data_19878 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Structure of Platypus 'Intermediate' Defensin-like Peptide (Int-DLP) ; _BMRB_accession_number 19878 _BMRB_flat_file_name bmr19878.str _Entry_type original _Submission_date 2014-03-27 _Accession_date 2014-03-27 _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 Torres Allan M. . 2 Bansal Paramjit S. . 3 Koh Jennifer MS . 4 Pages Guilhem . . 5 Wu Ming J. . 6 Kuchel Philip W. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 196 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2014-09-15 original author . stop_ _Original_release_date 2014-09-15 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title "Structure and antimicrobial activity of platypus 'intermediate' defensin-like peptide" _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 24694388 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Torres Allan M. . 2 Bansal Paramjit S. . 3 Koh Jennifer MS . 4 Pages Guilhem . . 5 Wu Ming J. . 6 Kuchel Philip W. . stop_ _Journal_abbreviation 'FEBS Lett.' _Journal_volume 588 _Journal_issue 9 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 1821 _Page_last 1826 _Year 2014 _Details . save_ ####################################### # Cited references within the entry # ####################################### save_citation_2 _Saveframe_category citation _Citation_full . _Citation_title 'Defensins and the convergent evolution of platypus and reptile venom genes' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 18463304 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Whittington Camilla M. . 2 Papenfuss Anthony T. . 3 Bansal Paramjit . . 4 Torres Allan M. . 5 Wong Emily SW . 6 Deakin Janine E. . 7 Graves Tina . . 8 Alsop Amber . . 9 Schatzkamer Kyriena . . 10 Kremitzki Colin . . 11 Ponting Chris P. . 12 Temple-Smith Peter . . 13 Warren Wesley C. . 14 Kuchel Philip W. . 15 Katherine Belov . . stop_ _Journal_abbreviation 'Genome Res' _Journal_name_full . _Journal_volume 18 _Journal_issue 6 _Journal_CSD . _Book_title . _Book_chapter_title . _Book_volume . _Book_series . _Book_publisher . _Book_publisher_city . _Book_ISBN . _Conference_title . _Conference_site . _Conference_state_province . _Conference_country . _Conference_start_date . _Conference_end_date . _Conference_abstract_number . _Thesis_institution . _Thesis_institution_city . _Thesis_institution_country . _Page_first 986 _Page_last 994 _Year 2008 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name Int-DLP _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label Int-DLP $Int-DLP 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_Int-DLP _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common Int-DLP _Molecular_mass 5000.910 _Mol_thiol_state 'all disulfide bound' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 44 _Mol_residue_sequence ; RRRRRRPPCEDVNGQCQPRG NPCLRLRGACPRGSRCCMPT VAAH ; loop_ _Residue_seq_code _Residue_label 1 ARG 2 ARG 3 ARG 4 ARG 5 ARG 6 ARG 7 PRO 8 PRO 9 CYS 10 GLU 11 ASP 12 VAL 13 ASN 14 GLY 15 GLN 16 CYS 17 GLN 18 PRO 19 ARG 20 GLY 21 ASN 22 PRO 23 CYS 24 LEU 25 ARG 26 LEU 27 ARG 28 GLY 29 ALA 30 CYS 31 PRO 32 ARG 33 GLY 34 SER 35 ARG 36 CYS 37 CYS 38 MET 39 PRO 40 THR 41 VAL 42 ALA 43 ALA 44 HIS stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2014-11-09 loop_ _Database_name _Database_accession_code _Database_entry_mol_name _Sequence_query_to_submitted_percentage _Sequence_subject_length _Sequence_identity _Sequence_positive _Sequence_homology_expectation_value PDB 2MN3 "Structure Of Platypus 'intermediate' Defensin-like Peptide (int-dlp)" 100.00 44 100.00 100.00 1.52e-20 SP P0C8B1 "RecName: Full=Defensin-BvL; Short=DefB-vL; Short=OaDefB-vL; Flags: Precursor [Ornithorhynchus anatinus]" 100.00 68 100.00 100.00 1.84e-21 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species _Details $Int-DLP platypus 9258 Eukaryota Metazoa Ornithorhynchus anatinus platypus 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 $Int-DLP 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details 'chemically synthesized Int-DLP' loop_ _Mol_label _Concentration_value _Concentration_value_units _Concentration_min_value _Concentration_max_value _Isotopic_labeling $Int-DLP . mM 1 2 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_CYANA _Saveframe_category software _Name CYANA _Version 2.1 loop_ _Vendor _Address _Electronic_address 'Guntert, Mumenthaler and Wuthrich' . . stop_ loop_ _Task 'chemical shift assignment' 'data analysis' 'structure solution' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 500 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 800 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _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-1H_COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H COSY' _Sample_label $sample_1 save_ save_2D_1H-1H_TOCSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _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 temperature 298 . K pH 3.5 . pH pressure 1 . atm 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 water H 1 protons ppm 4.78 na direct . . . 1.0 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_ _Software_label $CYANA stop_ loop_ _Experiment_label '2D 1H-1H NOESY' '2D 1H-1H COSY' '2D 1H-1H TOCSY' 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 Int-DLP _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 2 2 ARG H H 8.518 0.000 . 2 2 2 ARG HA H 4.349 0.000 . 3 3 3 ARG H H 8.502 0.000 . 4 3 3 ARG HA H 4.579 0.000 . 5 4 4 ARG H H 8.495 0.000 . 6 4 4 ARG HA H 4.334 0.000 . 7 5 5 ARG HA H 4.070 0.002 . 8 5 5 ARG HB2 H 1.676 0.000 . 9 5 5 ARG HB3 H 1.938 0.001 . 10 5 5 ARG HD2 H 3.244 0.000 . 11 6 6 ARG H H 8.815 0.000 . 12 6 6 ARG HA H 4.390 0.000 . 13 6 6 ARG HB2 H 1.668 0.000 . 14 6 6 ARG HB3 H 1.801 0.000 . 15 7 7 PRO HB3 H 2.370 0.003 . 16 7 7 PRO HD2 H 3.666 0.004 . 17 7 7 PRO HD3 H 3.810 0.002 . 18 8 8 PRO HB2 H 2.060 0.000 . 19 8 8 PRO HB3 H 2.507 0.001 . 20 8 8 PRO HG2 H 1.944 0.000 . 21 8 8 PRO HD2 H 3.699 0.008 . 22 8 8 PRO HD3 H 3.889 0.004 . 23 9 9 CYS HA H 4.049 0.007 . 24 9 9 CYS HB2 H 2.671 0.004 . 25 9 9 CYS HB3 H 2.977 0.004 . 26 10 10 GLU HA H 4.365 0.000 . 27 10 10 GLU HB3 H 2.119 0.001 . 28 10 10 GLU HG2 H 2.506 0.000 . 29 10 10 GLU HG3 H 2.535 0.007 . 30 11 11 ASP H H 7.970 0.002 . 31 11 11 ASP HA H 4.679 0.000 . 32 11 11 ASP HB2 H 2.974 0.000 . 33 12 12 VAL H H 7.452 0.003 . 34 12 12 VAL HA H 4.596 0.002 . 35 12 12 VAL HB H 2.509 0.002 . 36 12 12 VAL HG2 H 0.850 0.003 . 37 13 13 ASN H H 7.709 0.000 . 38 13 13 ASN HA H 4.369 0.003 . 39 13 13 ASN HB2 H 2.980 0.000 . 40 13 13 ASN HB3 H 3.088 0.001 . 41 13 13 ASN HD21 H 6.876 0.000 . 42 13 13 ASN HD22 H 7.480 0.000 . 43 14 14 GLY H H 7.550 0.000 . 44 14 14 GLY HA2 H 3.313 0.000 . 45 14 14 GLY HA3 H 4.578 0.000 . 46 15 15 GLN H H 8.861 0.003 . 47 15 15 GLN HA H 4.554 0.000 . 48 15 15 GLN HB2 H 1.859 0.006 . 49 15 15 GLN HB3 H 1.930 0.001 . 50 15 15 GLN HG2 H 2.278 0.001 . 51 15 15 GLN HE21 H 6.893 0.003 . 52 15 15 GLN HE22 H 7.568 0.002 . 53 16 16 CYS H H 9.086 0.001 . 54 16 16 CYS HA H 5.233 0.002 . 55 16 16 CYS HB2 H 2.909 0.009 . 56 16 16 CYS HB3 H 2.954 0.006 . 57 17 17 GLN H H 9.471 0.001 . 58 17 17 GLN HA H 5.105 0.001 . 59 17 17 GLN HB2 H 1.993 0.000 . 60 17 17 GLN HB3 H 2.161 0.003 . 61 17 17 GLN HG2 H 2.258 0.002 . 62 17 17 GLN HG3 H 2.426 0.002 . 63 17 17 GLN HE21 H 6.792 0.001 . 64 17 17 GLN HE22 H 7.133 0.001 . 65 18 18 PRO HA H 4.623 0.001 . 66 18 18 PRO HB2 H 2.064 0.003 . 67 18 18 PRO HB3 H 2.417 0.002 . 68 18 18 PRO HG2 H 1.968 0.000 . 69 18 18 PRO HD2 H 3.732 0.005 . 70 18 18 PRO HD3 H 3.872 0.007 . 71 19 19 ARG H H 8.284 0.000 . 72 19 19 ARG HA H 3.927 0.001 . 73 19 19 ARG HB2 H 1.734 0.002 . 74 19 19 ARG HB3 H 1.807 0.002 . 75 19 19 ARG HG2 H 1.570 0.002 . 76 19 19 ARG HD2 H 3.181 0.000 . 77 20 20 GLY H H 8.550 0.002 . 78 20 20 GLY HA2 H 3.879 0.004 . 79 20 20 GLY HA3 H 4.002 0.003 . 80 21 21 ASN H H 7.667 0.000 . 81 21 21 ASN HA H 5.007 0.002 . 82 21 21 ASN HB2 H 2.731 0.000 . 83 21 21 ASN HB3 H 2.837 0.003 . 84 21 21 ASN HD21 H 7.119 0.001 . 85 21 21 ASN HD22 H 7.525 0.001 . 86 22 22 PRO HA H 4.368 0.002 . 87 22 22 PRO HB2 H 2.117 0.003 . 88 22 22 PRO HB3 H 2.276 0.004 . 89 22 22 PRO HG2 H 1.906 0.005 . 90 22 22 PRO HG3 H 2.023 0.000 . 91 22 22 PRO HD2 H 3.632 0.002 . 92 22 22 PRO HD3 H 3.921 0.006 . 93 23 23 CYS H H 8.354 0.001 . 94 23 23 CYS HA H 4.820 0.002 . 95 23 23 CYS HB2 H 2.981 0.002 . 96 23 23 CYS HB3 H 3.218 0.007 . 97 24 24 LEU H H 9.047 0.001 . 98 24 24 LEU HA H 4.595 0.003 . 99 24 24 LEU HB2 H 1.721 0.002 . 100 24 24 LEU HD1 H 0.937 0.001 . 101 24 24 LEU HD2 H 0.992 0.001 . 102 25 25 ARG H H 8.252 0.001 . 103 25 25 ARG HA H 4.498 0.000 . 104 25 25 ARG HB2 H 1.793 0.007 . 105 25 25 ARG HB3 H 1.840 0.002 . 106 25 25 ARG HG2 H 1.669 0.008 . 107 25 25 ARG HD2 H 3.240 0.000 . 108 25 25 ARG HE H 7.382 0.001 . 109 26 26 LEU H H 7.995 0.002 . 110 26 26 LEU HA H 4.648 0.006 . 111 26 26 LEU HB2 H 1.293 0.004 . 112 26 26 LEU HB3 H 1.368 0.000 . 113 26 26 LEU HG H 1.569 0.006 . 114 26 26 LEU HD1 H 0.806 0.002 . 115 26 26 LEU HD2 H 0.923 0.006 . 116 27 27 ARG H H 8.615 0.001 . 117 27 27 ARG HA H 4.351 0.002 . 118 27 27 ARG HB2 H 1.771 0.004 . 119 27 27 ARG HB3 H 1.811 0.012 . 120 27 27 ARG HG2 H 1.637 0.006 . 121 27 27 ARG HD2 H 3.217 0.004 . 122 28 28 GLY H H 8.372 0.000 . 123 28 28 GLY HA3 H 3.954 0.000 . 124 29 29 ALA H H 8.963 0.008 . 125 29 29 ALA HA H 4.559 0.003 . 126 29 29 ALA HB H 1.269 0.003 . 127 30 30 CYS H H 8.550 0.003 . 128 30 30 CYS HA H 5.075 0.000 . 129 30 30 CYS HB2 H 2.313 0.000 . 130 30 30 CYS HB3 H 3.265 0.003 . 131 31 31 PRO HA H 4.492 0.003 . 132 31 31 PRO HB2 H 2.025 0.002 . 133 31 31 PRO HB3 H 2.411 0.001 . 134 31 31 PRO HG2 H 1.857 0.008 . 135 31 31 PRO HG3 H 1.982 0.001 . 136 31 31 PRO HD2 H 3.570 0.005 . 137 31 31 PRO HD3 H 3.867 0.009 . 138 32 32 ARG H H 8.549 0.000 . 139 32 32 ARG HA H 4.119 0.004 . 140 32 32 ARG HB2 H 1.786 0.001 . 141 32 32 ARG HB3 H 1.872 0.004 . 142 32 32 ARG HG2 H 1.647 0.004 . 143 32 32 ARG HD2 H 3.263 0.001 . 144 33 33 GLY H H 9.072 0.001 . 145 33 33 GLY HA2 H 3.703 0.003 . 146 33 33 GLY HA3 H 4.431 0.002 . 147 34 34 SER H H 8.285 0.001 . 148 34 34 SER HA H 5.177 0.001 . 149 34 34 SER HB2 H 3.636 0.003 . 150 34 34 SER HB3 H 3.636 0.003 . 151 35 35 ARG H H 9.225 0.001 . 152 35 35 ARG HA H 4.725 0.000 . 153 35 35 ARG HB2 H 1.636 0.000 . 154 35 35 ARG HB3 H 1.809 0.003 . 155 35 35 ARG HD2 H 3.147 0.000 . 156 35 35 ARG HE H 7.607 0.000 . 157 36 36 CYS H H 8.578 0.001 . 158 36 36 CYS HA H 4.694 0.001 . 159 36 36 CYS HB2 H 2.981 0.003 . 160 36 36 CYS HB3 H 3.164 0.000 . 161 37 37 CYS H H 8.779 0.000 . 162 37 37 CYS HA H 5.389 0.002 . 163 37 37 CYS HB2 H 2.746 0.003 . 164 37 37 CYS HB3 H 3.426 0.006 . 165 38 38 MET H H 9.100 0.003 . 166 38 38 MET HA H 4.694 0.002 . 167 38 38 MET HB2 H 2.017 0.002 . 168 38 38 MET HB3 H 2.280 0.002 . 169 38 38 MET HG2 H 2.737 0.005 . 170 39 39 PRO HA H 4.496 0.001 . 171 39 39 PRO HB2 H 2.104 0.004 . 172 39 39 PRO HB3 H 2.241 0.003 . 173 39 39 PRO HG2 H 1.885 0.000 . 174 39 39 PRO HG3 H 1.910 0.000 . 175 39 39 PRO HD2 H 3.888 0.001 . 176 39 39 PRO HD3 H 4.192 0.003 . 177 40 40 THR H H 8.335 0.001 . 178 40 40 THR HA H 4.341 0.002 . 179 40 40 THR HB H 4.194 0.001 . 180 40 40 THR HG2 H 1.236 0.001 . 181 41 41 VAL H H 8.168 0.000 . 182 41 41 VAL HA H 4.147 0.001 . 183 41 41 VAL HB H 2.068 0.001 . 184 41 41 VAL HG2 H 0.948 0.002 . 185 42 42 ALA H H 8.399 0.000 . 186 42 42 ALA HA H 4.300 0.003 . 187 42 42 ALA HB H 1.377 0.001 . 188 43 43 ALA H H 8.299 0.000 . 189 43 43 ALA HA H 4.261 0.002 . 190 43 43 ALA HB H 1.356 0.002 . 191 44 44 HIS H H 8.449 0.000 . 192 44 44 HIS HA H 4.687 0.000 . 193 44 44 HIS HB2 H 3.196 0.001 . 194 44 44 HIS HB3 H 3.306 0.001 . 195 44 44 HIS HD2 H 7.332 0.001 . 196 44 44 HIS HE1 H 8.623 0.002 . stop_ save_