data_4640 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution structure and activity of the four disulfide bond Mediterranean mussel defensin MGD-1 ; _BMRB_accession_number 4640 _BMRB_flat_file_name bmr4640.str _Entry_type original _Submission_date 2000-08-08 _Accession_date 2001-03-16 _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 Yang Y. S. . 2 Mitta G. . . 3 Chavanieu A. . . 4 Calas B. . . 5 Sanchez J. F. . 6 Roch P. . . 7 Aumelas A. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 226 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2008-07-16 update BMRB 'Updating non-standard residue' stop_ _Original_release_date 2001-03-16 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Solution structure and activity of the four disulfide bond Mediterranean mussel defensin MGD-1 ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 11087396 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Yang Y. S. . 2 Mitta G. . . 3 Chavanieu A. . . 4 Calas B. . . 5 Sanchez J. F. . 6 Roch P. . . 7 Aumelas A. . . stop_ _Journal_abbreviation Biochemistry _Journal_volume 39 _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 14436 _Page_last 14447 _Year 2000 _Details . loop_ _Keyword 'Cystine stabilized alpha-beta motif' Defensin antibacterial 'disulfide bond' synthesis stop_ save_ ################################## # Molecular system description # ################################## save_system_MGD-1 _Saveframe_category molecular_system _Mol_system_name 'DEFENSIN MGD-1' _Abbreviation_common MGD-1 _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'DEFENSIN MGD-1' $MGD-1 stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state monomer _System_paramagnetic no _System_thiol_state 'all disulfide bound' _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_MGD-1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common 'DEFENSIN MGD-1' _Abbreviation_common MGD-1 _Molecular_mass . _Mol_thiol_state 'all disulfide bound' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 40 _Mol_residue_sequence ; GFGCPNNYQCHRHCKSIPGR CGGYCGGWHRLRCTCYRCGX ; loop_ _Residue_seq_code _Residue_label 1 GLY 2 PHE 3 GLY 4 CYS 5 PRO 6 ASN 7 ASN 8 TYR 9 GLN 10 CYS 11 HIS 12 ARG 13 HIS 14 CYS 15 LYS 16 SER 17 ILE 18 PRO 19 GLY 20 ARG 21 CYS 22 GLY 23 GLY 24 TYR 25 CYS 26 GLY 27 GLY 28 TRP 29 HIS 30 ARG 31 LEU 32 ARG 33 CYS 34 THR 35 CYS 36 TYR 37 ARG 38 CYS 39 GLY 40 NH2 stop_ _Sequence_homology_query_date 2008-03-24 _Sequence_homology_query_revised_last_date 2008-03-03 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 1FJN 'A Chain A, Solution Structure And ActivityOf The Four Disulfide Bond Mediterranean MusselDefensin Mgd-1' 100.00 39 100 100 7e-21 GenBank AAD45117.1 'MGD1 antimicrobial peptide precursor[Mytilus galloprovincialis]' 68.42 57 100 100 9e-19 SWISS-PROT P80571 'DEFI_MYTGA Defensin MGD-1 precursor' 65.00 60 100 100 7e-21 stop_ save_ ###################### # Polymer residues # ###################### save_chem_comp_NH2 _Saveframe_category polymer_residue _Mol_type NON-POLYMER _Name_common 'AMINO GROUP' _BMRB_code NH2 _PDB_code NH2 _Standard_residue_derivative . _Molecular_mass 16.023 _Mol_paramagnetic . _Details . 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 $MGD-1 'Mediterranean mussel' 29158 Eukaryota Metazoa Mytilus galloprovincialis 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 $MGD-1 '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 $MGD-1 3 mM . H2O 95 % . D2O 5 % . stop_ save_ ############################ # Computer software used # ############################ save_X-PLOR _Saveframe_category software _Name X-PLOR _Version 3.1 loop_ _Task refinement stop_ _Details Brunger save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AMX _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_COSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D COSY' _Sample_label $sample_1 save_ save_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name TOCSY _Sample_label $sample_1 save_ save_NOESY_3 _Saveframe_category NMR_applied_experiment _Experiment_name NOESY _Sample_label $sample_1 save_ ####################### # Sample conditions # ####################### save_sample_cond_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 3.3 . pH pressure 1 . atm temperature 285 . 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 TSP H 1 'methyl protons' ppm 0.0 . . . . . 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_chemical_shift_set_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D COSY' TOCSY NOESY stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_cond_1 _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name 'DEFENSIN MGD-1' _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 GLY HA2 H 3.76 0.01 1 2 . 1 GLY HA3 H 3.64 0.01 1 3 . 2 PHE H H 8.55 0.01 1 4 . 2 PHE HA H 3.96 0.01 1 5 . 2 PHE HB2 H 2.99 0.01 1 6 . 2 PHE HB3 H 2.72 0.01 1 7 . 2 PHE HD1 H 7.18 0.01 1 8 . 2 PHE HD2 H 7.18 0.01 1 9 . 2 PHE HE1 H 6.82 0.01 1 10 . 2 PHE HE2 H 6.82 0.01 1 11 . 3 GLY H H 8.25 0.01 1 12 . 3 GLY HA2 H 4.34 0.01 1 13 . 3 GLY HA3 H 3.53 0.01 1 14 . 4 CYS H H 7.99 0.01 1 15 . 4 CYS HA H 4.79 0.01 1 16 . 4 CYS HB2 H 4.29 0.01 1 17 . 4 CYS HB3 H 2.81 0.01 1 18 . 5 PRO HA H 4.88 0.01 1 19 . 5 PRO HB2 H 2.43 0.01 2 20 . 5 PRO HB3 H 2.25 0.01 2 21 . 5 PRO HG2 H 1.92 0.01 2 22 . 5 PRO HG3 H 1.71 0.01 2 23 . 5 PRO HD2 H 3.49 0.01 1 24 . 5 PRO HD3 H 3.49 0.01 1 25 . 6 ASN H H 9.00 0.01 1 26 . 6 ASN HA H 4.77 0.01 1 27 . 6 ASN HB2 H 3.13 0.01 1 28 . 6 ASN HB3 H 2.79 0.01 1 29 . 6 ASN HD21 H 7.94 0.01 2 30 . 6 ASN HD22 H 7.23 0.01 2 31 . 7 ASN H H 9.78 0.01 1 32 . 7 ASN HA H 4.58 0.01 1 33 . 7 ASN HB2 H 3.04 0.01 1 34 . 7 ASN HB3 H 2.83 0.01 1 35 . 7 ASN HD21 H 7.82 0.01 2 36 . 7 ASN HD22 H 7.25 0.01 2 37 . 8 TYR H H 8.32 0.01 1 38 . 8 TYR HA H 4.37 0.01 1 39 . 8 TYR HB2 H 3.28 0.01 1 40 . 8 TYR HB3 H 3.17 0.01 1 41 . 8 TYR HD1 H 7.19 0.01 1 42 . 8 TYR HD2 H 7.19 0.01 1 43 . 8 TYR HE1 H 6.86 0.01 1 44 . 8 TYR HE2 H 6.86 0.01 1 45 . 9 GLN H H 7.96 0.01 1 46 . 9 GLN HA H 3.98 0.01 1 47 . 9 GLN HB2 H 2.30 0.01 1 48 . 9 GLN HB3 H 2.12 0.01 1 49 . 9 GLN HG2 H 2.56 0.01 2 50 . 9 GLN HG3 H 2.46 0.01 2 51 . 9 GLN HE21 H 7.62 0.01 2 52 . 9 GLN HE22 H 7.07 0.01 2 53 . 10 CYS H H 7.45 0.01 1 54 . 10 CYS HA H 4.70 0.01 1 55 . 10 CYS HB2 H 3.44 0.01 2 56 . 10 CYS HB3 H 2.64 0.01 2 57 . 11 HIS H H 9.01 0.01 1 58 . 11 HIS HA H 3.80 0.01 1 59 . 11 HIS HB2 H 3.36 0.01 1 60 . 11 HIS HB3 H 3.24 0.01 1 61 . 11 HIS HD2 H 8.13 0.01 1 62 . 11 HIS HE1 H 7.05 0.01 1 63 . 12 ARG H H 7.99 0.01 1 64 . 12 ARG HA H 3.67 0.01 1 65 . 12 ARG HB2 H 1.80 0.01 2 66 . 12 ARG HB3 H 1.68 0.01 2 67 . 12 ARG HG2 H 1.59 0.01 2 68 . 12 ARG HG3 H 1.48 0.01 2 69 . 12 ARG HD2 H 3.09 0.01 2 70 . 12 ARG HD3 H 3.03 0.01 2 71 . 12 ARG HE H 7.25 0.01 1 72 . 13 HIS H H 7.95 0.01 1 73 . 13 HIS HA H 4.29 0.01 1 74 . 13 HIS HB2 H 3.34 0.01 1 75 . 13 HIS HB3 H 3.50 0.01 1 76 . 13 HIS HD2 H 8.21 0.01 1 77 . 13 HIS HE1 H 6.54 0.01 1 78 . 14 CYS H H 8.69 0.01 1 79 . 14 CYS HA H 3.67 0.01 1 80 . 14 CYS HB2 H 2.26 0.01 1 81 . 14 CYS HB3 H 2.26 0.01 1 82 . 15 LYS H H 7.53 0.01 1 83 . 15 LYS HA H 3.66 0.01 1 84 . 15 LYS HB2 H 1.67 0.01 1 85 . 15 LYS HB3 H 1.47 0.01 1 86 . 15 LYS HG2 H 1.00 0.01 1 87 . 15 LYS HG3 H 1.00 0.01 1 88 . 15 LYS HD2 H 1.16 0.01 1 89 . 15 LYS HD3 H 1.16 0.01 1 90 . 15 LYS HE2 H 2.87 0.01 1 91 . 15 LYS HE3 H 2.87 0.01 1 92 . 16 SER H H 7.30 0.01 1 93 . 16 SER HA H 4.37 0.01 1 94 . 16 SER HB2 H 4.01 0.01 2 95 . 16 SER HB3 H 3.84 0.01 2 96 . 17 ILE H H 7.47 0.01 1 97 . 17 ILE HA H 4.33 0.01 1 98 . 17 ILE HB H 1.80 0.01 1 99 . 17 ILE HG12 H 1.23 0.01 1 100 . 17 ILE HG13 H 1.23 0.01 1 101 . 17 ILE HG2 H 0.81 0.01 1 102 . 17 ILE HD1 H 0.51 0.01 1 103 . 18 PRO HA H 4.25 0.01 1 104 . 18 PRO HB2 H 2.30 0.01 2 105 . 18 PRO HB3 H 1.88 0.01 2 106 . 18 PRO HG2 H 2.12 0.01 2 107 . 18 PRO HG3 H 1.99 0.01 2 108 . 18 PRO HD2 H 4.09 0.01 2 109 . 18 PRO HD3 H 3.62 0.01 2 110 . 19 GLY H H 9.00 0.01 1 111 . 19 GLY HA2 H 4.24 0.01 1 112 . 19 GLY HA3 H 3.77 0.01 1 113 . 20 ARG H H 8.38 0.01 1 114 . 20 ARG HA H 4.97 0.01 1 115 . 20 ARG HB2 H 2.60 0.01 1 116 . 20 ARG HB3 H 1.26 0.01 1 117 . 20 ARG HG2 H 1.42 0.01 2 118 . 20 ARG HG3 H 1.36 0.01 2 119 . 20 ARG HD2 H 2.79 0.01 2 120 . 20 ARG HD3 H 2.57 0.01 2 121 . 20 ARG HE H 7.45 0.01 1 122 . 21 CYS H H 8.05 0.01 1 123 . 21 CYS HA H 4.96 0.01 1 124 . 21 CYS HB2 H 3.41 0.01 1 125 . 21 CYS HB3 H 2.60 0.01 1 126 . 22 GLY H H 6.72 0.01 1 127 . 22 GLY HA2 H 4.04 0.01 1 128 . 22 GLY HA3 H 3.02 0.01 1 129 . 23 GLY H H 9.00 0.01 1 130 . 23 GLY HA2 H 4.71 0.01 1 131 . 23 GLY HA3 H 4.36 0.01 1 132 . 24 TYR H H 8.43 0.01 1 133 . 24 TYR HA H 4.89 0.01 1 134 . 24 TYR HB2 H 3.19 0.01 2 135 . 24 TYR HB3 H 3.03 0.01 2 136 . 24 TYR HD1 H 7.01 0.01 1 137 . 24 TYR HD2 H 7.01 0.01 1 138 . 24 TYR HE1 H 6.78 0.01 1 139 . 24 TYR HE2 H 6.78 0.01 1 140 . 25 CYS H H 8.86 0.01 1 141 . 25 CYS HA H 5.33 0.01 1 142 . 25 CYS HB2 H 3.67 0.01 1 143 . 25 CYS HB3 H 2.89 0.01 1 144 . 26 GLY H H 9.02 0.01 1 145 . 26 GLY HA2 H 4.50 0.01 1 146 . 26 GLY HA3 H 4.08 0.01 1 147 . 27 GLY H H 8.66 0.01 1 148 . 27 GLY HA2 H 4.21 0.01 1 149 . 27 GLY HA3 H 3.97 0.01 1 150 . 28 TRP H H 8.91 0.01 1 151 . 28 TRP HA H 4.40 0.01 1 152 . 28 TRP HB2 H 3.25 0.01 1 153 . 28 TRP HB3 H 3.25 0.01 1 154 . 28 TRP HD1 H 7.25 0.01 1 155 . 28 TRP HE1 H 10.04 0.01 1 156 . 28 TRP HE3 H 7.15 0.01 1 157 . 28 TRP HZ2 H 7.47 0.01 1 158 . 28 TRP HZ3 H 7.15 0.01 1 159 . 28 TRP HH2 H 7.01 0.01 1 160 . 29 HIS H H 9.38 0.01 1 161 . 29 HIS HA H 3.93 0.01 1 162 . 29 HIS HB2 H 3.00 0.01 2 163 . 29 HIS HB3 H 2.51 0.01 2 164 . 29 HIS HD2 H 8.39 0.01 1 165 . 29 HIS HE1 H 6.08 0.01 1 166 . 30 ARG H H 8.44 0.01 1 167 . 30 ARG HA H 3.24 0.01 1 168 . 30 ARG HB2 H 1.62 0.01 2 169 . 30 ARG HB3 H 1.50 0.01 2 170 . 30 ARG HG2 H 1.91 0.01 2 171 . 30 ARG HG3 H 1.87 0.01 2 172 . 30 ARG HD2 H 3.24 0.01 1 173 . 30 ARG HD3 H 3.24 0.01 1 174 . 30 ARG HE H 7.19 0.01 1 175 . 31 LEU H H 6.80 0.01 1 176 . 31 LEU HA H 4.03 0.01 1 177 . 31 LEU HB2 H 1.90 0.01 1 178 . 31 LEU HB3 H 1.60 0.01 1 179 . 31 LEU HG H 1.66 0.01 1 180 . 31 LEU HD1 H 1.05 0.01 2 181 . 31 LEU HD2 H 0.72 0.01 2 182 . 32 ARG H H 8.69 0.01 1 183 . 32 ARG HA H 4.59 0.01 1 184 . 32 ARG HB2 H 1.75 0.01 2 185 . 32 ARG HB3 H 1.69 0.01 2 186 . 32 ARG HG2 H 1.33 0.01 1 187 . 32 ARG HG3 H 1.33 0.01 1 188 . 32 ARG HD2 H 3.23 0.01 1 189 . 32 ARG HD3 H 3.23 0.01 1 190 . 32 ARG HE H 7.08 0.01 1 191 . 33 CYS H H 9.52 0.01 1 192 . 33 CYS HA H 4.93 0.01 1 193 . 33 CYS HB2 H 3.46 0.01 1 194 . 33 CYS HB3 H 2.81 0.01 1 195 . 34 THR H H 9.10 0.01 1 196 . 34 THR HA H 4.32 0.01 1 197 . 34 THR HB H 3.45 0.01 1 198 . 34 THR HG2 H 1.13 0.01 1 199 . 35 CYS H H 8.86 0.01 1 200 . 35 CYS HA H 4.45 0.01 1 201 . 35 CYS HB2 H 2.76 0.01 1 202 . 36 TYR H H 8.32 0.01 1 203 . 36 TYR HA H 5.18 0.01 1 204 . 36 TYR HB2 H 3.24 0.01 2 205 . 36 TYR HB3 H 2.98 0.01 2 206 . 36 TYR HD1 H 6.98 0.01 1 207 . 36 TYR HD2 H 6.98 0.01 1 208 . 36 TYR HE1 H 6.60 0.01 1 209 . 36 TYR HE2 H 6.60 0.01 1 210 . 37 ARG H H 9.10 0.01 1 211 . 37 ARG HA H 4.60 0.01 1 212 . 37 ARG HB2 H 2.07 0.01 2 213 . 37 ARG HB3 H 1.86 0.01 2 214 . 37 ARG HG2 H 1.77 0.01 2 215 . 37 ARG HG3 H 1.62 0.01 2 216 . 37 ARG HD2 H 3.23 0.01 1 217 . 37 ARG HD3 H 3.23 0.01 1 218 . 37 ARG HE H 7.29 0.01 1 219 . 38 CYS H H 8.33 0.01 1 220 . 38 CYS HA H 4.72 0.01 1 221 . 38 CYS HB2 H 3.30 0.01 2 222 . 38 CYS HB3 H 2.78 0.01 2 223 . 39 GLY H H 8.92 0.01 1 224 . 39 GLY HA2 H 3.95 0.01 1 225 . 40 NH2 HN1 H 7.57 0.01 2 226 . 40 NH2 HN2 H 7.18 0.01 2 stop_ save_