data_16073 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution structure of cycloviolacin O2 ; _BMRB_accession_number 16073 _BMRB_flat_file_name bmr16073.str _Entry_type original _Submission_date 2008-12-21 _Accession_date 2008-12-21 _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 Wang Conan K. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 155 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-05-27 update BMRB 'edit entity/assembly name' 2009-09-04 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_citations _Saveframe_category entry_citation _Citation_full . _Citation_title 'Despite a conserved cystine knot motif, different cyclotides have different membrane binding modes' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 19720036 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Wang Conan K. . 2 Colgrave Michelle L. . 3 Ireland David C. . 4 Kaas Quentin . . 5 Craik David J. . stop_ _Journal_abbreviation 'Biophys. J.' _Journal_volume 97 _Journal_issue 5 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 1471 _Page_last 1481 _Year 2009 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'cycloviolacin O2' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'cycloviolacin O2' $entity 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_entity _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common 'cycloviolacin O2' _Molecular_mass . _Mol_thiol_state 'all disulfide bound' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 30 _Mol_residue_sequence ; GIPCGESCVWIPCISSAIGC SCKSKVCYRN ; loop_ _Residue_seq_code _Residue_label 1 GLY 2 ILE 3 PRO 4 CYS 5 GLY 6 GLU 7 SER 8 CYS 9 VAL 10 TRP 11 ILE 12 PRO 13 CYS 14 ILE 15 SER 16 SER 17 ALA 18 ILE 19 GLY 20 CYS 21 SER 22 CYS 23 LYS 24 SER 25 LYS 26 VAL 27 CYS 28 TYR 29 ARG 30 ASN stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-09-30 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 2KCG "Solution Structure Of Cycloviolacin O2" 100.00 30 100.00 100.00 1.01e-10 PDB 2KNM "Solution Structure Of The Cyclotide Cycloviolacin O2" 100.00 30 100.00 100.00 1.01e-10 GB AGI97139 "cyclotide B, partial [Viola odorata]" 96.67 79 100.00 100.00 6.50e-11 GB AGI97141 "cyclotide B, partial [Viola odorata]" 96.67 79 100.00 100.00 6.50e-11 SP P58434 "RecName: Full=Cycloviolacin-O2" 100.00 30 100.00 100.00 1.01e-10 SP P85526 "RecName: Full=Cycloviolacin-O2" 100.00 30 100.00 100.00 1.01e-10 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $entity 'Viola odorata' 97441 Eukaryota Viridiplantae Viola odorata 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 $entity '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 _Isotopic_labeling $entity 2 mM 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_CNS _Saveframe_category software _Name CNS _Version . loop_ _Vendor _Address _Electronic_address 'Brunger A. T. et.al.' . . stop_ loop_ _Task refinement stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DMX _Field_strength 750 _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_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 5 . pH pressure 1 . atm temperature 303 . 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 4.7 internal direct . . . 1 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 NOESY' 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 'cycloviolacin O2' _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 H H 8.531 0.000 . 2 1 1 GLY HA2 H 4.138 0.000 . 3 1 1 GLY HA3 H 3.455 0.000 . 4 2 2 ILE H H 8.038 0.000 . 5 2 2 ILE HA H 4.766 0.000 . 6 2 2 ILE HB H 2.148 0.000 . 7 2 2 ILE HD1 H 0.876 0.000 . 8 2 2 ILE HG12 H 1.542 0.000 . 9 2 2 ILE HG13 H 1.280 0.000 . 10 2 2 ILE HG2 H 1.004 0.000 . 11 3 3 PRO HA H 4.128 0.000 . 12 3 3 PRO HB2 H 2.150 0.000 . 13 3 3 PRO HB3 H 2.117 0.000 . 14 3 3 PRO HD2 H 4.059 0.000 . 15 3 3 PRO HD3 H 3.831 0.000 . 16 3 3 PRO HG2 H 1.951 0.000 . 17 3 3 PRO HG3 H 1.840 0.000 . 18 4 4 CYS H H 8.441 0.000 . 19 4 4 CYS HA H 4.541 0.000 . 20 4 4 CYS HB2 H 3.169 0.000 . 21 4 4 CYS HB3 H 3.046 0.000 . 22 5 5 GLY H H 8.861 0.000 . 23 5 5 GLY HA2 H 4.035 0.000 . 24 5 5 GLY HA3 H 3.645 0.000 . 25 6 6 GLU H H 7.629 0.000 . 26 6 6 GLU HA H 4.563 0.000 . 27 6 6 GLU HB2 H 1.832 0.000 . 28 6 6 GLU HB3 H 1.690 0.000 . 29 6 6 GLU HG2 H 2.381 0.000 . 30 6 6 GLU HG3 H 2.238 0.000 . 31 7 7 SER H H 8.775 0.000 . 32 7 7 SER HA H 4.689 0.000 . 33 7 7 SER HB2 H 3.974 0.000 . 34 7 7 SER HB3 H 3.900 0.000 . 35 8 8 CYS H H 8.006 0.000 . 36 8 8 CYS HA H 5.324 0.000 . 37 8 8 CYS HB2 H 3.232 0.000 . 38 8 8 CYS HB3 H 3.133 0.000 . 39 9 9 VAL H H 7.917 0.000 . 40 9 9 VAL HA H 3.376 0.000 . 41 9 9 VAL HB H 1.594 0.000 . 42 9 9 VAL HG1 H 0.871 0.000 . 43 9 9 VAL HG2 H 0.097 0.000 . 44 10 10 TRP H H 8.181 0.000 . 45 10 10 TRP HA H 4.835 0.000 . 46 10 10 TRP HB2 H 3.443 0.000 . 47 10 10 TRP HB3 H 3.106 0.000 . 48 10 10 TRP HD1 H 7.200 0.000 . 49 10 10 TRP HE1 H 10.085 0.000 . 50 10 10 TRP HE3 H 7.695 0.000 . 51 10 10 TRP HZ2 H 7.451 0.000 . 52 11 11 ILE H H 7.502 0.000 . 53 11 11 ILE HA H 4.715 0.000 . 54 11 11 ILE HB H 1.926 0.000 . 55 11 11 ILE HD1 H 0.874 0.000 . 56 11 11 ILE HG2 H 0.975 0.000 . 57 12 12 PRO HA H 4.376 0.000 . 58 12 12 PRO HB2 H 2.360 0.000 . 59 12 12 PRO HB3 H 1.785 0.000 . 60 12 12 PRO HD2 H 3.732 0.000 . 61 12 12 PRO HG2 H 1.955 0.000 . 62 12 12 PRO HG3 H 1.892 0.000 . 63 13 13 CYS H H 8.302 0.000 . 64 13 13 CYS HA H 4.230 0.000 . 65 13 13 CYS HB2 H 3.000 0.000 . 66 13 13 CYS HB3 H 2.653 0.000 . 67 14 14 ILE H H 9.342 0.000 . 68 14 14 ILE HA H 4.223 0.000 . 69 15 15 SER H H 9.647 0.000 . 70 15 15 SER HA H 4.401 0.000 . 71 15 15 SER HB2 H 4.180 0.000 . 72 15 15 SER HB3 H 3.942 0.000 . 73 16 16 SER H H 7.753 0.000 . 74 16 16 SER HA H 4.651 0.000 . 75 16 16 SER HB2 H 3.932 0.000 . 76 16 16 SER HB3 H 3.932 0.000 . 77 17 17 ALA H H 8.329 0.000 . 78 17 17 ALA HA H 4.278 0.000 . 79 17 17 ALA HB H 1.443 0.000 . 80 18 18 ILE H H 7.275 0.000 . 81 18 18 ILE HA H 4.421 0.000 . 82 18 18 ILE HB H 2.106 0.000 . 83 18 18 ILE HD1 H 1.151 0.000 . 84 18 18 ILE HG12 H 1.427 0.000 . 85 18 18 ILE HG13 H 1.427 0.000 . 86 18 18 ILE HG2 H 0.878 0.000 . 87 19 19 GLY H H 7.870 0.000 . 88 19 19 GLY HA2 H 4.310 0.000 . 89 19 19 GLY HA3 H 3.742 0.000 . 90 20 20 CYS H H 7.618 0.000 . 91 20 20 CYS HA H 4.797 0.000 . 92 20 20 CYS HB2 H 3.195 0.000 . 93 20 20 CYS HB3 H 2.452 0.000 . 94 21 21 SER H H 9.389 0.000 . 95 21 21 SER HA H 4.710 0.000 . 96 21 21 SER HB2 H 3.832 0.000 . 97 21 21 SER HB3 H 3.832 0.000 . 98 22 22 CYS H H 8.752 0.000 . 99 22 22 CYS HA H 4.645 0.000 . 100 22 22 CYS HB2 H 3.081 0.000 . 101 22 22 CYS HB3 H 3.081 0.000 . 102 23 23 LYS H H 9.574 0.000 . 103 23 23 LYS HA H 4.604 0.000 . 104 23 23 LYS HB2 H 1.861 0.000 . 105 23 23 LYS HB3 H 1.861 0.000 . 106 23 23 LYS HD2 H 1.501 0.000 . 107 23 23 LYS HD3 H 1.440 0.000 . 108 23 23 LYS HE2 H 2.790 0.000 . 109 23 23 LYS HE3 H 2.790 0.000 . 110 23 23 LYS HG2 H 1.282 0.000 . 111 23 23 LYS HG3 H 1.282 0.000 . 112 23 23 LYS HZ H 7.342 0.000 . 113 24 24 SER H H 9.233 0.000 . 114 24 24 SER HA H 4.714 0.000 . 115 24 24 SER HB2 H 4.070 0.000 . 116 24 24 SER HB3 H 3.844 0.000 . 117 25 25 LYS H H 8.111 0.000 . 118 25 25 LYS HA H 3.501 0.000 . 119 25 25 LYS HB2 H 2.228 0.000 . 120 25 25 LYS HB3 H 1.865 0.000 . 121 25 25 LYS HD2 H 1.589 0.000 . 122 25 25 LYS HD3 H 1.535 0.000 . 123 25 25 LYS HE2 H 2.879 0.000 . 124 25 25 LYS HE3 H 2.879 0.000 . 125 25 25 LYS HG2 H 1.235 0.000 . 126 25 25 LYS HG3 H 1.235 0.000 . 127 25 25 LYS HZ H 7.433 0.000 . 128 26 26 VAL H H 7.957 0.000 . 129 26 26 VAL HA H 4.191 0.000 . 130 26 26 VAL HB H 1.996 0.000 . 131 26 26 VAL HG1 H 0.923 0.000 . 132 26 26 VAL HG2 H 0.518 0.000 . 133 27 27 CYS H H 7.700 0.000 . 134 27 27 CYS HA H 5.068 0.000 . 135 27 27 CYS HB2 H 3.073 0.000 . 136 27 27 CYS HB3 H 2.625 0.000 . 137 28 28 TYR H H 9.577 0.000 . 138 28 28 TYR HA H 5.110 0.000 . 139 28 28 TYR HB2 H 2.780 0.000 . 140 28 28 TYR HB3 H 2.645 0.000 . 141 28 28 TYR HD1 H 6.869 0.000 . 142 28 28 TYR HD2 H 6.769 0.000 . 143 29 29 ARG H H 9.293 0.000 . 144 29 29 ARG HA H 4.712 0.000 . 145 29 29 ARG HB2 H 1.824 0.000 . 146 29 29 ARG HB3 H 1.725 0.000 . 147 29 29 ARG HD2 H 3.206 0.000 . 148 29 29 ARG HD3 H 3.115 0.000 . 149 29 29 ARG HE H 7.133 0.000 . 150 29 29 ARG HG2 H 1.609 0.000 . 151 29 29 ARG HG3 H 1.418 0.000 . 152 30 30 ASN H H 9.524 0.000 . 153 30 30 ASN HA H 4.338 0.000 . 154 30 30 ASN HB2 H 3.067 0.000 . 155 30 30 ASN HB3 H 2.802 0.000 . stop_ save_