data_17152 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Helical hairpin structure of a novel antimicrobial peptide EcAMP1 from seeds of barnyard grass (Echinochloa crus-galli) ; _BMRB_accession_number 17152 _BMRB_flat_file_name bmr17152.str _Entry_type original _Submission_date 2010-08-27 _Accession_date 2010-08-27 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details 'Micromolar concentrations of EcAMP1 were shown to inhibit growth of several fungal phytopathogens.' loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Nolde Svetlana B. . 2 Barinov Nikolay A. . 3 Balashova Tamara A. . 4 Arseniev Alexander S. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 217 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2011-05-18 update BMRB 'update entry citation' 2011-05-04 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Disulfide-stabilized helical hairpin structure and activity of a novel antifungal peptide EcAMP1 from seeds of barnyard grass (Echinochloa crus-galli).' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 21561864 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Nolde Svetlana B. . 2 Vassilevski Alexander A. . 3 Rogozhin Eugene A. . 4 Barinov Nikolay A. . 5 Balashova Tamara A. . 6 Samsonova Olga V. . 7 Baranov Yuri V. . 8 Feofanov Alexey V. . 9 Egorov Tsezi A. . 10 Arseniev Alexander S. . 11 Grishin Eugene V. . stop_ _Journal_abbreviation 'J. Biol. Chem.' _Journal_name_full 'The Journal of biological chemistry' _Journal_volume 286 _Journal_issue 28 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 25145 _Page_last 25153 _Year 2011 _Details . loop_ _Keyword 'antifungal peptide' 'antimicrobial peptide' 'disulfide-stabilized helical hairpin' stop_ save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name EcAMP1 _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label EcAMP1 $EcAMP1 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_EcAMP1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common EcAMP1 _Molecular_mass 4288.794 _Mol_thiol_state 'all disulfide bound' loop_ _Biological_function 'antimicrobial peptide' stop_ _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 37 _Mol_residue_sequence ; GSGRGSCRSQCMRRHEDEPW RVQECVSQCRRRRGGGD ; loop_ _Residue_seq_code _Residue_label 1 GLY 2 SER 3 GLY 4 ARG 5 GLY 6 SER 7 CYS 8 ARG 9 SER 10 GLN 11 CYS 12 MET 13 ARG 14 ARG 15 HIS 16 GLU 17 ASP 18 GLU 19 PRO 20 TRP 21 ARG 22 VAL 23 GLN 24 GLU 25 CYS 26 VAL 27 SER 28 GLN 29 CYS 30 ARG 31 ARG 32 ARG 33 ARG 34 GLY 35 GLY 36 GLY 37 ASP stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-10-28 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 2L2R "Helical Hairpin Structure Of A Novel Antimicrobial Peptide Ecamp1 From Seeds Of Barnyard Grass (Echinochloa Crus-Galli)" 100.00 37 100.00 100.00 1.81e-15 GB AFU90746 "antimicrobial peptide polyprotein, partial [Echinochloa crus-galli]" 100.00 87 100.00 100.00 2.76e-15 GB AFU90747 "antimicrobial peptide polyprotein, partial [Echinochloa crus-galli]" 100.00 87 100.00 100.00 2.48e-15 GB AFU90748 "antimicrobial peptide polyprotein, partial [Echinochloa crus-galli]" 100.00 87 97.30 97.30 1.33e-14 GB AFU90750 "antimicrobial peptide polyprotein, partial [Echinochloa crus-galli]" 59.46 92 100.00 100.00 1.47e-05 GB AFU90751 "antimicrobial peptide polyprotein, partial [Echinochloa crus-galli]" 59.46 92 100.00 100.00 1.47e-05 SP B3EWR6 "RecName: Full=Antimicrobial peptides; Contains: RecName: Full=Antimicrobial peptide 1; Short=EcAMP1; Contains: RecName: Full=An" 100.00 361 100.00 100.00 4.94e-14 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 $EcAMP1 'Barnyard grass' 90397 Eukaryota Viridiplantae Echinochloa crus-galli 'Seeds of Echinochloa crus-galli (L.) P. Beauv. (family Poaceae)' 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 $EcAMP1 'purified from the natural source' 'Barnyard grass' Echinochloa crusgalli . . 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 $EcAMP1 0.7 mg/ml 'natural abundance' KOH 10 mM 'natural abundance' H2O 95 % 'natural abundance' D2O 5 % '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 'structure solution' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _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_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 'ionic strength' 10 . mM pH 6.62 . pH pressure 1 . atm temperature 293 . 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 water H 1 protons ppm 4.85 internal direct . . . 1.000000000 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 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 EcAMP1 _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 GLY HA2 H 3.936 0.020 1 2 1 1 GLY HA3 H 3.936 0.020 1 3 2 2 SER H H 8.761 0.020 1 4 2 2 SER HA H 4.570 0.020 1 5 2 2 SER HB2 H 3.914 0.020 2 6 2 2 SER HB3 H 3.944 0.020 2 7 3 3 GLY H H 8.670 0.020 1 8 3 3 GLY HA2 H 4.013 0.020 2 9 3 3 GLY HA3 H 4.004 0.020 2 10 4 4 ARG H H 8.454 0.020 1 11 4 4 ARG HA H 4.350 0.020 1 12 4 4 ARG HB2 H 1.794 0.020 2 13 4 4 ARG HB3 H 1.885 0.020 2 14 4 4 ARG HD2 H 3.205 0.020 1 15 4 4 ARG HD3 H 3.205 0.020 1 16 4 4 ARG HG2 H 1.698 0.020 2 17 4 4 ARG HG3 H 1.667 0.020 2 18 5 5 GLY H H 8.603 0.020 1 19 5 5 GLY HA2 H 4.055 0.020 2 20 5 5 GLY HA3 H 4.006 0.020 2 21 6 6 SER H H 8.449 0.020 1 22 6 6 SER HA H 4.489 0.020 1 23 6 6 SER HB2 H 4.279 0.020 1 24 6 6 SER HB3 H 4.039 0.020 1 25 7 7 CYS H H 9.917 0.020 1 26 7 7 CYS HA H 4.458 0.020 1 27 7 7 CYS HB2 H 3.321 0.020 1 28 7 7 CYS HB3 H 2.849 0.020 1 29 8 8 ARG H H 9.001 0.020 1 30 8 8 ARG HA H 3.767 0.020 1 31 8 8 ARG HB2 H 1.834 0.020 1 32 8 8 ARG HB3 H 1.788 0.020 1 33 8 8 ARG HD2 H 3.214 0.020 1 34 8 8 ARG HD3 H 3.214 0.020 1 35 8 8 ARG HE H 7.399 0.020 1 36 8 8 ARG HG2 H 1.572 0.020 1 37 8 8 ARG HG3 H 1.572 0.020 1 38 9 9 SER H H 8.157 0.020 1 39 9 9 SER HA H 4.151 0.020 1 40 9 9 SER HB2 H 3.944 0.020 1 41 9 9 SER HB3 H 3.944 0.020 1 42 10 10 GLN H H 8.341 0.020 1 43 10 10 GLN HA H 4.077 0.020 1 44 10 10 GLN HB2 H 2.217 0.020 1 45 10 10 GLN HB3 H 2.132 0.020 1 46 10 10 GLN HE21 H 7.175 0.020 1 47 10 10 GLN HE22 H 6.847 0.020 1 48 10 10 GLN HG2 H 2.503 0.020 1 49 10 10 GLN HG3 H 2.366 0.020 1 50 11 11 CYS H H 8.445 0.020 1 51 11 11 CYS HA H 4.408 0.020 1 52 11 11 CYS HB2 H 3.186 0.020 1 53 11 11 CYS HB3 H 2.880 0.020 1 54 12 12 MET H H 8.564 0.020 1 55 12 12 MET HA H 4.059 0.020 1 56 12 12 MET HB2 H 2.125 0.020 1 57 12 12 MET HB3 H 2.125 0.020 1 58 12 12 MET HE H 2.116 0.020 1 59 12 12 MET HG2 H 2.573 0.020 1 60 12 12 MET HG3 H 2.730 0.020 1 61 13 13 ARG H H 7.324 0.020 1 62 13 13 ARG HA H 4.233 0.020 1 63 13 13 ARG HB2 H 1.889 0.020 1 64 13 13 ARG HB3 H 1.889 0.020 1 65 13 13 ARG HD2 H 3.237 0.020 1 66 13 13 ARG HD3 H 3.237 0.020 1 67 13 13 ARG HG2 H 1.738 0.020 2 68 13 13 ARG HG3 H 1.700 0.020 2 69 14 14 ARG H H 7.860 0.020 1 70 14 14 ARG HA H 3.985 0.020 1 71 14 14 ARG HB2 H 1.748 0.020 1 72 14 14 ARG HB3 H 1.443 0.020 1 73 14 14 ARG HD2 H 3.009 0.020 1 74 14 14 ARG HD3 H 3.009 0.020 1 75 14 14 ARG HE H 7.122 0.020 1 76 14 14 ARG HG2 H 1.077 0.020 2 77 14 14 ARG HG3 H 0.937 0.020 2 78 15 15 HIS H H 7.554 0.020 1 79 15 15 HIS HA H 5.015 0.020 1 80 15 15 HIS HB2 H 2.686 0.020 1 81 15 15 HIS HB3 H 3.372 0.020 1 82 15 15 HIS HD2 H 6.667 0.020 1 83 16 16 GLU H H 7.192 0.020 1 84 16 16 GLU HA H 4.006 0.020 1 85 16 16 GLU HB2 H 2.167 0.020 1 86 16 16 GLU HB3 H 2.038 0.020 1 87 16 16 GLU HG2 H 2.376 0.020 2 88 16 16 GLU HG3 H 2.301 0.020 2 89 17 17 ASP H H 8.606 0.020 1 90 17 17 ASP HA H 4.642 0.020 1 91 17 17 ASP HB2 H 2.695 0.020 2 92 17 17 ASP HB3 H 2.815 0.020 2 93 18 18 GLU H H 7.311 0.020 1 94 18 18 GLU HA H 3.843 0.020 1 95 18 18 GLU HB2 H 1.560 0.020 2 96 18 18 GLU HB3 H 0.858 0.020 2 97 18 18 GLU HG2 H 2.136 0.020 2 98 18 18 GLU HG3 H 2.064 0.020 2 99 19 19 PRO HA H 4.286 0.020 1 100 19 19 PRO HB2 H 2.420 0.020 1 101 19 19 PRO HB3 H 2.420 0.020 1 102 19 19 PRO HD2 H 3.566 0.020 1 103 19 19 PRO HD3 H 3.381 0.020 1 104 19 19 PRO HG2 H 2.147 0.020 1 105 19 19 PRO HG3 H 2.208 0.020 1 106 20 20 TRP H H 7.244 0.020 1 107 20 20 TRP HA H 4.678 0.020 1 108 20 20 TRP HB2 H 3.435 0.020 1 109 20 20 TRP HB3 H 3.522 0.020 1 110 20 20 TRP HD1 H 7.295 0.020 1 111 20 20 TRP HE1 H 10.605 0.020 1 112 20 20 TRP HE3 H 7.721 0.020 1 113 20 20 TRP HH2 H 7.441 0.020 1 114 20 20 TRP HZ2 H 7.651 0.020 1 115 20 20 TRP HZ3 H 7.360 0.020 1 116 21 21 ARG H H 7.626 0.020 1 117 21 21 ARG HA H 4.089 0.020 1 118 21 21 ARG HB2 H 0.938 0.020 1 119 21 21 ARG HB3 H 1.050 0.020 1 120 21 21 ARG HD2 H 2.902 0.020 2 121 21 21 ARG HD3 H 2.743 0.020 2 122 21 21 ARG HE H 7.167 0.020 1 123 21 21 ARG HG2 H 0.737 0.020 1 124 21 21 ARG HG3 H 0.816 0.020 1 125 22 22 VAL H H 7.414 0.020 1 126 22 22 VAL HA H 3.292 0.020 1 127 22 22 VAL HB H 2.203 0.020 1 128 22 22 VAL HG1 H 0.895 0.020 1 129 22 22 VAL HG2 H 1.107 0.020 1 130 23 23 GLN H H 8.638 0.020 1 131 23 23 GLN HA H 4.006 0.020 1 132 23 23 GLN HB2 H 2.204 0.020 1 133 23 23 GLN HB3 H 2.157 0.020 1 134 23 23 GLN HE21 H 7.572 0.020 1 135 23 23 GLN HE22 H 6.915 0.020 1 136 23 23 GLN HG2 H 2.472 0.020 1 137 23 23 GLN HG3 H 2.472 0.020 1 138 24 24 GLU H H 8.612 0.020 1 139 24 24 GLU HA H 4.228 0.020 1 140 24 24 GLU HB2 H 2.107 0.020 1 141 24 24 GLU HB3 H 1.979 0.020 1 142 24 24 GLU HG2 H 2.325 0.020 1 143 24 24 GLU HG3 H 2.325 0.020 1 144 25 25 CYS H H 7.628 0.020 1 145 25 25 CYS HA H 4.362 0.020 1 146 25 25 CYS HB2 H 3.278 0.020 1 147 25 25 CYS HB3 H 3.674 0.020 1 148 26 26 VAL H H 9.104 0.020 1 149 26 26 VAL HA H 3.367 0.020 1 150 26 26 VAL HB H 2.262 0.020 1 151 26 26 VAL HG1 H 0.918 0.020 1 152 26 26 VAL HG2 H 0.979 0.020 1 153 27 27 SER H H 8.301 0.020 1 154 27 27 SER HA H 4.203 0.020 1 155 27 27 SER HB2 H 4.070 0.020 1 156 27 27 SER HB3 H 4.070 0.020 1 157 28 28 GLN H H 8.218 0.020 1 158 28 28 GLN HA H 4.107 0.020 1 159 28 28 GLN HB2 H 2.187 0.020 1 160 28 28 GLN HB3 H 2.187 0.020 1 161 28 28 GLN HE21 H 7.757 0.020 1 162 28 28 GLN HE22 H 6.890 0.020 1 163 28 28 GLN HG2 H 2.645 0.020 2 164 28 28 GLN HG3 H 2.495 0.020 2 165 29 29 CYS H H 8.419 0.020 1 166 29 29 CYS HA H 4.279 0.020 1 167 29 29 CYS HB2 H 3.293 0.020 1 168 29 29 CYS HB3 H 3.335 0.020 1 169 30 30 ARG H H 8.886 0.020 1 170 30 30 ARG HA H 4.074 0.020 1 171 30 30 ARG HB2 H 1.959 0.020 1 172 30 30 ARG HB3 H 1.903 0.020 1 173 30 30 ARG HD2 H 3.140 0.020 1 174 30 30 ARG HD3 H 3.204 0.020 1 175 30 30 ARG HE H 7.243 0.020 1 176 30 30 ARG HG2 H 1.676 0.020 1 177 30 30 ARG HG3 H 1.676 0.020 1 178 31 31 ARG H H 7.796 0.020 1 179 31 31 ARG HA H 4.182 0.020 1 180 31 31 ARG HB2 H 2.013 0.020 1 181 31 31 ARG HB3 H 2.013 0.020 1 182 31 31 ARG HD2 H 3.270 0.020 1 183 31 31 ARG HD3 H 3.270 0.020 1 184 31 31 ARG HE H 7.232 0.020 1 185 31 31 ARG HG2 H 1.847 0.020 1 186 31 31 ARG HG3 H 1.727 0.020 1 187 32 32 ARG H H 7.815 0.020 1 188 32 32 ARG HA H 4.298 0.020 1 189 32 32 ARG HB2 H 2.025 0.020 1 190 32 32 ARG HB3 H 2.025 0.020 1 191 32 32 ARG HD2 H 3.269 0.020 1 192 32 32 ARG HD3 H 3.269 0.020 1 193 32 32 ARG HE H 7.317 0.020 1 194 32 32 ARG HG2 H 1.847 0.020 1 195 32 32 ARG HG3 H 1.745 0.020 1 196 33 33 ARG H H 8.066 0.020 1 197 33 33 ARG HA H 4.420 0.020 1 198 33 33 ARG HB2 H 2.019 0.020 1 199 33 33 ARG HB3 H 1.965 0.020 1 200 33 33 ARG HD2 H 3.208 0.020 1 201 33 33 ARG HD3 H 3.208 0.020 1 202 33 33 ARG HE H 7.163 0.020 1 203 33 33 ARG HG2 H 1.721 0.020 2 204 33 33 ARG HG3 H 1.876 0.020 2 205 34 34 GLY H H 8.257 0.020 1 206 34 34 GLY HA2 H 4.132 0.020 1 207 34 34 GLY HA3 H 3.981 0.020 1 208 35 35 GLY H H 8.381 0.020 1 209 35 35 GLY HA2 H 4.228 0.020 2 210 35 35 GLY HA3 H 3.847 0.020 2 211 36 36 GLY H H 8.083 0.020 1 212 36 36 GLY HA2 H 4.059 0.020 2 213 36 36 GLY HA3 H 3.977 0.020 2 214 37 37 ASP H H 7.977 0.020 1 215 37 37 ASP HA H 4.453 0.020 1 216 37 37 ASP HB2 H 2.696 0.020 1 217 37 37 ASP HB3 H 2.569 0.020 1 stop_ save_