data_4461 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; 1H NMR Solution Structure of Cycloviolacin O1 - A Macro-cyclic Polypeptide Isolated from Viola odorat ; _BMRB_accession_number 4461 _BMRB_flat_file_name bmr4461.str _Entry_type original _Submission_date 1999-11-17 _Accession_date 1999-11-17 _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 Craik David J. . 2 Daly Norelle L. . 3 Bond Trudy . . 4 Waine Clement . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 126 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2000-03-23 original BMRB . stop_ _Original_release_date 1999-11-21 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Plant Cyclotides - a unique family of cyclic and knotted proteins that defines the cyclic cystine knot structural moti ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code 20069951 _PubMed_ID 10600388 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Craik David J. . 2 Daly Norelle L. . 3 Bond Trudy . . 4 Waine Clement . . stop_ _Journal_abbreviation 'J. Mol. Biol.' _Journal_volume 294 _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 1327 _Page_last 1336 _Year 1999 _Details . save_ ################################## # Molecular system description # ################################## save_cck_system _Saveframe_category molecular_system _Mol_system_name 'Cycloviolacin O1' _Abbreviation_common cck _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label cck $cck 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_cck _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common cyclotide _Abbreviation_common cck _Molecular_mass 3116 _Mol_thiol_state 'all disulfide bound' _Details 'three disulfide bonds that form a knotted core and the backbone is cyclic via a covalent peptide bond' ############################## # Polymer residue sequence # ############################## _Residue_count 30 _Mol_residue_sequence ; SCVYIPCTVTALLGCSCSNR VCYNGIPCAE ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 4 SER 2 5 CYS 3 6 VAL 4 7 TYR 5 8 ILE 6 9 PRO 7 10 CYS 8 11 THR 9 12 VAL 10 13 THR 11 14 ALA 12 15 LEU 13 16 LEU 14 17 GLY 15 18 CYS 16 19 SER 17 20 CYS 18 21 SER 19 22 ASN 20 23 ARG 21 24 VAL 22 25 CYS 23 26 TYR 24 27 ASN 25 28 GLY 26 29 ILE 27 30 PRO 28 1 CYS 29 2 ALA 30 3 GLU 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 1DF6 '1h Nmr Solution Structure Of Cycloviolacin O1' 96.67 30 100.00 100.00 1.16e-07 PDB 1NBJ 'High-Resolution Solution Structure Of Cycloviolacin O1' 90.00 30 100.00 100.00 1.62e-06 SWISS-PROT P82230 Cycloviolacin-O1 80.00 30 100.00 100.00 1.89e-04 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $cck Viola 97441 Eukaryota . Violaceae 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 $cck 'purified from the natural source' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_ss1559 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $cck 1.6 mM . stop_ save_ ############################ # Computer software used # ############################ save_PROCHECK-NMR _Saveframe_category software _Name ProcheckNMR _Version . loop_ _Task 'Ramachandran plot' stop_ _Details . save_ save_X-PLOR _Saveframe_category software _Name X-PLOR _Version . loop_ _Task 'Structure Calculations and energy minimizations' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_one _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AMX _Field_strength 500 _Details . save_ save_NMR_spectrometer_two _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DMX _Field_strength 750 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_TOCSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label . save_ save_2D_1H-1H_NOESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label . save_ save_2D_1H-1H_E-COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H E-COSY' _Sample_label . save_ save_2D_1H-1H_DQF-COSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H DQF-COSY' _Sample_label . save_ ####################### # Sample conditions # ####################### save_ss1559-cond_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 3.6 0.3 na temperature 298 2 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 DSS H 1 'methyl protons' ppm 0.0 internal direct . . . 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_shift1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H TOCSY' stop_ loop_ _Sample_label $ss1559 stop_ _Sample_conditions_label $ss1559-cond_1 _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name cck _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 SER H H 8.91 0.01 1 2 . 1 SER HA H 4.69 0.01 1 3 . 1 SER HB2 H 3.88 0.01 2 4 . 1 SER HB3 H 4.01 0.01 2 5 . 2 CYS H H 8.24 0.01 1 6 . 2 CYS HA H 5.35 0.01 1 7 . 2 CYS HB2 H 3.13 0.01 2 8 . 2 CYS HB3 H 3.27 0.01 2 9 . 3 VAL H H 7.94 0.01 1 10 . 3 VAL HA H 3.43 0.01 1 11 . 3 VAL HB H 1.44 0.01 1 12 . 3 VAL HG1 H 0.30 0.01 2 13 . 3 VAL HG2 H 0.93 0.01 2 14 . 4 TYR H H 8.20 0.01 1 15 . 4 TYR HA H 4.61 0.01 1 16 . 4 TYR HB2 H 2.89 0.01 2 17 . 4 TYR HB3 H 3.19 0.01 2 18 . 5 ILE H H 7.58 0.01 1 19 . 5 ILE HA H 4.67 0.01 1 20 . 5 ILE HB H 1.90 0.01 1 21 . 5 ILE HG12 H 1.50 0.01 2 22 . 5 ILE HG13 H 1.01 0.01 2 23 . 6 PRO HA H 4.44 0.01 1 24 . 6 PRO HB2 H 2.31 0.01 2 25 . 6 PRO HG2 H 1.87 0.01 2 26 . 6 PRO HD2 H 3.51 0.01 2 27 . 6 PRO HD3 H 3.69 0.01 2 28 . 7 CYS H H 8.33 0.01 1 29 . 7 CYS HA H 4.05 0.01 1 30 . 7 CYS HB2 H 2.70 0.01 2 31 . 7 CYS HB3 H 2.87 0.01 2 32 . 8 THR H H 8.73 0.01 1 33 . 8 THR HA H 4.11 0.01 1 34 . 8 THR HG2 H 1.19 0.01 1 35 . 9 VAL H H 8.84 0.01 1 36 . 9 VAL HA H 3.95 0.01 1 37 . 9 VAL HB H 2.00 0.01 1 38 . 9 VAL HG1 H 0.93 0.01 2 39 . 9 VAL HG2 H 1.00 0.01 2 40 . 10 THR H H 8.54 0.01 1 41 . 10 THR HA H 4.27 0.01 1 42 . 10 THR HB H 4.83 0.01 1 43 . 10 THR HG2 H 1.13 0.01 1 44 . 11 ALA H H 7.99 0.01 1 45 . 11 ALA HA H 4.40 0.01 1 46 . 11 ALA HB H 1.41 0.01 1 47 . 12 LEU H H 7.95 0.01 1 48 . 12 LEU HA H 4.18 0.01 1 49 . 12 LEU HB2 H 1.72 0.01 2 50 . 12 LEU HG H 1.59 0.01 1 51 . 12 LEU HD1 H 0.88 0.01 2 52 . 13 LEU H H 7.52 0.01 1 53 . 13 LEU HA H 4.40 0.01 1 54 . 13 LEU HB2 H 1.75 0.01 2 55 . 13 LEU HB3 H 1.86 0.01 2 56 . 13 LEU HG H 1.56 0.01 1 57 . 13 LEU HD1 H 0.83 0.01 2 58 . 13 LEU HD2 H 0.91 0.01 2 59 . 14 GLY H H 8.19 0.01 1 60 . 14 GLY HA2 H 3.76 0.01 2 61 . 14 GLY HA3 H 4.13 0.01 2 62 . 15 CYS H H 7.69 0.01 1 63 . 15 CYS HA H 4.69 0.01 1 64 . 15 CYS HB2 H 2.49 0.01 2 65 . 15 CYS HB3 H 3.52 0.01 2 66 . 16 SER H H 9.09 0.01 1 67 . 16 SER HA H 4.63 0.01 1 68 . 16 SER HB2 H 3.80 0.01 2 69 . 17 CYS H H 8.77 0.01 1 70 . 17 CYS HA H 4.54 0.01 1 71 . 17 CYS HB2 H 3.00 0.01 2 72 . 18 SER H H 9.47 0.01 1 73 . 18 SER HA H 4.57 0.01 1 74 . 18 SER HB2 H 3.60 0.01 2 75 . 19 ASN H H 9.38 0.01 1 76 . 19 ASN HA H 4.20 0.01 1 77 . 19 ASN HB2 H 2.61 0.01 2 78 . 19 ASN HB3 H 2.93 0.01 2 79 . 20 ARG H H 8.25 0.01 1 80 . 20 ARG HA H 3.44 0.01 1 81 . 20 ARG HB2 H 2.27 0.01 2 82 . 20 ARG HB3 H 1.89 0.01 2 83 . 20 ARG HG2 H 1.49 0.01 2 84 . 21 VAL H H 8.12 0.01 1 85 . 21 VAL HA H 4.35 0.01 1 86 . 21 VAL HB H 2.09 0.01 1 87 . 21 VAL HG1 H 0.91 0.01 2 88 . 21 VAL HG2 H 0.99 0.01 2 89 . 22 CYS H H 8.21 0.01 1 90 . 22 CYS HA H 4.74 0.01 1 91 . 22 CYS HB2 H 2.69 0.01 2 92 . 22 CYS HB3 H 2.97 0.01 2 93 . 23 TYR H H 9.86 0.01 1 94 . 23 TYR HA H 5.02 0.01 1 95 . 23 TYR HB2 H 2.91 0.01 2 96 . 23 TYR HB3 H 2.99 0.01 2 97 . 24 ASN H H 8.66 0.01 1 98 . 24 ASN HA H 4.78 0.01 1 99 . 24 ASN HB2 H 2.71 0.01 2 100 . 24 ASN HB3 H 2.93 0.01 2 101 . 25 GLY H H 7.77 0.01 1 102 . 25 GLY HA2 H 3.33 0.01 2 103 . 25 GLY HA3 H 4.46 0.01 2 104 . 26 ILE H H 7.74 0.01 1 105 . 26 ILE HA H 4.53 0.01 1 106 . 26 ILE HB H 1.94 0.01 1 107 . 26 ILE HG12 H 0.97 0.01 2 108 . 27 PRO HA H 4.19 0.01 1 109 . 27 PRO HB2 H 2.16 0.01 2 110 . 27 PRO HB3 H 2.23 0.01 2 111 . 27 PRO HG2 H 1.78 0.01 2 112 . 27 PRO HG3 H 1.94 0.01 2 113 . 27 PRO HD2 H 3.64 0.01 2 114 . 27 PRO HD3 H 3.84 0.01 2 115 . 28 CYS H H 9.08 0.01 1 116 . 28 CYS HB2 H 3.06 0.01 2 117 . 28 CYS HB3 H 3.17 0.01 2 118 . 29 ALA H H 8.51 0.01 1 119 . 29 ALA HA H 4.14 0.01 1 120 . 29 ALA HB H 1.29 0.01 1 121 . 30 GLU H H 7.91 0.01 1 122 . 30 GLU HA H 4.38 0.01 1 123 . 30 GLU HB2 H 1.61 0.01 2 124 . 30 GLU HB3 H 1.91 0.01 2 125 . 30 GLU HG2 H 2.55 0.01 2 126 . 30 GLU HG3 H 2.76 0.01 2 stop_ save_