data_15318 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Antibacterial Peptide from Eggshell Matrix: Structure and Self-assembly of a - defensin Like Peptide from the Chinese Soft-shelled Turtle Eggshell ; _BMRB_accession_number 15318 _BMRB_flat_file_name bmr15318.str _Entry_type original _Submission_date 2007-06-20 _Accession_date 2007-06-20 _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 Vivekanandan Subramanian . . 2 Lakshminarayanan Rajamani . . 3 Jois Seetharama 'D S' . 4 Perumalsamy Ramar . . 5 Banerjee Yajnavalka . . 6 'Ooi Chi-Jin' Emma . . 7 'Wah Teo' Kay . . 8 Kini Manjunatha R. . 9 Valiyaveettil Suresh . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 206 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2008-06-12 original author . stop_ _Original_release_date 2008-06-12 save_ ############################# # Citation for this entry # ############################# save_citations _Saveframe_category entry_citation _Citation_full . _Citation_title 'Structure, self-assembly, and dual role of a beta-defensin-like peptide from the Chinese soft-shelled turtle eggshell matrix' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 18341335 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Lakshminarayanan Rajamani . . 2 Vivekanandan Subramanian . . 3 Samy Ramar Perumal . 4 Banerjee Yajnavalka . . 5 'Ooi Chi-Jin' Emma . . 6 'Wah Teo' Kay . . 7 Jois Seetharama D.S. . 8 Kini R. Manjunatha . 9 Valiyaveettil Suresh . . stop_ _Journal_abbreviation 'J. Am. Chem. Soc.' _Journal_volume 130 _Journal_issue 14 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 4660 _Page_last 4668 _Year 2008 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name Pelovaterin _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label Pelovaterin $Pelovaterin 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_Pelovaterin _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common Pelovaterin _Molecular_mass 4201.883 _Mol_thiol_state 'all disulfide bound' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 42 _Mol_residue_sequence ; DDTPSSRCGSGGWGPCLPIV DLLCIVHVTVGCSGGFGCCR IG ; loop_ _Residue_seq_code _Residue_label 1 ASP 2 ASP 3 THR 4 PRO 5 SER 6 SER 7 ARG 8 CYS 9 GLY 10 SER 11 GLY 12 GLY 13 TRP 14 GLY 15 PRO 16 CYS 17 LEU 18 PRO 19 ILE 20 VAL 21 ASP 22 LEU 23 LEU 24 CYS 25 ILE 26 VAL 27 HIS 28 VAL 29 THR 30 VAL 31 GLY 32 CYS 33 SER 34 GLY 35 GLY 36 PHE 37 GLY 38 CYS 39 CYS 40 ARG 41 ILE 42 GLY stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-10-07 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 2JR3 "Antibacterial Peptide From Eggshell Matrix: Structure And Self-Assembly Of Beta-Defensin Like Peptide From The Chinese Soft-She" 100.00 42 100.00 100.00 3.51e-19 SP P84818 "RecName: Full=Pelovaterin" 100.00 42 100.00 100.00 3.51e-19 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $Pelovaterin 'Pelodiscus sinensis' 13735 Eukaryota Metazoa Pelodiscus sinensis 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 $Pelovaterin 'purified from the natural source' . Pelodiscus sinensis . 'not applicable' 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 $Pelovaterin 1 mM 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % . stop_ save_ ############################ # Computer software used # ############################ save_CYANA _Saveframe_category software _Name CYANA _Version 2.1 loop_ _Vendor _Address _Electronic_address 'P.GUNTERT ET AL.' . . stop_ loop_ _Task refinement 'structure solution' stop_ _Details . save_ save_SPARKY _Saveframe_category software _Name SPARKY _Version 3.110 loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'data analysis' 'peak picking' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 800 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 500 _Details . save_ ############################# # NMR applied experiments # ############################# save_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name 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 pH 4.5 . pH pressure 1 . atm temperature 308 . 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 DSS H 1 'methyl protons' ppm 0.00 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_ _Software_label $CYANA $SPARKY stop_ loop_ _Experiment_label 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 Pelovaterin _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 ASP HA H 4.242 0.020 1 2 1 1 ASP HB3 H 2.907 0.020 2 3 2 2 ASP H H 8.819 0.020 1 4 2 2 ASP HA H 4.742 0.020 1 5 2 2 ASP HB2 H 2.740 0.020 2 6 2 2 ASP HB3 H 2.832 0.020 2 7 3 3 THR H H 8.176 0.020 1 8 3 3 THR HA H 4.489 0.020 1 9 3 3 THR HB H 4.068 0.020 1 10 3 3 THR HG2 H 1.171 0.020 1 11 4 4 PRO HA H 4.386 0.020 1 12 4 4 PRO HB2 H 2.251 0.020 2 13 4 4 PRO HD2 H 3.633 0.020 2 14 4 4 PRO HD3 H 3.786 0.020 2 15 4 4 PRO HG2 H 1.857 0.020 2 16 4 4 PRO HG3 H 1.930 0.020 2 17 5 5 SER H H 8.356 0.020 1 18 5 5 SER HA H 4.371 0.020 1 19 5 5 SER HB2 H 3.788 0.020 2 20 5 5 SER HB3 H 3.788 0.020 2 21 6 6 SER H H 7.901 0.020 1 22 6 6 SER HA H 4.246 0.020 1 23 6 6 SER HB2 H 3.048 0.020 2 24 6 6 SER HB3 H 3.148 0.020 2 25 7 7 ARG H H 8.262 0.020 1 26 7 7 ARG HA H 4.023 0.020 1 27 7 7 ARG HB2 H 1.401 0.020 2 28 7 7 ARG HB3 H 1.450 0.020 2 29 7 7 ARG HD2 H 3.036 0.020 2 30 7 7 ARG HD3 H 3.036 0.020 2 31 7 7 ARG HG2 H 1.221 0.020 2 32 7 7 ARG HG3 H 1.221 0.020 2 33 7 7 ARG HH11 H 7.090 0.020 2 34 7 7 ARG HH21 H 7.089 0.020 2 35 8 8 CYS H H 7.983 0.020 1 36 8 8 CYS HA H 4.613 0.020 1 37 8 8 CYS HB2 H 2.328 0.020 2 38 8 8 CYS HB3 H 3.075 0.020 2 39 9 9 GLY H H 8.047 0.020 1 40 9 9 GLY HA2 H 3.438 0.020 2 41 9 9 GLY HA3 H 4.053 0.020 2 42 10 10 SER H H 7.961 0.020 1 43 10 10 SER HA H 4.816 0.020 1 44 10 10 SER HB2 H 3.723 0.020 2 45 10 10 SER HB3 H 3.750 0.020 2 46 11 11 GLY H H 8.988 0.020 1 47 11 11 GLY HA2 H 3.944 0.020 2 48 11 11 GLY HA3 H 4.002 0.020 2 49 12 12 GLY H H 8.676 0.020 1 50 12 12 GLY HA2 H 3.549 0.020 2 51 12 12 GLY HA3 H 4.016 0.020 2 52 13 13 TRP H H 7.768 0.020 1 53 13 13 TRP HA H 4.518 0.020 1 54 13 13 TRP HB2 H 3.647 0.020 2 55 13 13 TRP HB3 H 3.773 0.020 2 56 13 13 TRP HD1 H 7.261 0.020 1 57 13 13 TRP HE1 H 9.801 0.020 1 58 13 13 TRP HE3 H 7.125 0.020 1 59 13 13 TRP HH2 H 6.964 0.020 1 60 13 13 TRP HZ2 H 7.216 0.020 1 61 14 14 GLY H H 8.954 0.020 1 62 14 14 GLY HA2 H 4.186 0.020 2 63 14 14 GLY HA3 H 4.104 0.020 2 64 15 15 PRO HA H 4.410 0.020 1 65 15 15 PRO HB2 H 1.987 0.020 2 66 15 15 PRO HB3 H 2.193 0.020 2 67 15 15 PRO HD2 H 3.478 0.020 2 68 15 15 PRO HD3 H 3.599 0.020 2 69 15 15 PRO HG2 H 1.818 0.020 2 70 15 15 PRO HG3 H 1.818 0.020 2 71 16 16 CYS H H 8.238 0.020 1 72 16 16 CYS HA H 4.412 0.020 1 73 16 16 CYS HB2 H 2.779 0.020 2 74 16 16 CYS HB3 H 2.854 0.020 2 75 17 17 LEU H H 10.009 0.020 1 76 17 17 LEU HA H 4.908 0.020 1 77 17 17 LEU HB2 H 1.653 0.020 2 78 17 17 LEU HB3 H 1.565 0.020 2 79 17 17 LEU HD1 H 0.922 0.020 2 80 17 17 LEU HD2 H 0.811 0.020 2 81 17 17 LEU HG H 1.335 0.020 1 82 18 18 PRO HA H 3.517 0.020 1 83 18 18 PRO HB2 H 1.534 0.020 2 84 18 18 PRO HB3 H 1.865 0.020 2 85 18 18 PRO HD2 H 3.684 0.020 2 86 18 18 PRO HD3 H 3.419 0.020 2 87 18 18 PRO HG2 H 1.429 0.020 2 88 18 18 PRO HG3 H 1.429 0.020 2 89 19 19 ILE H H 7.968 0.020 1 90 19 19 ILE HA H 3.231 0.020 1 91 19 19 ILE HB H 1.437 0.020 1 92 19 19 ILE HD1 H 0.455 0.020 1 93 19 19 ILE HG12 H 1.144 0.020 2 94 19 19 ILE HG13 H 1.153 0.020 2 95 19 19 ILE HG2 H 0.520 0.020 1 96 20 20 VAL H H 7.645 0.020 1 97 20 20 VAL HA H 3.915 0.020 1 98 20 20 VAL HB H 2.092 0.020 1 99 20 20 VAL HG1 H 0.783 0.020 2 100 20 20 VAL HG2 H 0.783 0.020 2 101 21 21 ASP H H 7.869 0.020 1 102 21 21 ASP HA H 4.684 0.020 1 103 21 21 ASP HB2 H 2.677 0.020 2 104 21 21 ASP HB3 H 3.003 0.020 2 105 22 22 LEU H H 7.385 0.020 1 106 22 22 LEU HA H 4.220 0.020 1 107 22 22 LEU HB2 H 1.712 0.020 2 108 22 22 LEU HB3 H 1.817 0.020 2 109 22 22 LEU HD1 H 0.328 0.020 1 110 22 22 LEU HD2 H 0.803 0.020 1 111 22 22 LEU HG H 1.371 0.020 1 112 23 23 LEU H H 8.736 0.020 1 113 23 23 LEU HA H 4.460 0.020 1 114 23 23 LEU HB2 H 1.587 0.020 2 115 23 23 LEU HB3 H 1.587 0.020 2 116 23 23 LEU HD2 H 0.737 0.020 1 117 23 23 LEU HD1 H 0.858 0.020 1 118 24 24 CYS H H 7.455 0.020 1 119 24 24 CYS HA H 4.837 0.020 1 120 24 24 CYS HB2 H 3.381 0.020 2 121 24 24 CYS HB3 H 3.558 0.020 2 122 25 25 ILE H H 8.293 0.020 1 123 25 25 ILE HA H 3.905 0.020 1 124 25 25 ILE HB H 1.799 0.020 1 125 25 25 ILE HD1 H 0.806 0.020 1 126 25 25 ILE HG12 H 1.209 0.020 2 127 25 25 ILE HG13 H 1.493 0.020 2 128 25 25 ILE HG2 H 0.881 0.020 1 129 26 26 VAL H H 7.777 0.020 1 130 26 26 VAL HA H 4.036 0.020 1 131 26 26 VAL HB H 2.003 0.020 1 132 26 26 VAL HG1 H 0.889 0.020 2 133 26 26 VAL HG2 H 0.889 0.020 2 134 27 27 HIS H H 8.274 0.020 1 135 27 27 HIS HA H 5.713 0.020 1 136 27 27 HIS HB2 H 3.313 0.020 2 137 27 27 HIS HB3 H 2.938 0.020 2 138 27 27 HIS HD1 H 7.216 0.020 1 139 27 27 HIS HD2 H 6.693 0.020 1 140 27 27 HIS HE1 H 8.675 0.020 1 141 28 28 VAL H H 8.212 0.020 1 142 28 28 VAL HA H 4.178 0.020 1 143 28 28 VAL HB H 1.431 0.020 1 144 28 28 VAL HG1 H 0.438 0.020 2 145 28 28 VAL HG2 H -0.344 0.020 2 146 29 29 THR H H 8.806 0.020 1 147 29 29 THR HA H 4.593 0.020 1 148 29 29 THR HG2 H 1.163 0.020 1 149 30 30 VAL H H 6.585 0.020 1 150 30 30 VAL HA H 3.607 0.020 1 151 30 30 VAL HB H 1.857 0.020 1 152 30 30 VAL HG1 H 0.956 0.020 2 153 30 30 VAL HG2 H 0.823 0.020 2 154 31 31 GLY H H 8.704 0.020 1 155 31 31 GLY HA2 H 3.481 0.020 2 156 31 31 GLY HA3 H 4.304 0.020 2 157 32 32 CYS H H 7.848 0.020 1 158 32 32 CYS HA H 5.006 0.020 1 159 32 32 CYS HB2 H 2.594 0.020 2 160 32 32 CYS HB3 H 3.264 0.020 2 161 33 33 SER H H 8.751 0.020 1 162 33 33 SER HA H 4.399 0.020 1 163 33 33 SER HB2 H 3.515 0.020 2 164 33 33 SER HB3 H 3.730 0.020 2 165 34 34 GLY H H 8.520 0.020 1 166 34 34 GLY HA2 H 3.740 0.020 2 167 34 34 GLY HA3 H 3.916 0.020 2 168 35 35 GLY H H 8.555 0.020 1 169 35 35 GLY HA2 H 3.582 0.020 2 170 35 35 GLY HA3 H 4.271 0.020 2 171 36 36 PHE H H 8.249 0.020 1 172 36 36 PHE HA H 5.205 0.020 1 173 36 36 PHE HB2 H 3.455 0.020 2 174 36 36 PHE HB3 H 2.581 0.020 2 175 36 36 PHE HD1 H 7.255 0.020 1 176 36 36 PHE HD2 H 7.255 0.020 1 177 37 37 GLY H H 9.380 0.020 1 178 37 37 GLY HA2 H 3.484 0.020 2 179 37 37 GLY HA3 H 4.565 0.020 2 180 38 38 CYS H H 9.528 0.020 1 181 38 38 CYS HA H 5.559 0.020 1 182 38 38 CYS HB2 H 2.691 0.020 2 183 38 38 CYS HB3 H 3.333 0.020 2 184 39 39 CYS H H 8.528 0.020 1 185 39 39 CYS HA H 5.481 0.020 1 186 39 39 CYS HB2 H 2.643 0.020 2 187 39 39 CYS HB3 H 3.421 0.020 2 188 40 40 ARG H H 8.761 0.020 1 189 40 40 ARG HA H 3.652 0.020 1 190 40 40 ARG HB2 H 1.231 0.020 2 191 40 40 ARG HB3 H 0.775 0.020 2 192 40 40 ARG HD2 H 2.241 0.020 2 193 40 40 ARG HD3 H 2.393 0.020 2 194 40 40 ARG HG2 H 0.473 0.020 2 195 40 40 ARG HG3 H 0.451 0.020 2 196 40 40 ARG HH11 H 6.780 0.020 2 197 41 41 ILE H H 8.038 0.020 1 198 41 41 ILE HA H 4.011 0.020 1 199 41 41 ILE HB H 1.645 0.020 1 200 41 41 ILE HD1 H 0.718 0.020 1 201 41 41 ILE HG12 H 0.896 0.020 2 202 41 41 ILE HG13 H 1.257 0.020 2 203 41 41 ILE HG2 H 0.778 0.020 1 204 42 42 GLY H H 8.230 0.020 1 205 42 42 GLY HA2 H 3.790 0.020 2 206 42 42 GLY HA3 H 3.797 0.020 2 stop_ save_