data_5491 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Structural basis for new pattern of the conserved amino acid residues related to chitin-binding in the antifungal peptide from the coconut rhinoceros beetle, Oryctes rhinoceros ; _BMRB_accession_number 5491 _BMRB_flat_file_name bmr5491.str _Entry_type original _Submission_date 2002-08-05 _Accession_date 2002-08-05 _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 Hemmi Hikaru . . 2 Ishibashi Jun . . 3 Tomie Tetsuya . . 4 Yamakawa Minoru . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 238 "13C chemical shifts" 36 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2003-06-24 original BMRB . stop_ _Original_release_date 2002-08-05 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Structural basis for new pattern of the conserved amino acid residues related to chitin-binding in the antifungal peptide from the coconut rhinoceros beetle, Oryctes rhinoceros ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 12676931 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Hemmi Hikaru . . 2 Ishibashi Jun . . 3 Tomie Tetsuya . . 4 Yamakawa Minoru . . stop_ _Journal_abbreviation 'J. Biol. Chem.' _Journal_volume 278 _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 22820 _Page_last 22827 _Year 2003 _Details . save_ ################################## # Molecular system description # ################################## save_system_scarabaecin _Saveframe_category molecular_system _Mol_system_name 'scarabaecin monomer' _Abbreviation_common scarabaecin _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'scarabaecin monomer' $scarabaecin stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state monomer _System_paramagnetic no _System_thiol_state 'all disulfide bound' loop_ _Biological_function 'antifungal peptide' stop_ _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_scarabaecin _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common scarabaecin _Abbreviation_common scarabaecin _Molecular_mass . _Mol_thiol_state 'all disulfide bound' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 36 _Mol_residue_sequence ; ELPKLPDDKVLIRSRSNCPK GKVWNGFDCKSPFAFS ; loop_ _Residue_seq_code _Residue_label 1 GLU 2 LEU 3 PRO 4 LYS 5 LEU 6 PRO 7 ASP 8 ASP 9 LYS 10 VAL 11 LEU 12 ILE 13 ARG 14 SER 15 ARG 16 SER 17 ASN 18 CYS 19 PRO 20 LYS 21 GLY 22 LYS 23 VAL 24 TRP 25 ASN 26 GLY 27 PHE 28 ASP 29 CYS 30 LYS 31 SER 32 PRO 33 PHE 34 ALA 35 PHE 36 SER stop_ _Sequence_homology_query_date 2008-08-19 _Sequence_homology_query_revised_last_date 2008-08-19 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 1IYC 'Solution Structure Of Antifungal Peptide, Scarabaecin' 100.00 36 100.00 100.00 1.76e-12 DBJ BAC54897 'scarabaecin [Oryctes rhinoceros]' 100.00 66 100.00 100.00 4.26e-13 SWISS-PROT Q86SC0 'Scarabaecin precursor [Contains: Scarabaecin, minor form; Scarabaecin, major form]' 100.00 66 100.00 100.00 4.26e-13 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $scarabaecin 'rhinoceros beetle' 72550 Eukaryota Metazoa Oryctes rhinoceros 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 $scarabaecin '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 $scarabaecin 3 mM . stop_ save_ ############################ # Computer software used # ############################ save_XWINNMR _Saveframe_category software _Name XWINNMR _Version 2.6 loop_ _Task acquisition processing stop_ _Details . save_ save_FELIX _Saveframe_category software _Name FELIX _Version 2000 loop_ _Task processing stop_ _Details . save_ save_SPARKY _Saveframe_category software _Name SPARKY _Version 3.1 loop_ _Task 'peak assignment' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 800 _Details . save_ save_NMR_spectrometer2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 500 _Details . save_ ############################# # NMR applied experiments # ############################# save_1H-1H_TOCSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-1H TOCSY' _Sample_label $sample_1 save_ save_1H-1H_DQF-COSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-1H DQF-COSY' _Sample_label $sample_1 save_ save_1H-1H_NOESY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-1H NOESY' _Sample_label $sample_1 save_ save_1H-1H_E.COSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-1H E.COSY' _Sample_label $sample_1 save_ save_1H-1H_ROESY_5 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-1H ROESY' _Sample_label $sample_1 save_ ####################### # Sample conditions # ####################### save_Ex-cond_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 2.4 0.01 n/a temperature 298 0.01 K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference _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 0.0 . indirect . . . 0.251449530 DSS H 1 'methyl protons' ppm 0.0 internal 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_shift_set_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '1H-1H TOCSY' '1H-1H DQF-COSY' '1H-1H NOESY' '1H-1H E.COSY' '1H-1H ROESY' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $Ex-cond_1 _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name 'scarabaecin monomer' _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 GLU HA H 4.09 . 1 2 . 1 GLU HB2 H 2.16 . 1 3 . 1 GLU HB3 H 2.16 . 1 4 . 1 GLU HG2 H 2.54 . 1 5 . 1 GLU HG3 H 2.54 . 1 6 . 1 GLU CA C 55.2 . 1 7 . 2 LEU H H 8.74 . 1 8 . 2 LEU HA H 4.43 . 1 9 . 2 LEU HB2 H 1.61 . 1 10 . 2 LEU HB3 H 1.61 . 1 11 . 2 LEU HG H 1.71 . 1 12 . 2 LEU HD1 H 0.93 . 2 13 . 2 LEU HD2 H 0.98 . 2 14 . 2 LEU CA C 53.5 . 1 15 . 3 PRO HA H 4.43 . 1 16 . 3 PRO HB2 H 1.86 . 2 17 . 3 PRO HB3 H 2.29 . 2 18 . 3 PRO HG2 H 2.03 . 1 19 . 3 PRO HG3 H 2.03 . 1 20 . 3 PRO HD2 H 3.66 . 2 21 . 3 PRO HD3 H 3.86 . 2 22 . 3 PRO CA C 63.3 . 1 23 . 4 LYS H H 8.35 . 1 24 . 4 LYS HA H 4.30 . 1 25 . 4 LYS HB2 H 1.78 . 1 26 . 4 LYS HB3 H 1.78 . 1 27 . 4 LYS HG2 H 1.44 . 1 28 . 4 LYS HG3 H 1.44 . 1 29 . 4 LYS HD2 H 1.69 . 1 30 . 4 LYS HD3 H 1.69 . 1 31 . 4 LYS HE2 H 3.08 . 1 32 . 4 LYS HE3 H 3.08 . 1 33 . 4 LYS HZ H 7.54 . 1 34 . 4 LYS CA C 56.3 . 1 35 . 5 LEU H H 8.30 . 1 36 . 5 LEU HA H 4.64 . 1 37 . 5 LEU HB2 H 1.61 . 1 38 . 5 LEU HB3 H 1.61 . 1 39 . 5 LEU HG H 1.54 . 1 40 . 5 LEU HD1 H 0.92 . 2 41 . 5 LEU HD2 H 0.94 . 2 42 . 5 LEU CA C 53.3 . 1 43 . 6 PRO HA H 4.40 . 1 44 . 6 PRO HB2 H 1.89 . 2 45 . 6 PRO HB3 H 2.28 . 2 46 . 6 PRO HG2 H 2.03 . 1 47 . 6 PRO HG3 H 2.03 . 1 48 . 6 PRO HD2 H 3.65 . 2 49 . 6 PRO HD3 H 3.84 . 2 50 . 6 PRO CA C 63.4 . 1 51 . 7 ASP H H 8.51 . 1 52 . 7 ASP HA H 4.67 . 1 53 . 7 ASP HB2 H 2.86 . 2 54 . 7 ASP HB3 H 2.90 . 2 55 . 7 ASP CA C 53.2 . 1 56 . 8 ASP H H 8.40 . 1 57 . 8 ASP HA H 4.69 . 1 58 . 8 ASP HB2 H 2.90 . 1 59 . 8 ASP HB3 H 2.90 . 1 60 . 8 ASP CA C 53.3 . 1 61 . 9 LYS H H 8.16 . 1 62 . 9 LYS HA H 4.29 . 1 63 . 9 LYS HB2 H 1.78 . 1 64 . 9 LYS HB3 H 1.78 . 1 65 . 9 LYS HG2 H 1.42 . 1 66 . 9 LYS HG3 H 1.42 . 1 67 . 9 LYS HD2 H 1.68 . 1 68 . 9 LYS HD3 H 1.68 . 1 69 . 9 LYS HE2 H 3.00 . 1 70 . 9 LYS HE3 H 3.00 . 1 71 . 9 LYS HZ H 7.54 . 1 72 . 9 LYS CA C 56.9 . 1 73 . 10 VAL H H 7.97 . 1 74 . 10 VAL HA H 4.03 . 1 75 . 10 VAL HB H 2.03 . 1 76 . 10 VAL HG1 H 0.90 . 2 77 . 10 VAL HG2 H 0.93 . 2 78 . 10 VAL CA C 62.8 . 1 79 . 11 LEU H H 8.26 . 1 80 . 11 LEU HA H 4.37 . 1 81 . 11 LEU HB2 H 1.60 . 1 82 . 11 LEU HB3 H 1.60 . 1 83 . 11 LEU HG H 1.56 . 1 84 . 11 LEU HD1 H 0.84 . 2 85 . 11 LEU HD2 H 0.90 . 2 86 . 11 LEU CA C 55.3 . 1 87 . 12 ILE H H 8.16 . 1 88 . 12 ILE HA H 4.11 . 1 89 . 12 ILE HB H 1.84 . 1 90 . 12 ILE HG12 H 1.18 . 1 91 . 12 ILE HG13 H 1.18 . 1 92 . 12 ILE HG2 H 0.88 . 1 93 . 12 ILE HD1 H 0.84 . 1 94 . 12 ILE CA C 61.4 . 1 95 . 13 ARG H H 8.42 . 1 96 . 13 ARG HA H 4.35 . 1 97 . 13 ARG HB2 H 1.75 . 2 98 . 13 ARG HB3 H 1.84 . 2 99 . 13 ARG HG2 H 1.62 . 1 100 . 13 ARG HG3 H 1.62 . 1 101 . 13 ARG HD2 H 3.16 . 1 102 . 13 ARG HD3 H 3.16 . 1 103 . 13 ARG HE H 7.18 . 1 104 . 13 ARG CA C 56.3 . 1 105 . 14 SER H H 8.26 . 1 106 . 14 SER HA H 4.34 . 1 107 . 14 SER HB2 H 3.78 . 2 108 . 14 SER HB3 H 3.82 . 2 109 . 14 SER CA C 58.5 . 1 110 . 15 ARG H H 8.21 . 1 111 . 15 ARG HA H 4.06 . 1 112 . 15 ARG HB2 H 1.54 . 2 113 . 15 ARG HB3 H 1.65 . 2 114 . 15 ARG HG2 H 1.45 . 1 115 . 15 ARG HG3 H 1.45 . 1 116 . 15 ARG HD2 H 3.04 . 1 117 . 15 ARG HD3 H 3.04 . 1 118 . 15 ARG HE H 7.08 . 1 119 . 15 ARG CA C 56.6 . 1 120 . 16 SER H H 7.63 . 1 121 . 16 SER HA H 3.93 . 1 122 . 16 SER HB2 H 3.24 . 2 123 . 16 SER HB3 H 3.31 . 2 124 . 16 SER CA C 58.0 . 1 125 . 17 ASN H H 8.07 . 1 126 . 17 ASN HA H 4.60 . 1 127 . 17 ASN HB2 H 2.51 . 1 128 . 17 ASN HB3 H 2.58 . 1 129 . 17 ASN HD21 H 6.67 . 2 130 . 17 ASN HD22 H 7.20 . 2 131 . 17 ASN CA C 53.3 . 1 132 . 18 CYS H H 8.34 . 1 133 . 18 CYS HA H 5.20 . 1 134 . 18 CYS HB2 H 2.69 . 1 135 . 18 CYS HB3 H 2.88 . 1 136 . 18 CYS CA C 52.4 . 1 137 . 19 PRO HA H 4.49 . 1 138 . 19 PRO HB2 H 1.82 . 2 139 . 19 PRO HB3 H 2.36 . 2 140 . 19 PRO HG2 H 1.93 . 2 141 . 19 PRO HG3 H 2.07 . 2 142 . 19 PRO HD2 H 3.35 . 2 143 . 19 PRO HD3 H 3.98 . 2 144 . 19 PRO CA C 62.6 . 1 145 . 20 LYS H H 8.34 . 1 146 . 20 LYS HA H 4.05 . 1 147 . 20 LYS HB2 H 1.78 . 1 148 . 20 LYS HB3 H 1.78 . 1 149 . 20 LYS HG2 H 1.44 . 1 150 . 20 LYS HG3 H 1.44 . 1 151 . 20 LYS HD2 H 1.73 . 1 152 . 20 LYS HD3 H 1.73 . 1 153 . 20 LYS HE2 H 2.98 . 1 154 . 20 LYS HE3 H 2.98 . 1 155 . 20 LYS HZ H 7.54 . 1 156 . 20 LYS CA C 58.5 . 1 157 . 21 GLY H H 8.87 . 1 158 . 21 GLY HA2 H 3.66 . 2 159 . 21 GLY HA3 H 4.31 . 2 160 . 21 GLY CA C 45.3 . 1 161 . 22 LYS H H 8.08 . 1 162 . 22 LYS HA H 4.78 . 1 163 . 22 LYS HB2 H 1.77 . 1 164 . 22 LYS HB3 H 1.77 . 1 165 . 22 LYS HG2 H 1.15 . 1 166 . 22 LYS HG3 H 1.15 . 1 167 . 22 LYS HD2 H 1.40 . 2 168 . 22 LYS HD3 H 1.51 . 2 169 . 22 LYS HE2 H 2.92 . 1 170 . 22 LYS HE3 H 2.92 . 1 171 . 22 LYS HZ H 7.60 . 1 172 . 22 LYS CA C 54.9 . 1 173 . 23 VAL H H 8.92 . 1 174 . 23 VAL HA H 4.54 . 1 175 . 23 VAL HB H 2.02 . 1 176 . 23 VAL HG1 H 0.84 . 2 177 . 23 VAL HG2 H 0.90 . 2 178 . 23 VAL CA C 60.6 . 1 179 . 24 TRP H H 8.93 . 1 180 . 24 TRP HA H 5.13 . 1 181 . 24 TRP HB2 H 3.23 . 1 182 . 24 TRP HB3 H 3.33 . 1 183 . 24 TRP HD1 H 7.17 . 1 184 . 24 TRP HE1 H 10.26 . 1 185 . 24 TRP HE3 H 7.40 . 1 186 . 24 TRP HZ2 H 7.21 . 1 187 . 24 TRP HZ3 H 6.97 . 1 188 . 24 TRP HH2 H 7.01 . 1 189 . 24 TRP CA C 57.2 . 1 190 . 25 ASN H H 8.08 . 1 191 . 25 ASN HA H 4.81 . 1 192 . 25 ASN HB2 H 2.57 . 2 193 . 25 ASN HB3 H 3.25 . 2 194 . 25 ASN HD21 H 6.83 . 2 195 . 25 ASN HD22 H 7.58 . 2 196 . 25 ASN CA C 51.8 . 1 197 . 26 GLY H H 8.07 . 1 198 . 26 GLY HA2 H 3.13 . 2 199 . 26 GLY HA3 H 4.04 . 2 200 . 26 GLY CA C 45.5 . 1 201 . 27 PHE H H 7.55 . 1 202 . 27 PHE HA H 4.30 . 1 203 . 27 PHE HB2 H 2.70 . 2 204 . 27 PHE HB3 H 2.93 . 2 205 . 27 PHE HD1 H 7.02 . 1 206 . 27 PHE HD2 H 7.02 . 1 207 . 27 PHE HE1 H 7.28 . 1 208 . 27 PHE HE2 H 7.28 . 1 209 . 27 PHE HZ H 7.26 . 1 210 . 27 PHE CA C 58.9 . 1 211 . 28 ASP H H 8.19 . 1 212 . 28 ASP HA H 4.73 . 1 213 . 28 ASP HB2 H 2.69 . 2 214 . 28 ASP HB3 H 2.78 . 2 215 . 28 ASP CA C 52.6 . 1 216 . 29 CYS H H 8.65 . 1 217 . 29 CYS HA H 5.23 . 1 218 . 29 CYS HB2 H 3.14 . 1 219 . 29 CYS HB3 H 2.71 . 1 220 . 29 CYS CA C 55.0 . 1 221 . 30 LYS H H 9.07 . 1 222 . 30 LYS HA H 4.71 . 1 223 . 30 LYS HB2 H 1.71 . 1 224 . 30 LYS HB3 H 1.71 . 1 225 . 30 LYS HG2 H 1.36 . 2 226 . 30 LYS HG3 H 1.64 . 2 227 . 30 LYS HD2 H 1.84 . 1 228 . 30 LYS HD3 H 1.84 . 1 229 . 30 LYS HE2 H 2.94 . 1 230 . 30 LYS HE3 H 2.94 . 1 231 . 30 LYS HZ H 7.51 . 1 232 . 30 LYS CA C 54.7 . 1 233 . 31 SER H H 8.90 . 1 234 . 31 SER HA H 4.87 . 1 235 . 31 SER HB2 H 3.87 . 2 236 . 31 SER HB3 H 3.90 . 2 237 . 31 SER CA C 57.4 . 1 238 . 32 PRO HA H 4.34 . 1 239 . 32 PRO HB2 H 1.72 . 2 240 . 32 PRO HB3 H 2.12 . 2 241 . 32 PRO HG2 H 1.78 . 2 242 . 32 PRO HG3 H 1.89 . 2 243 . 32 PRO HD2 H 3.79 . 2 244 . 32 PRO HD3 H 3.91 . 2 245 . 32 PRO CA C 63.7 . 1 246 . 33 PHE H H 7.97 . 1 247 . 33 PHE HA H 4.56 . 1 248 . 33 PHE HB2 H 2.92 . 1 249 . 33 PHE HB3 H 3.08 . 1 250 . 33 PHE HD1 H 7.20 . 1 251 . 33 PHE HD2 H 7.20 . 1 252 . 33 PHE HE1 H 7.32 . 1 253 . 33 PHE HE2 H 7.32 . 1 254 . 33 PHE HZ H 7.31 . 1 255 . 33 PHE CA C 57.7 . 1 256 . 34 ALA H H 7.98 . 1 257 . 34 ALA HA H 4.29 . 1 258 . 34 ALA HB H 1.27 . 1 259 . 34 ALA CA C 52.4 . 1 260 . 35 PHE H H 8.04 . 1 261 . 35 PHE HA H 4.63 . 1 262 . 35 PHE HB2 H 3.04 . 1 263 . 35 PHE HB3 H 3.17 . 1 264 . 35 PHE HD1 H 7.36 . 1 265 . 35 PHE HD2 H 7.36 . 1 266 . 35 PHE HE1 H 7.28 . 1 267 . 35 PHE HE2 H 7.28 . 1 268 . 35 PHE HZ H 7.35 . 1 269 . 35 PHE CA C 57.8 . 1 270 . 36 SER H H 8.22 . 1 271 . 36 SER HA H 4.46 . 1 272 . 36 SER HB2 H 3.84 . 2 273 . 36 SER HB3 H 3.92 . 2 274 . 36 SER CA C 58.1 . 1 stop_ save_