data_6849 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Crassostrea gigas defensin ; _BMRB_accession_number 6849 _BMRB_flat_file_name bmr6849.str _Entry_type original _Submission_date 2005-10-03 _Accession_date 2005-10-03 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details 'Crassostrea gigas defensin' loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Gueguen Yannick . . 2 Amaury Herpin . . 3 Aumelas Andre . . 4 Garnier Julien . . 5 Fievet Julie . . 6 Escoubas Jean-Michel . . 7 Bulet Philippe . . 8 Gonzales Marcelo . . 9 Lelong Christophe . . 10 Favrel Pascal . . 11 Bachere Evelyne . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 243 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2007-01-29 original author . stop_ _Original_release_date 2007-01-29 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Characterization of a Defensin from the Oyster Crassostrea gigas: RECOMBINANT PRODUCTION, FOLDING, SOLUTION STRUCTURE, ANTIMICROBIAL ACTIVITIES, AND GENE EXPRESSION. ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 16246846 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Gueguen Yannick . . 2 Herpin Amaury . . 3 Aumelas Andre . . 4 Garnier Julien . . 5 Fievet Julie . . 6 Escoubas Jean-Michel . . 7 Bulet Philippe . . 8 Gonzalez Marcelo . . 9 Lelong Christophe . . 10 Favrel Pascal . . 11 Bachere Evelyne . . stop_ _Journal_abbreviation 'J. Biol. Chem.' _Journal_volume 281 _Journal_issue 1 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 313 _Page_last 323 _Year 2006 _Details . loop_ _Keyword antimicrobial 'Crassotrea gigas' defensin oyster structure stop_ save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'Grassostrea gigas defensin' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'Grassostrea gigas defensin' $Grassostrea_gigas_defensin stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state 'disulfide and other bound' _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_Grassostrea_gigas_defensin _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common 'Grassostrea gigas defensin' _Molecular_mass . _Mol_thiol_state 'disulfide and other bound' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 43 _Mol_residue_sequence ; GFGCPGNQLKCNNHCKSISC RAGYCDAATLWLRCTCTDCN GKK ; loop_ _Residue_seq_code _Residue_label 1 GLY 2 PHE 3 GLY 4 CYS 5 PRO 6 GLY 7 ASN 8 GLN 9 LEU 10 LYS 11 CYS 12 ASN 13 ASN 14 HIS 15 CYS 16 LYS 17 SER 18 ILE 19 SER 20 CYS 21 ARG 22 ALA 23 GLY 24 TYR 25 CYS 26 ASP 27 ALA 28 ALA 29 THR 30 LEU 31 TRP 32 LEU 33 ARG 34 CYS 35 THR 36 CYS 37 THR 38 ASP 39 CYS 40 ASN 41 GLY 42 LYS 43 LYS stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-01-28 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 2B68 "Solution Structure Of The Recombinant Crassostrea Gigas Defensin" 100.00 43 100.00 100.00 9.86e-22 EMBL CAJ19280 "defensin [Crassostrea gigas]" 100.00 65 100.00 100.00 6.32e-23 GB ACQ72990 "defs [Crassostrea gigas]" 100.00 65 100.00 100.00 6.32e-23 GB ACQ72991 "defs [Crassostrea gigas]" 100.00 65 100.00 100.00 6.32e-23 GB ACQ72992 "defs [Crassostrea gigas]" 100.00 65 97.67 97.67 4.77e-22 GB ACQ72993 "defs [Crassostrea gigas]" 100.00 65 100.00 100.00 6.32e-23 GB ACQ72994 "defs [Crassostrea gigas]" 100.00 65 100.00 100.00 6.32e-23 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $Grassostrea_gigas_defensin Oyster 29159 Eukaryota Metazoa Crassostrea gigas 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 $Grassostrea_gigas_defensin 'recombinant technology' . . . . . 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 _Concentration_min_value _Concentration_max_value _Isotopic_labeling $Grassostrea_gigas_defensin 0.8 mM 0.7 0.9 . stop_ save_ ############################ # Computer software used # ############################ save_Wxinnmr _Saveframe_category software _Name xwinnmr _Version 3.1 loop_ _Vendor _Address _Electronic_address bruker . . stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_600MHz _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_TOCSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name TOCSY _Sample_label . save_ save_COSY-DQF_2 _Saveframe_category NMR_applied_experiment _Experiment_name COSY-DQF _Sample_label . save_ save_NOESY_3 _Saveframe_category NMR_applied_experiment _Experiment_name NOESY _Sample_label . save_ ####################### # Sample conditions # ####################### save_sample_condition_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 3.25 0.1 pH temperature 303 0.1 K stop_ save_ save_sample_condition_2 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 3.25 0.1 pH temperature 283 0.1 K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_referencing _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 TSP H 1 'methyl protons' ppm 0.0 internal . . . . 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_chem_shift_list_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_condition_1 _Chem_shift_reference_set_label $chemical_shift_referencing _Mol_system_component_name 'Grassostrea gigas defensin' _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 3.69 0.01 1 2 1 1 GLY HA3 H 3.69 0.01 1 3 2 2 PHE H H 8.62 0.01 1 4 2 2 PHE HA H 3.91 0.01 1 5 2 2 PHE HB2 H 2.94 0.01 2 6 2 2 PHE HB3 H 2.68 0.01 2 7 2 2 PHE HD1 H 6.77 0.01 1 8 2 2 PHE HD2 H 6.77 0.01 1 9 2 2 PHE HE1 H 7.09 0.01 1 10 2 2 PHE HE2 H 7.09 0.01 1 11 2 2 PHE HZ H 7.09 0.01 1 12 3 3 GLY H H 8.04 0.01 1 13 3 3 GLY HA2 H 4.65 0.01 2 14 3 3 GLY HA3 H 3.41 0.01 2 15 4 4 CYS H H 7.62 0.01 1 16 4 4 CYS HA H 4.67 0.01 1 17 4 4 CYS HB2 H 3.71 0.01 2 18 4 4 CYS HB3 H 2.50 0.01 2 19 5 5 PRO HA H 4.99 0.01 1 20 5 5 PRO HB2 H 2.34 0.01 2 21 5 5 PRO HB3 H 2.02 0.01 2 22 5 5 PRO HG2 H 1.90 0.01 1 23 5 5 PRO HG3 H 1.90 0.01 1 24 5 5 PRO HD2 H 3.63 0.01 2 25 5 5 PRO HD3 H 3.48 0.01 2 26 6 6 GLY H H 8.90 0.01 1 27 6 6 GLY HA2 H 4.15 0.01 2 28 6 6 GLY HA3 H 3.72 0.01 2 29 7 7 ASN H H 8.47 0.01 1 30 7 7 ASN HA H 4.92 0.01 1 31 7 7 ASN HB2 H 3.15 0.01 2 32 7 7 ASN HB3 H 2.53 0.01 2 33 7 7 ASN HD21 H 7.71 0.01 1 34 7 7 ASN HD22 H 6.88 0.01 1 35 8 8 GLN H H 8.58 0.01 1 36 8 8 GLN HA H 3.88 0.01 1 37 8 8 GLN HB2 H 2.12 0.01 1 38 8 8 GLN HB3 H 2.12 0.01 1 39 8 8 GLN HG2 H 3.15 0.01 2 40 8 8 GLN HG3 H 2.53 0.01 2 41 8 8 GLN HE21 H 7.77 0.01 1 42 8 8 GLN HE22 H 7.15 0.01 1 43 9 9 LEU H H 8.30 0.01 1 44 9 9 LEU HA H 4.12 0.01 1 45 9 9 LEU HB2 H 1.71 0.01 1 46 9 9 LEU HB3 H 1.71 0.01 1 47 9 9 LEU HG H 1.61 0.01 1 48 9 9 LEU HD1 H 0.93 0.01 2 49 9 9 LEU HD2 H 0.87 0.01 2 50 10 10 LYS H H 7.39 0.01 1 51 10 10 LYS HA H 3.97 0.01 1 52 10 10 LYS HB2 H 1.76 0.01 1 53 10 10 LYS HB3 H 1.76 0.01 1 54 10 10 LYS HG2 H 1.42 0.01 2 55 10 10 LYS HG3 H 1.23 0.01 2 56 10 10 LYS HD2 H 1.54 0.01 1 57 10 10 LYS HD3 H 1.54 0.01 1 58 10 10 LYS HE2 H 2.87 0.01 1 59 10 10 LYS HE3 H 2.87 0.01 1 60 10 10 LYS HZ H 7.57 0.01 1 61 11 11 CYS H H 7.19 0.01 1 62 11 11 CYS HA H 4.88 0.01 1 63 11 11 CYS HB2 H 3.66 0.01 2 64 11 11 CYS HB3 H 2.64 0.01 2 65 12 12 ASN H H 8.80 0.01 1 66 12 12 ASN HA H 3.92 0.01 1 67 12 12 ASN HB2 H 2.88 0.01 1 68 12 12 ASN HB3 H 2.88 0.01 1 69 12 12 ASN HD21 H 7.41 0.01 1 70 12 12 ASN HD22 H 6.94 0.01 1 71 13 13 ASN H H 8.64 0.01 1 72 13 13 ASN HA H 4.35 0.01 1 73 13 13 ASN HB2 H 2.85 0.01 2 74 13 13 ASN HB3 H 2.78 0.01 2 75 13 13 ASN HD21 H 7.57 0.01 1 76 13 13 ASN HD22 H 6.93 0.01 1 77 14 14 HIS H H 8.41 0.01 1 78 14 14 HIS HA H 4.28 0.01 1 79 14 14 HIS HB2 H 3.63 0.01 2 80 14 14 HIS HB3 H 3.21 0.01 2 81 14 14 HIS HD2 H 6.57 0.01 1 82 14 14 HIS HE1 H 8.15 0.01 1 83 15 15 CYS H H 8.45 0.01 1 84 15 15 CYS HA H 3.85 0.01 1 85 15 15 CYS HB2 H 2.39 0.01 1 86 15 15 CYS HB3 H 2.39 0.01 1 87 16 16 LYS H H 8.19 0.01 1 88 16 16 LYS HA H 4.52 0.01 1 89 16 16 LYS HB2 H 1.78 0.01 2 90 16 16 LYS HB3 H 1.68 0.01 2 91 16 16 LYS HG2 H 1.47 0.01 2 92 16 16 LYS HG3 H 1.31 0.01 2 93 16 16 LYS HD2 H 1.64 0.01 2 94 16 16 LYS HD3 H 1.61 0.01 2 95 16 16 LYS HE2 H 2.94 0.01 1 96 16 16 LYS HE3 H 2.94 0.01 1 97 16 16 LYS HZ H 7.51 0.01 1 98 17 17 SER H H 7.79 0.01 1 99 17 17 SER HA H 4.29 0.01 1 100 17 17 SER HB2 H 4.01 0.01 2 101 17 17 SER HB3 H 3.92 0.01 2 102 18 18 ILE H H 6.91 0.01 1 103 18 18 ILE HA H 4.59 0.01 1 104 18 18 ILE HB H 2.00 0.01 1 105 18 18 ILE HG12 H 1.35 0.01 2 106 18 18 ILE HG13 H 0.68 0.01 2 107 18 18 ILE HG2 H 0.55 0.01 1 108 18 18 ILE HD1 H 0.61 0.01 1 109 19 19 SER H H 7.56 0.01 1 110 19 19 SER HA H 3.91 0.01 1 111 19 19 SER HB2 H 4.06 0.01 2 112 19 19 SER HB3 H 3.99 0.01 2 113 20 20 CYS H H 7.78 0.01 1 114 20 20 CYS HA H 5.23 0.01 1 115 20 20 CYS HB2 H 3.12 0.01 2 116 20 20 CYS HB3 H 2.68 0.01 2 117 21 21 ARG H H 7.79 0.01 1 118 21 21 ARG HA H 4.02 0.01 1 119 21 21 ARG HB2 H 1.91 0.01 2 120 21 21 ARG HB3 H 1.82 0.01 2 121 21 21 ARG HG2 H 1.78 0.01 2 122 21 21 ARG HG3 H 1.62 0.01 2 123 21 21 ARG HD2 H 3.18 0.01 1 124 21 21 ARG HD3 H 3.18 0.01 1 125 21 21 ARG HE H 7.32 0.01 1 126 22 22 ALA H H 7.53 0.01 1 127 22 22 ALA HA H 4.59 0.01 1 128 22 22 ALA HB H 1.32 0.01 1 129 23 23 GLY H H 8.54 0.01 1 130 23 23 GLY HA2 H 5.22 0.01 2 131 23 23 GLY HA3 H 3.93 0.01 2 132 24 24 TYR H H 8.58 0.01 1 133 24 24 TYR HA H 4.76 0.01 1 134 24 24 TYR HB2 H 3.33 0.01 2 135 24 24 TYR HB3 H 2.93 0.01 2 136 24 24 TYR HD1 H 6.84 0.01 1 137 24 24 TYR HD2 H 6.84 0.01 1 138 24 24 TYR HE1 H 6.58 0.01 1 139 24 24 TYR HE2 H 6.58 0.01 1 140 25 25 CYS H H 8.92 0.01 1 141 25 25 CYS HA H 5.33 0.01 1 142 25 25 CYS HB2 H 3.39 0.01 2 143 25 25 CYS HB3 H 3.07 0.01 2 144 26 26 ASP H H 8.32 0.01 1 145 26 26 ASP HA H 4.65 0.01 1 146 26 26 ASP HB2 H 2.81 0.01 2 147 26 26 ASP HB3 H 2.66 0.01 2 148 27 27 ALA H H 9.84 0.01 1 149 27 27 ALA HA H 1.87 0.01 1 150 27 27 ALA HB H 1.18 0.01 1 151 28 28 ALA H H 8.32 0.01 1 152 28 28 ALA HA H 4.03 0.01 1 153 28 28 ALA HB H 1.36 0.01 1 154 29 29 THR H H 7.36 0.01 1 155 29 29 THR HA H 4.45 0.01 1 156 29 29 THR HB H 4.52 0.01 1 157 29 29 THR HG2 H 0.98 0.01 1 158 30 30 LEU H H 7.76 0.01 1 159 30 30 LEU HA H 3.31 0.01 1 160 30 30 LEU HB2 H 1.99 0.01 2 161 30 30 LEU HB3 H 1.69 0.01 2 162 30 30 LEU HG H 1.43 0.01 1 163 30 30 LEU HD1 H 0.85 0.01 2 164 30 30 LEU HD2 H 0.76 0.01 2 165 31 31 TRP H H 7.22 0.01 1 166 31 31 TRP HA H 3.17 0.01 1 167 31 31 TRP HB2 H 3.45 0.01 1 168 31 31 TRP HB3 H 3.57 0.01 1 169 31 31 TRP HD1 H 7.02 0.01 1 170 31 31 TRP HE1 H 10.35 0.01 1 171 31 31 TRP HE3 H 7.27 0.01 1 172 31 31 TRP HZ2 H 7.48 0.01 1 173 31 31 TRP HZ3 H 7.10 0.01 1 174 31 31 TRP HH2 H 7.18 0.01 1 175 32 32 LEU H H 7.07 0.01 1 176 32 32 LEU HA H 3.83 0.01 1 177 32 32 LEU HB2 H 1.65 0.01 2 178 32 32 LEU HB3 H 1.39 0.01 2 179 32 32 LEU HG H 1.80 0.01 1 180 32 32 LEU HD1 H 0.88 0.01 2 181 32 32 LEU HD2 H 0.77 0.01 2 182 33 33 ARG H H 7.86 0.01 1 183 33 33 ARG HA H 4.36 0.01 1 184 33 33 ARG HB2 H 1.84 0.01 2 185 33 33 ARG HB3 H 1.62 0.01 2 186 33 33 ARG HG2 H 1.54 0.01 2 187 33 33 ARG HG3 H 1.29 0.01 2 188 33 33 ARG HD2 H 3.10 0.01 1 189 33 33 ARG HD3 H 3.10 0.01 1 190 33 33 ARG HE H 6.88 0.01 1 191 34 34 CYS H H 8.57 0.01 1 192 34 34 CYS HA H 4.95 0.01 1 193 34 34 CYS HB2 H 3.21 0.01 2 194 34 34 CYS HB3 H 2.58 0.01 2 195 35 35 THR H H 9.31 0.01 1 196 35 35 THR HA H 4.14 0.01 1 197 35 35 THR HB H 3.08 0.01 1 198 35 35 THR HG2 H 0.95 0.01 1 199 36 36 CYS H H 8.56 0.01 1 200 36 36 CYS HA H 5.59 0.01 1 201 36 36 CYS HB2 H 3.05 0.01 2 202 36 36 CYS HB3 H 2.59 0.01 2 203 37 37 THR H H 8.95 0.01 1 204 37 37 THR HA H 4.61 0.01 1 205 37 37 THR HB H 4.05 0.01 1 206 37 37 THR HG2 H 1.15 0.01 1 207 38 38 ASP H H 8.89 0.01 1 208 38 38 ASP HA H 4.29 0.01 1 209 38 38 ASP HB2 H 2.95 0.01 2 210 38 38 ASP HB3 H 2.76 0.01 2 211 39 39 CYS H H 8.81 0.01 1 212 39 39 CYS HA H 4.82 0.01 1 213 39 39 CYS HB2 H 3.08 0.01 2 214 39 39 CYS HB3 H 2.81 0.01 2 215 40 40 ASN H H 8.48 0.01 1 216 40 40 ASN HA H 4.66 0.01 1 217 40 40 ASN HB2 H 2.82 0.01 2 218 40 40 ASN HB3 H 2.77 0.01 2 219 41 41 GLY H H 8.48 0.01 1 220 41 41 GLY HA2 H 3.91 0.01 2 221 41 41 GLY HA3 H 3.83 0.01 2 222 42 42 LYS H H 8.20 0.01 1 223 42 42 LYS HA H 4.27 0.01 1 224 42 42 LYS HB2 H 1.77 0.01 2 225 42 42 LYS HB3 H 1.69 0.01 2 226 42 42 LYS HG2 H 1.36 0.01 1 227 42 42 LYS HG3 H 1.36 0.01 1 228 42 42 LYS HD2 H 1.69 0.01 2 229 42 42 LYS HD3 H 1.60 0.01 2 230 42 42 LYS HE2 H 2.92 0.01 1 231 42 42 LYS HE3 H 2.92 0.01 1 232 42 42 LYS HZ H 7.46 0.01 1 233 43 43 LYS H H 8.14 0.01 1 234 43 43 LYS HA H 4.14 0.01 1 235 43 43 LYS HB2 H 1.78 0.01 1 236 43 43 LYS HB3 H 1.78 0.01 1 237 43 43 LYS HG2 H 1.33 0.01 1 238 43 43 LYS HG3 H 1.33 0.01 1 239 43 43 LYS HD2 H 1.65 0.01 2 240 43 43 LYS HD3 H 1.60 0.01 2 241 43 43 LYS HE2 H 2.92 0.01 1 242 43 43 LYS HE3 H 2.92 0.01 1 243 43 43 LYS HZ H 7.45 0.01 1 stop_ save_