data_17500 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Papiliocin ; _BMRB_accession_number 17500 _BMRB_flat_file_name bmr17500.str _Entry_type original _Submission_date 2011-03-01 _Accession_date 2011-03-01 _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 Kim Yangmee . . 2 Kim Jin-Kyoung . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 222 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2012-03-08 update BMRB 'update entry citation' 2011-11-03 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title 'Structure and function of papiliocin with antimicrobial and anti-inflammatory activities isolated from the swallowtail butterfly, Papilio xuthus.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 21965682 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Kim Jin-Kyoung . . 2 Lee Eunjung . . 3 Shin Soyoung . . 4 Jeong Ki-woong . . 5 Lee Jee-Young . . 6 Bae Su-Young . . 7 Kim Soo-Hyun . . 8 Lee Juneyoung . . 9 Kim 'Seong Ryul' . . 10 Lee 'Dong Gun' . . 11 Hwang Jae-Sam . . 12 Kim Yangmee . . stop_ _Journal_abbreviation 'J. Biol. Chem.' _Journal_name_full 'The Journal of biological chemistry' _Journal_volume 286 _Journal_issue 48 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 41296 _Page_last 41311 _Year 2011 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name papiliocin _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label papiliocin $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 papiliocin _Molecular_mass 4010.906 _Mol_thiol_state . _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 38 _Mol_residue_sequence ; RWKIFKKIEKVGRNVRDGII KAGPAVAVVGQAATVVKX ; loop_ _Residue_seq_code _Residue_label 1 ARG 2 TRP 3 LYS 4 ILE 5 PHE 6 LYS 7 LYS 8 ILE 9 GLU 10 LYS 11 VAL 12 GLY 13 ARG 14 ASN 15 VAL 16 ARG 17 ASP 18 GLY 19 ILE 20 ILE 21 LYS 22 ALA 23 GLY 24 PRO 25 ALA 26 VAL 27 ALA 28 VAL 29 VAL 30 GLY 31 GLN 32 ALA 33 ALA 34 THR 35 VAL 36 VAL 37 LYS 38 NH2 stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-06-23 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 2LA2 "Solution Structure Of Papiliocin Isolated From The Swallowtail Butterfly, Papilio Xuthus" 97.37 38 100.00 100.00 1.24e-14 DBJ BAM18456 "unknown secreted protein [Papilio xuthus]" 97.37 62 97.30 97.30 5.07e-14 GB ACR82292 "cecropin [Papilio xuthus]" 97.37 62 100.00 100.00 3.82e-15 stop_ save_ ###################### # Polymer residues # ###################### save_chem_comp_NH2 _Saveframe_category polymer_residue _Mol_type non-polymer _Name_common 'AMINO GROUP' _BMRB_code . _PDB_code NH2 _Standard_residue_derivative . _Molecular_mass 16.023 _Mol_paramagnetic . _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Wed Mar 23 12:59:18 2011 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons N N N . 0 . ? HN1 HN1 H . 0 . ? HN2 HN2 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 HN1 ? ? SING N HN2 ? ? 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 butterfly 66420 Eukaryota Metazoa Papilio xuthus 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 'chemical synthesis' . . . . . 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 1 mM 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_CYANA _Saveframe_category software _Name CYANA _Version . loop_ _Vendor _Address _Electronic_address 'Guntert, Mumenthaler 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 500 _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_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _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 temperature 303 . K pH 5.5 . 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 DSS H 1 'methyl protons' ppm 0 internal direct . . . 1.0000000 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 1H-1H NOESY' '2D 1H-1H TOCSY' '2D DQF-COSY' 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 papiliocin _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 ARG HB2 H 1.807 0.002 2 2 1 1 ARG HB3 H 1.580 0.004 2 3 1 1 ARG HD2 H 3.069 0.001 2 4 1 1 ARG HD3 H 3.069 0.001 2 5 2 2 TRP HA H 4.823 0.001 1 6 2 2 TRP HB2 H 3.339 0.008 2 7 2 2 TRP HB3 H 3.220 0.004 2 8 2 2 TRP HD1 H 7.347 0.015 1 9 2 2 TRP HE1 H 10.683 0.000 1 10 2 2 TRP HE3 H 7.487 0.003 1 11 2 2 TRP HZ2 H 7.380 0.001 1 12 2 2 TRP HZ3 H 6.912 0.003 1 13 2 2 TRP HH2 H 7.069 0.002 1 14 3 3 LYS H H 9.136 0.004 1 15 3 3 LYS HA H 4.226 0.008 1 16 3 3 LYS HB2 H 1.903 0.001 2 17 3 3 LYS HB3 H 1.903 0.001 2 18 3 3 LYS HG2 H 1.504 0.001 2 19 3 3 LYS HG3 H 1.504 0.001 2 20 3 3 LYS HE2 H 2.998 0.004 2 21 3 3 LYS HE3 H 2.998 0.004 2 22 4 4 ILE H H 8.062 0.006 1 23 4 4 ILE HA H 3.940 0.001 1 24 4 4 ILE HB H 1.669 0.004 1 25 4 4 ILE HG12 H 1.316 0.015 2 26 4 4 ILE HG13 H 1.086 0.006 2 27 4 4 ILE HG2 H 0.814 0.002 1 28 4 4 ILE HD1 H 0.640 0.002 1 29 5 5 PHE H H 7.770 0.002 1 30 5 5 PHE HA H 4.319 0.001 1 31 5 5 PHE HB2 H 3.273 0.006 2 32 5 5 PHE HB3 H 3.156 0.005 2 33 5 5 PHE HD1 H 7.278 0.001 3 34 5 5 PHE HE1 H 7.274 0.001 3 35 5 5 PHE HE2 H 7.274 0.001 3 36 5 5 PHE HZ H 7.246 0.001 1 37 6 6 LYS H H 7.957 0.003 1 38 6 6 LYS HA H 4.162 0.006 1 39 6 6 LYS HB2 H 1.917 0.008 2 40 6 6 LYS HB3 H 1.917 0.008 2 41 6 6 LYS HG2 H 1.541 0.010 2 42 6 6 LYS HG3 H 1.541 0.010 2 43 6 6 LYS HD2 H 1.733 0.008 2 44 6 6 LYS HD3 H 1.733 0.008 2 45 6 6 LYS HE2 H 3.005 0.001 2 46 6 6 LYS HE3 H 3.005 0.001 2 47 7 7 LYS H H 7.696 0.004 1 48 7 7 LYS HA H 4.168 0.002 1 49 7 7 LYS HB2 H 1.960 0.005 2 50 7 7 LYS HB3 H 1.891 0.009 2 51 7 7 LYS HG2 H 1.524 0.010 2 52 7 7 LYS HG3 H 1.524 0.010 2 53 7 7 LYS HD2 H 1.681 0.002 2 54 7 7 LYS HD3 H 1.681 0.002 2 55 7 7 LYS HE2 H 2.901 0.004 2 56 7 7 LYS HE3 H 2.901 0.004 2 57 8 8 ILE H H 7.761 0.002 1 58 8 8 ILE HA H 3.771 0.002 1 59 8 8 ILE HB H 1.967 0.003 1 60 8 8 ILE HG12 H 1.692 0.003 2 61 8 8 ILE HG13 H 1.114 0.006 2 62 8 8 ILE HG2 H 0.886 0.008 1 63 8 8 ILE HD1 H 0.810 0.002 1 64 9 9 GLU H H 8.101 0.003 1 65 9 9 GLU HA H 3.857 0.006 1 66 9 9 GLU HB2 H 2.283 0.005 2 67 9 9 GLU HB3 H 2.172 0.005 2 68 9 9 GLU HG2 H 2.055 0.006 2 69 9 9 GLU HG3 H 2.055 0.006 2 70 10 10 LYS H H 7.664 0.002 1 71 10 10 LYS HA H 4.071 0.010 1 72 10 10 LYS HB2 H 1.951 0.012 2 73 10 10 LYS HB3 H 1.951 0.012 2 74 10 10 LYS HG2 H 1.535 0.006 2 75 10 10 LYS HG3 H 1.449 0.003 2 76 10 10 LYS HD2 H 1.687 0.003 2 77 10 10 LYS HD3 H 1.687 0.003 2 78 10 10 LYS HE2 H 2.979 0.003 2 79 10 10 LYS HE3 H 2.979 0.003 2 80 11 11 VAL H H 7.840 0.003 1 81 11 11 VAL HA H 3.885 0.004 1 82 11 11 VAL HB H 2.192 0.007 1 83 11 11 VAL HG1 H 1.058 0.009 2 84 11 11 VAL HG2 H 0.943 0.002 2 85 12 12 GLY H H 8.591 0.002 1 86 12 12 GLY HA2 H 3.728 0.011 2 87 12 12 GLY HA3 H 3.728 0.011 2 88 13 13 ARG H H 8.254 0.004 1 89 13 13 ARG HA H 3.982 0.005 1 90 13 13 ARG HB2 H 1.916 0.006 2 91 13 13 ARG HB3 H 1.754 0.007 2 92 13 13 ARG HG2 H 1.667 0.005 2 93 13 13 ARG HG3 H 1.667 0.005 2 94 13 13 ARG HD2 H 3.208 0.016 2 95 13 13 ARG HD3 H 3.208 0.016 2 96 13 13 ARG HE H 7.588 0.003 1 97 14 14 ASN H H 8.060 0.002 1 98 14 14 ASN HA H 4.577 0.003 1 99 14 14 ASN HB2 H 2.967 0.003 2 100 14 14 ASN HB3 H 2.765 0.008 2 101 14 14 ASN HD21 H 6.953 0.006 2 102 14 14 ASN HD22 H 7.681 0.001 2 103 15 15 VAL H H 8.252 0.004 1 104 15 15 VAL HA H 3.838 0.011 1 105 15 15 VAL HB H 2.221 0.012 1 106 15 15 VAL HG1 H 1.023 0.002 2 107 15 15 VAL HG2 H 0.926 0.004 2 108 16 16 ARG H H 8.244 0.004 1 109 16 16 ARG HA H 3.888 0.002 1 110 16 16 ARG HB2 H 2.040 0.004 2 111 16 16 ARG HB3 H 1.845 0.005 2 112 16 16 ARG HG2 H 1.718 0.010 2 113 16 16 ARG HG3 H 1.610 0.007 2 114 16 16 ARG HD2 H 3.180 0.002 2 115 16 16 ARG HD3 H 3.180 0.002 2 116 16 16 ARG HE H 7.535 0.002 1 117 17 17 ASP H H 8.288 0.001 1 118 17 17 ASP HA H 4.495 0.003 1 119 17 17 ASP HB2 H 2.706 0.016 2 120 17 17 ASP HB3 H 2.706 0.016 2 121 18 18 GLY H H 7.989 0.002 1 122 18 18 GLY HA2 H 3.937 0.002 2 123 18 18 GLY HA3 H 3.832 0.002 2 124 19 19 ILE H H 8.024 0.001 1 125 19 19 ILE HA H 3.882 0.003 1 126 19 19 ILE HB H 1.971 0.006 1 127 19 19 ILE HG12 H 1.680 0.005 2 128 19 19 ILE HG13 H 1.178 0.014 2 129 19 19 ILE HG2 H 0.898 0.003 1 130 19 19 ILE HD1 H 0.824 0.004 1 131 20 20 ILE H H 7.709 0.005 1 132 20 20 ILE HA H 3.973 0.007 1 133 20 20 ILE HB H 1.900 0.000 1 134 20 20 ILE HG12 H 1.579 0.003 2 135 20 20 ILE HG13 H 1.579 0.003 2 136 20 20 ILE HG2 H 1.215 0.010 1 137 20 20 ILE HD1 H 0.907 0.013 1 138 21 21 LYS H H 7.954 0.004 1 139 21 21 LYS HA H 4.256 0.006 1 140 21 21 LYS HB2 H 1.909 0.004 2 141 21 21 LYS HB3 H 1.831 0.006 2 142 21 21 LYS HG2 H 1.504 0.007 2 143 21 21 LYS HG3 H 1.504 0.007 2 144 21 21 LYS HD2 H 1.675 0.002 2 145 21 21 LYS HD3 H 1.675 0.002 2 146 21 21 LYS HE2 H 2.983 0.001 2 147 21 21 LYS HE3 H 2.983 0.001 2 148 22 22 ALA H H 8.056 0.003 1 149 22 22 ALA HA H 4.265 0.003 1 150 22 22 ALA HB H 1.442 0.002 1 151 23 23 GLY H H 8.168 0.002 1 152 23 23 GLY HA2 H 4.123 0.002 2 153 23 23 GLY HA3 H 3.938 0.003 2 154 24 24 PRO HA H 4.392 0.002 1 155 24 24 PRO HB2 H 2.061 0.002 2 156 24 24 PRO HB3 H 2.354 0.004 2 157 24 24 PRO HG2 H 1.985 0.001 2 158 24 24 PRO HG3 H 1.899 0.005 2 159 24 24 PRO HD2 H 3.675 0.009 2 160 24 24 PRO HD3 H 3.675 0.009 2 161 25 25 ALA H H 8.092 0.001 1 162 25 25 ALA HA H 4.197 0.008 1 163 25 25 ALA HB H 1.454 0.003 1 164 26 26 VAL H H 7.794 0.001 1 165 26 26 VAL HA H 3.937 0.004 1 166 26 26 VAL HB H 2.199 0.003 1 167 26 26 VAL HG1 H 1.043 0.002 2 168 26 26 VAL HG2 H 0.945 0.004 2 169 27 27 ALA H H 7.986 0.007 1 170 27 27 ALA HA H 4.213 0.004 1 171 27 27 ALA HB H 1.457 0.002 1 172 28 28 VAL H H 7.968 0.003 1 173 28 28 VAL HA H 3.768 0.003 1 174 28 28 VAL HB H 2.155 0.008 1 175 28 28 VAL HG1 H 1.022 0.003 2 176 28 28 VAL HG2 H 0.950 0.003 2 177 29 29 VAL H H 7.998 0.002 1 178 29 29 VAL HA H 3.762 0.014 1 179 29 29 VAL HB H 2.177 0.008 1 180 29 29 VAL HG1 H 1.012 0.014 2 181 29 29 VAL HG2 H 0.916 0.016 2 182 30 30 GLY H H 8.285 0.002 1 183 30 30 GLY HA2 H 3.942 0.003 2 184 30 30 GLY HA3 H 3.839 0.004 2 185 31 31 GLN H H 7.965 0.002 1 186 31 31 GLN HA H 4.242 0.004 1 187 31 31 GLN HB2 H 2.141 0.007 2 188 31 31 GLN HB3 H 2.141 0.007 2 189 31 31 GLN HG2 H 2.410 0.003 2 190 31 31 GLN HG3 H 2.410 0.003 2 191 31 31 GLN HE21 H 6.762 0.001 2 192 31 31 GLN HE22 H 7.413 0.000 2 193 32 32 ALA H H 8.265 0.005 1 194 32 32 ALA HA H 4.106 0.020 1 195 32 32 ALA HB H 1.458 0.007 1 196 33 33 ALA H H 8.244 0.002 1 197 33 33 ALA HA H 4.083 0.011 1 198 33 33 ALA HB H 1.461 0.005 1 199 34 34 THR H H 7.763 0.001 1 200 34 34 THR HA H 4.278 0.005 1 201 34 34 THR HB H 4.066 0.002 1 202 34 34 THR HG2 H 1.256 0.002 1 203 35 35 VAL H H 7.738 0.001 1 204 35 35 VAL HA H 3.940 0.007 1 205 35 35 VAL HB H 2.191 0.006 1 206 35 35 VAL HG1 H 1.033 0.006 2 207 35 35 VAL HG2 H 0.944 0.001 2 208 36 36 VAL H H 7.796 0.003 1 209 36 36 VAL HA H 3.935 0.006 1 210 36 36 VAL HB H 2.136 0.003 1 211 36 36 VAL HG1 H 0.983 0.003 2 212 36 36 VAL HG2 H 0.947 0.003 2 213 37 37 LYS H H 7.898 0.002 1 214 37 37 LYS HA H 4.167 0.002 1 215 37 37 LYS HB2 H 1.859 0.008 2 216 37 37 LYS HB3 H 1.805 0.011 2 217 37 37 LYS HG2 H 1.528 0.005 2 218 37 37 LYS HG3 H 1.471 0.027 2 219 37 37 LYS HD2 H 1.670 0.003 2 220 37 37 LYS HD3 H 1.670 0.003 2 221 37 37 LYS HE2 H 2.958 0.012 2 222 37 37 LYS HE3 H 2.958 0.012 2 stop_ save_