PRO HB3 H 2.0000 0.01 2 58 13 13 PRO HG2 H 2.1800 0.01 2 59 13 13 PRO HG3 H 2.0000 0.01 2 60 13 13 PRO HD2 H 3.8700 0.01 2 61 13 13 PRO HD3 H 3.8700 0.01 2 62 14 14 GLN H H 8.7350 0.01 1 63 14 14 GLN HA H 4.2140 0.01 1 64 14 14 GLN HB2 H 2.0730 0.01 2 65 14 14 GLN HB3 H 2.0730 0.01 2 66 14 14 GLN HG2 H 2.4250 0.01 2 67 14 14 GLN HG3 H 2.3740 0.01 2 68 14 14 GLN HE21 H 6.8950 0.01 2 69 14 14 GLN HE22 H 7.5540 0.01 2 70 15 15 CYS H H 8.0740 0.01 1 71 15 15 CYS HA H 4.8850 0.01 1 72 15 15 CYS HB2 H 3.1640 0.01 2 73 15 15 CYS HB3 H 3.0240 0.01 2 74 16 16 ARG H H 7.7250 0.01 1 75 16 16 ARG HA H 4.2800 0.01 1 76 16 16 ARG HB2 H 1.8500 0.01 2 77 16 16 ARG HB3 H 1.8100 0.01 2 78 16 16 ARG HG2 H 1.6570 0.01 2 79 16 16 ARG HG3 H 1.6380 0.01 2 80 16 16 ARG HD2 H 3.1400 0.01 2 81 16 16 ARG HD3 H 3.1400 0.01 2 82 16 16 ARG HE H 7.1630 0.01 1 83 17 17 LYS H H 8.0980 0.01 1 84 17 17 LYS HA H 4.2230 0.01 1 85 17 17 LYS HB2 H 1.6930 0.01 2 86 17 17 LYS HB3 H 1.7000 0.01 2 87 17 17 LYS HG2 H 1.2000 0.01 2 88 17 17 LYS HG3 H 1.2020 0.01 2 89 17 17 LYS HD2 H 1.5830 0.01 2 90 17 17 LYS HD3 H 1.5830 0.01 2 91 17 17 LYS HE2 H 2.9000 0.01 2 92 17 17 LYS HE3 H 2.9000 0.01 2 93 17 17 LYS HZ H 7.2540 0.01 1 94 18 18 PHE H H 7.9660 0.01 1 95 18 18 PHE HA H 4.5530 0.01 1 96 18 18 PHE HB2 H 3.1620 0.01 2 97 18 18 PHE HB3 H 3.0340 0.01 2 98 18 18 PHE HD1 H 7.2550 0.01 3 99 18 18 PHE HD2 H 7.2550 0.01 3 100 18 18 PHE HE1 H 7.2550 0.01 3 101 18 18 PHE HE2 H 7.2550 0.01 3 102 18 18 PHE HZ H 7.3420 0.01 1 103 19 19 GLY H H 8.2510 0.01 1 104 19 19 GLY HA2 H 3.8830 0.01 2 105 19 19 GLY HA3 H 3.8830 0.01 2 106 20 20 ARG H H 8.1630 0.01 1 107 20 20 ARG HA H 4.3060 0.01 1 108 20 20 ARG HB2 H 1.8510 0.01 2 109 20 20 ARG HB3 H 1.7670 0.01 2 110 20 20 ARG HG2 H 1.6180 0.01 2 111 20 20 ARG HG3 H 1.6180 0.01 2 112 20 20 ARG HD2 H 3.1740 0.01 2 113 20 20 ARG HD3 H 3.1740 0.01 2 114 21 21 ARG H H 8.3920 0.01 1 115 21 21 ARG HA H 4.2780 0.01 1 116 21 21 ARG HB2 H 1.8540 0.01 2 117 21 21 ARG HB3 H 1.7720 0.01 2 118 21 21 ARG HG2 H 1.6600 0.01 2 119 21 21 ARG HG3 H 1.6120 0.01 2 120 21 21 ARG HD2 H 3.1700 0.01 2 121 21 21 ARG HD3 H 3.1700 0.01 2 122 21 21 ARG HE H 7.2540 0.01 1 stop_ save_