data_4587 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR STRUCTURAL DETERMINATION OF VISCOTOXIN A3 FROM VISCUM ALBUM L. ; _BMRB_accession_number 4587 _BMRB_flat_file_name bmr4587.str _Entry_type original _Submission_date 2000-05-05 _Accession_date 2000-09-07 _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 Ugolini R. . . 2 Fogolari F. . . 3 Schaller G. . . 4 Urech K. . . 5 Giannattasio M. . . 6 Ragona L. . . 7 Molinari H. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 264 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2000-12-29 original BMRB . stop_ _Original_release_date 2000-09-07 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; NMR structural determination of viscotoxin A3 from Viscum album L ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 10947973 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Romagnoli Silvia . . 2 Ugolini Raffaella . . 3 Fogolari Federico . . 4 Schaller Gerhard . . 5 Urech Konrad . . 6 Giannattasio Matteo . . 7 Ragona Laura . . 8 Molinari Henriette . . stop_ _Journal_abbreviation 'Biochem. J.' _Journal_volume 350 _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 569 _Page_last 577 _Year 2000 _Details . loop_ _Keyword 'ALPHA-BETA PROTEIN' 'AMPHIPATHIC HELIX' 'CONCENTRIC MOTIF' HELIX-TURN-HELIX THIONIN stop_ save_ ################################## # Molecular system description # ################################## save_system_VTA3 _Saveframe_category molecular_system _Mol_system_name 'Viscotoxin A3 from Viscum album L.' _Abbreviation_common VTA3 _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'Viscotoxin A3' $VTA3 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_VTA3 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common 'Viscotoxin A3' _Abbreviation_common VTA3 _Molecular_mass . _Mol_thiol_state 'all disulfide bound' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 46 _Mol_residue_sequence ; KSCCPNTTGRNIYNACRLTG APRPTCAKLSGCKIISGSTC PSDYPK ; loop_ _Residue_seq_code _Residue_label 1 LYS 2 SER 3 CYS 4 CYS 5 PRO 6 ASN 7 THR 8 THR 9 GLY 10 ARG 11 ASN 12 ILE 13 TYR 14 ASN 15 ALA 16 CYS 17 ARG 18 LEU 19 THR 20 GLY 21 ALA 22 PRO 23 ARG 24 PRO 25 THR 26 CYS 27 ALA 28 LYS 29 LEU 30 SER 31 GLY 32 CYS 33 LYS 34 ILE 35 ILE 36 SER 37 GLY 38 SER 39 THR 40 CYS 41 PRO 42 SER 43 ASP 44 TYR 45 PRO 46 LYS 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 1ED0 'Nmr Structural Determination Of Viscotoxin A3 From Viscum Album L.' 100.00 46 100.00 100.00 1.45e-17 PDB 1OKH 'Viscotoxin A3 From Viscum Album L' 100.00 46 100.00 100.00 1.45e-17 PRF 2007441A viscotoxin 100.00 111 100.00 100.00 1.12e-18 SWISS-PROT P01538 'Viscotoxin-A3 precursor [Contains: Viscotoxin-A3; Acidic protein]' 100.00 111 100.00 100.00 1.01e-18 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $VTA3 'European mistletoe' 3972 Eukaryota Viridiplantae Viscum album 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 $VTA3 'purified from the natural source' . . . . . 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 $VTA3 . mM 1.0 2.0 . 'H3PO4/NaOH aqueous buffer' 50 mM . . . H2O 90 % . . . D2O 10 % . . . stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Concentration_min_value _Concentration_max_value _Isotopic_labeling $VTA3 . mM 1.0 2.0 . 'H3PO4/NaOH aqueous buffer' 50 mM . . . D2O 100 % . . . stop_ save_ ############################ # Computer software used # ############################ save_DYANA _Saveframe_category software _Name DYANA _Version 1.4 loop_ _Task 'solution structure calculation' stop_ _Details . save_ save_DISCOVER _Saveframe_category software _Name DISCOVER _Version 98 loop_ _Task refinement stop_ _Details MSI save_ save_XWINNMR _Saveframe_category software _Name xwinnmr _Version 1.2 loop_ _Task collection stop_ _Details 'Bruker Spectrospin' save_ save_XEASY _Saveframe_category software _Name XEASY _Version 1.2 loop_ _Task 'data analysis' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DRX _Field_strength 500 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _Sample_label . save_ save_DQF-COSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name DQF-COSY _Sample_label . save_ save_TOCSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name TOCSY _Sample_label . save_ ####################### # Sample conditions # ####################### save_sample_cond_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 50 . mM pH 3.6 . n/a pressure 1 . atm temperature 285 0.1 K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_ref_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 TSP H 1 'methyl protons' ppm 0 internal direct . external parallel_to_Bo 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 NOESY' DQF-COSY TOCSY stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_cond_1 _Chem_shift_reference_set_label $chemical_shift_ref_1 _Mol_system_component_name 'Viscotoxin A3' _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 LYS HA H 4.17 . 1 2 . 1 LYS HB2 H 1.98 . 1 3 . 1 LYS HB3 H 1.98 . 1 4 . 1 LYS HG2 H 1.26 . 2 5 . 1 LYS HG3 H 1.73 . 2 6 . 1 LYS HD2 H 1.44 . 2 7 . 1 LYS HD3 H 1.56 . 2 8 . 1 LYS HE2 H 3.08 . 9 9 . 1 LYS HE3 H 3.08 . 9 10 . 1 LYS HZ H 7.59 . 1 11 . 2 SER H H 8.98 . 1 12 . 2 SER HA H 4.99 . 1 13 . 2 SER HB2 H 2.83 . 2 14 . 2 SER HB3 H 3.69 . 2 15 . 3 CYS H H 9.14 . 1 16 . 3 CYS HA H 5.00 . 1 17 . 3 CYS HB2 H 2.30 . 2 18 . 3 CYS HB3 H 4.37 . 2 19 . 4 CYS H H 9.44 . 1 20 . 4 CYS HA H 5.30 . 1 21 . 4 CYS HB2 H 2.65 . 2 22 . 4 CYS HB3 H 2.72 . 2 23 . 5 PRO HA H 4.45 . 1 24 . 5 PRO HB2 H 1.99 . 2 25 . 5 PRO HB3 H 2.12 . 2 26 . 5 PRO HG2 H 2.28 . 1 27 . 5 PRO HG3 H 2.28 . 1 28 . 5 PRO HD2 H 3.84 . 2 29 . 5 PRO HD3 H 4.02 . 2 30 . 6 ASN H H 6.98 . 1 31 . 6 ASN HA H 4.55 . 1 32 . 6 ASN HB2 H 3.31 . 1 33 . 6 ASN HB3 H 3.31 . 1 34 . 6 ASN HD21 H 7.91 . 2 35 . 6 ASN HD22 H 7.04 . 2 36 . 7 THR H H 9.13 . 1 37 . 7 THR HA H 3.91 . 1 38 . 7 THR HB H 4.16 . 1 39 . 7 THR HG2 H 1.30 . 1 40 . 8 THR H H 8.29 . 1 41 . 8 THR HA H 3.97 . 1 42 . 8 THR HB H 4.09 . 1 43 . 8 THR HG2 H 1.29 . 1 44 . 9 GLY H H 8.69 . 1 45 . 9 GLY HA2 H 3.60 . 2 46 . 9 GLY HA3 H 4.09 . 2 47 . 10 ARG H H 7.75 . 1 48 . 10 ARG HA H 4.59 . 1 49 . 10 ARG HB2 H 1.69 . 2 50 . 10 ARG HB3 H 2.19 . 2 51 . 10 ARG HG2 H 1.94 . 1 52 . 10 ARG HG3 H 1.94 . 1 53 . 10 ARG HD2 H 3.35 . 2 54 . 10 ARG HD3 H 3.51 . 2 55 . 10 ARG HE H 8.78 . 1 56 . 11 ASN H H 8.66 . 1 57 . 11 ASN HA H 4.60 . 1 58 . 11 ASN HB2 H 2.92 . 2 59 . 11 ASN HB3 H 3.15 . 2 60 . 11 ASN HD21 H 7.02 . 2 61 . 11 ASN HD22 H 7.79 . 2 62 . 12 ILE H H 8.54 . 1 63 . 12 ILE HA H 3.80 . 1 64 . 12 ILE HB H 1.87 . 1 65 . 12 ILE HG12 H 1.10 . 2 66 . 12 ILE HG13 H 1.99 . 2 67 . 12 ILE HG2 H 0.93 . 1 68 . 12 ILE HD1 H 0.87 . 1 69 . 13 TYR H H 9.09 . 1 70 . 13 TYR HA H 3.68 . 1 71 . 13 TYR HB2 H 3.16 . 2 72 . 13 TYR HB3 H 3.19 . 2 73 . 13 TYR HD1 H 6.92 . 1 74 . 13 TYR HD2 H 6.92 . 1 75 . 13 TYR HE1 H 6.78 . 1 76 . 13 TYR HE2 H 6.78 . 1 77 . 14 ASN H H 9.05 . 1 78 . 14 ASN HA H 4.33 . 1 79 . 14 ASN HB2 H 2.90 . 2 80 . 14 ASN HB3 H 3.07 . 2 81 . 14 ASN HD21 H 7.06 . 2 82 . 14 ASN HD22 H 7.89 . 2 83 . 15 ALA H H 8.11 . 1 84 . 15 ALA HA H 4.14 . 1 85 . 15 ALA HB H 1.50 . 1 86 . 16 CYS H H 8.18 . 1 87 . 16 CYS HA H 4.31 . 1 88 . 16 CYS HB2 H 3.04 . 2 89 . 16 CYS HB3 H 3.28 . 2 90 . 17 ARG H H 8.75 . 1 91 . 17 ARG HA H 3.97 . 1 92 . 17 ARG HB2 H 1.77 . 2 93 . 17 ARG HB3 H 1.86 . 2 94 . 17 ARG HG2 H 0.96 . 2 95 . 17 ARG HG3 H 1.47 . 2 96 . 17 ARG HD2 H 2.64 . 2 97 . 17 ARG HD3 H 3.18 . 2 98 . 17 ARG HE H 7.47 . 1 99 . 17 ARG HH11 H 6.62 . 1 100 . 17 ARG HH12 H 6.62 . 1 101 . 17 ARG HH21 H 7.14 . 1 102 . 17 ARG HH22 H 7.14 . 1 103 . 18 LEU H H 7.82 . 1 104 . 18 LEU HA H 4.22 . 1 105 . 18 LEU HB2 H 1.86 . 2 106 . 18 LEU HB3 H 1.92 . 2 107 . 18 LEU HG H 1.68 . 1 108 . 18 LEU HD1 H 0.92 . 2 109 . 18 LEU HD2 H 0.95 . 2 110 . 19 THR H H 7.49 . 1 111 . 19 THR HA H 4.45 . 1 112 . 19 THR HB H 4.51 . 1 113 . 19 THR HG2 H 1.44 . 1 114 . 20 GLY H H 7.97 . 1 115 . 20 GLY HA2 H 3.65 . 2 116 . 20 GLY HA3 H 4.35 . 2 117 . 21 ALA H H 6.93 . 1 118 . 21 ALA HA H 4.52 . 1 119 . 21 ALA HB H 1.21 . 1 120 . 22 PRO HA H 4.45 . 1 121 . 22 PRO HB2 H 2.00 . 2 122 . 22 PRO HB3 H 2.55 . 2 123 . 22 PRO HG2 H 2.12 . 1 124 . 22 PRO HG3 H 2.12 . 1 125 . 22 PRO HD2 H 3.50 . 2 126 . 22 PRO HD3 H 3.96 . 2 127 . 23 ARG H H 9.30 . 1 128 . 23 ARG HA H 3.88 . 1 129 . 23 ARG HB2 H 1.88 . 2 130 . 23 ARG HB3 H 1.98 . 2 131 . 23 ARG HG2 H 1.64 . 1 132 . 23 ARG HG3 H 1.64 . 1 133 . 23 ARG HD2 H 3.15 . 2 134 . 23 ARG HD3 H 3.27 . 2 135 . 23 ARG HE H 7.87 . 1 136 . 24 PRO HA H 4.37 . 1 137 . 24 PRO HB2 H 2.00 . 2 138 . 24 PRO HB3 H 2.40 . 2 139 . 24 PRO HG2 H 2.00 . 2 140 . 24 PRO HG3 H 2.14 . 2 141 . 24 PRO HD2 H 3.86 . 2 142 . 24 PRO HD3 H 3.96 . 2 143 . 25 THR H H 6.91 . 1 144 . 25 THR HA H 4.01 . 1 145 . 25 THR HB H 4.25 . 1 146 . 25 THR HG2 H 1.21 . 1 147 . 26 CYS H H 7.97 . 1 148 . 26 CYS HA H 4.72 . 1 149 . 26 CYS HB2 H 2.27 . 2 150 . 26 CYS HB3 H 2.73 . 2 151 . 27 ALA H H 9.61 . 1 152 . 27 ALA HA H 3.94 . 1 153 . 27 ALA HB H 1.51 . 1 154 . 28 LYS H H 7.67 . 1 155 . 28 LYS HA H 4.12 . 1 156 . 28 LYS HB2 H 2.03 . 1 157 . 28 LYS HB3 H 2.03 . 1 158 . 28 LYS HG2 H 1.52 . 2 159 . 28 LYS HG3 H 1.56 . 2 160 . 28 LYS HD2 H 1.74 . 1 161 . 28 LYS HD3 H 1.74 . 1 162 . 28 LYS HE2 H 3.02 . 9 163 . 28 LYS HE3 H 3.02 . 9 164 . 28 LYS HZ H 7.64 . 1 165 . 29 LEU H H 7.83 . 1 166 . 29 LEU HA H 4.20 . 1 167 . 29 LEU HB2 H 1.66 . 2 168 . 29 LEU HB3 H 1.73 . 2 169 . 29 LEU HG H 0.87 . 1 170 . 29 LEU HD1 H 0.87 . 2 171 . 29 LEU HD2 H 0.90 . 2 172 . 30 SER H H 7.63 . 1 173 . 30 SER HA H 4.32 . 1 174 . 30 SER HB2 H 3.75 . 2 175 . 30 SER HB3 H 4.80 . 2 176 . 30 SER HG H 5.82 . 1 177 . 31 GLY H H 8.03 . 1 178 . 31 GLY HA2 H 3.98 . 2 179 . 31 GLY HA3 H 4.39 . 2 180 . 32 CYS H H 8.09 . 1 181 . 32 CYS HA H 5.00 . 1 182 . 32 CYS HB2 H 2.40 . 2 183 . 32 CYS HB3 H 3.03 . 2 184 . 33 LYS H H 9.06 . 1 185 . 33 LYS HA H 4.53 . 1 186 . 33 LYS HB2 H 1.29 . 1 187 . 33 LYS HB3 H 1.29 . 1 188 . 33 LYS HG2 H 0.70 . 2 189 . 33 LYS HG3 H 1.04 . 2 190 . 33 LYS HD2 H 0.92 . 2 191 . 33 LYS HD3 H 1.12 . 2 192 . 33 LYS HE2 H 2.44 . 2 193 . 33 LYS HE3 H 2.51 . 2 194 . 33 LYS HZ H 7.49 . 1 195 . 34 ILE H H 8.63 . 1 196 . 34 ILE HA H 4.60 . 1 197 . 34 ILE HB H 1.89 . 1 198 . 34 ILE HG12 H 1.13 . 9 199 . 34 ILE HG13 H 1.3 . 9 200 . 34 ILE HG2 H 0.72 . 1 201 . 34 ILE HD1 H 0.65 . 1 202 . 35 ILE H H 8.82 . 1 203 . 35 ILE HA H 4.79 . 1 204 . 35 ILE HB H 2.03 . 1 205 . 35 ILE HG12 H 0.99 . 9 206 . 35 ILE HG13 H 1.29 . 9 207 . 35 ILE HG2 H 0.73 . 1 208 . 35 ILE HD1 H 0.58 . 1 209 . 36 SER H H 8.84 . 1 210 . 36 SER HA H 4.56 . 1 211 . 36 SER HB2 H 3.86 . 2 212 . 36 SER HB3 H 3.89 . 2 213 . 37 GLY H H 7.84 . 1 214 . 37 GLY HA2 H 4.05 . 2 215 . 37 GLY HA3 H 4.21 . 2 216 . 38 SER H H 8.40 . 1 217 . 38 SER HA H 4.54 . 1 218 . 38 SER HB2 H 3.89 . 2 219 . 38 SER HB3 H 3.92 . 2 220 . 39 THR H H 7.94 . 1 221 . 39 THR HA H 4.51 . 1 222 . 39 THR HB H 3.89 . 1 223 . 39 THR HG2 H 1.18 . 1 224 . 40 CYS H H 9.27 . 1 225 . 40 CYS HA H 4.80 . 1 226 . 40 CYS HB2 H 2.62 . 2 227 . 40 CYS HB3 H 3.69 . 2 228 . 41 PRO HA H 4.67 . 1 229 . 41 PRO HB2 H 2.33 . 2 230 . 41 PRO HB3 H 2.45 . 2 231 . 41 PRO HG2 H 2.04 . 2 232 . 41 PRO HG3 H 2.20 . 2 233 . 41 PRO HD2 H 3.64 . 2 234 . 41 PRO HD3 H 3.85 . 2 235 . 42 SER H H 8.97 . 1 236 . 42 SER HA H 4.05 . 1 237 . 42 SER HB2 H 3.93 . 1 238 . 42 SER HB3 H 3.93 . 1 239 . 43 ASP H H 8.65 . 1 240 . 43 ASP HA H 4.54 . 1 241 . 43 ASP HB2 H 2.77 . 2 242 . 43 ASP HB3 H 2.80 . 2 243 . 44 TYR H H 7.79 . 1 244 . 44 TYR HA H 4.38 . 1 245 . 44 TYR HB2 H 2.39 . 2 246 . 44 TYR HB3 H 2.46 . 2 247 . 45 PRO HA H 4.56 . 1 248 . 45 PRO HB2 H 2.07 . 1 249 . 45 PRO HB3 H 2.07 . 1 250 . 45 PRO HG2 H 1.67 . 2 251 . 45 PRO HG3 H 2.07 . 2 252 . 45 PRO HD2 H 3.41 . 1 253 . 45 PRO HD3 H 3.41 . 1 254 . 46 LYS H H 8.36 . 1 255 . 46 LYS HA H 4.36 . 1 256 . 46 LYS HB2 H 1.17 . 1 257 . 46 LYS HB3 H 1.17 . 1 258 . 46 LYS HG2 H 1.79 . 1 259 . 46 LYS HG3 H 1.79 . 1 260 . 46 LYS HD2 H 1.47 . 2 261 . 46 LYS HD3 H 1.61 . 2 262 . 46 LYS HE2 H 2.93 . 2 263 . 46 LYS HE3 H 3.00 . 2 264 . 46 LYS HZ H 7.67 . 1 stop_ save_