data_6596 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR solution structure of a leaf-specific-expressed cyclotide vhl-1 ; _BMRB_accession_number 6596 _BMRB_flat_file_name bmr6596.str _Entry_type original _Submission_date 2005-04-14 _Accession_date 2005-04-28 _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 Chen B. . . 2 Colgrave M. L. . 3 Daly N. L. . 4 Rosengren K. J. . 5 Gustafson K. R. . 6 Craik D. J. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 172 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2005-08-22 original BMRB . stop_ _Original_release_date 2005-04-28 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Isolation and characterisation of novel cyclotides from Viola hederaceae: solution structure and anti-HIV activity of vhl-1, a leaf-specific-expressed cyclotide ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 15824119 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Chen B. . . 2 Colgrave M. L. . 3 Daly N. L. . 4 Rosengren K. J. . 5 Gustafson K. R. . 6 Craik D. J. . stop_ _Journal_abbreviation 'J. Biol. Chem.' _Journal_volume 280 _Journal_issue 23 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 22395 _Page_last 22405 _Year 2005 _Details . loop_ _Keyword 'circular protein' 'cyclic cystine knot motif' stop_ save_ ################################## # Molecular system description # ################################## save_system_vhl-1 _Saveframe_category molecular_system _Mol_system_name vhl-1 _Abbreviation_common vhl-1 _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label vhl-1 $vhl-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_vhl-1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common vhl-1 _Abbreviation_common vhl-1 _Molecular_mass . _Mol_thiol_state 'all disulfide bound' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 31 _Mol_residue_sequence ; CGESCAMISFCFTEVIGCSC KNKVCYLNSIS ; loop_ _Residue_seq_code _Residue_label 1 CYS 2 GLY 3 GLU 4 SER 5 CYS 6 ALA 7 MET 8 ILE 9 SER 10 PHE 11 CYS 12 PHE 13 THR 14 GLU 15 VAL 16 ILE 17 GLY 18 CYS 19 SER 20 CYS 21 LYS 22 ASN 23 LYS 24 VAL 25 CYS 26 TYR 27 LEU 28 ASN 29 SER 30 ILE 31 SER 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 1ZA8 'Nmr Solution Structure Of A Leaf-Specific-Expressed Cyclotide Vhl-1' 100.00 31 100.00 100.00 2.04e-08 SWISS-PROT P84522 'Leaf cyclotide 1 (Vhl-1)' 90.32 31 100.00 100.00 3.52e-07 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $vhl-1 'Australian violet' 180952 Eukaryota Viridiplantae Viola hederacea 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 $vhl-1 . . . . . . 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 $vhl-1 1.4 mM . H2O 70 % . CD3CN 25 % . D2O 5 % . stop_ save_ ############################ # Computer software used # ############################ save_XWINNMR _Saveframe_category software _Name xwinnmr _Version 3.5 loop_ _Task collection stop_ _Details Bruker save_ save_Sparky _Saveframe_category software _Name SPARKY _Version 3.110 loop_ _Task 'data analysis' stop_ _Details 'Goddard, T. D. and Kneller, D. G.' save_ save_DYANA _Saveframe_category software _Name DYANA _Version 1.5 loop_ _Task 'iterative matrix relaxation' stop_ _Details 'Guntert, P., Mumenthaler, C and Wuthrich, K.' save_ save_CNS _Saveframe_category software _Name CNS _Version 1.1 loop_ _Task refinement stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AVANCE _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _Sample_label $sample_1 save_ save_2D_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D TOCSY' _Sample_label $sample_1 save_ save_DQF-COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name DQF-COSY _Sample_label $sample_1 save_ save_E-COSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name E-COSY _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 'ionic strength' 0 . M pH 3.3 . pH pressure 1 . atm temperature 298 . 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 . . . . . 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' '2D TOCSY' DQF-COSY E-COSY 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 vhl-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 CYS H H 8.943 0.004 1 2 . 1 CYS HA H 4.576 0.001 1 3 . 1 CYS HB2 H 3.058 0.008 1 4 . 1 CYS HB3 H 3.120 0.008 1 5 . 2 GLY H H 8.488 0.002 1 6 . 2 GLY HA2 H 3.786 0.004 1 7 . 2 GLY HA3 H 3.454 0.003 1 8 . 3 GLU H H 6.740 0.002 1 9 . 3 GLU HA H 4.461 0.001 1 10 . 3 GLU HB2 H 1.374 0.005 1 11 . 3 GLU HB3 H 1.680 0.003 1 12 . 3 GLU HG2 H 2.484 0.005 1 13 . 3 GLU HG3 H 2.484 0.005 1 14 . 4 SER H H 8.786 0.003 1 15 . 4 SER HA H 4.527 0.006 1 16 . 4 SER HB2 H 3.943 0.001 1 17 . 4 SER HB3 H 3.842 0.007 1 18 . 5 CYS H H 8.236 0.002 1 19 . 5 CYS HA H 5.150 0.002 1 20 . 5 CYS HB2 H 3.225 0.009 1 21 . 5 CYS HB3 H 3.308 0.011 1 22 . 6 ALA H H 7.928 0.002 1 23 . 6 ALA HA H 3.961 0.002 1 24 . 6 ALA HB H 1.428 0.002 1 25 . 7 MET H H 8.357 0.001 1 26 . 7 MET HA H 4.400 0.002 1 27 . 7 MET HB2 H 2.235 0.007 1 28 . 7 MET HB3 H 2.160 0.002 1 29 . 7 MET HG2 H 2.817 0.004 1 30 . 7 MET HG3 H 2.817 0.004 1 31 . 8 ILE H H 7.773 0.003 1 32 . 8 ILE HA H 4.291 0.002 1 33 . 8 ILE HB H 1.820 0.003 1 34 . 8 ILE HG12 H 1.050 0.003 1 35 . 8 ILE HG13 H 1.417 0.002 1 36 . 8 ILE HG2 H 0.864 0.002 1 37 . 8 ILE HD1 H 0.788 0.005 1 38 . 9 SER H H 8.235 0.003 1 39 . 9 SER HA H 4.640 0.002 1 40 . 9 SER HB2 H 3.814 0.006 1 41 . 9 SER HB3 H 3.865 0.004 1 42 . 10 PHE H H 7.829 0.003 1 43 . 10 PHE HA H 4.403 0.005 1 44 . 10 PHE HB2 H 2.447 0.008 1 45 . 10 PHE HB3 H 2.857 0.005 1 46 . 10 PHE HD1 H 6.802 0.003 1 47 . 10 PHE HD2 H 6.802 0.003 1 48 . 10 PHE HE1 H 6.610 0.001 1 49 . 10 PHE HE2 H 6.610 0.001 1 50 . 10 PHE HZ H 6.951 0.001 1 51 . 11 CYS H H 7.482 0.004 1 52 . 11 CYS HA H 4.489 0.003 1 53 . 11 CYS HB2 H 2.337 0.010 1 54 . 11 CYS HB3 H 2.735 0.003 1 55 . 12 PHE H H 10.931 0.005 1 56 . 12 PHE HA H 4.182 0.005 1 57 . 12 PHE HB2 H 3.102 0.003 1 58 . 12 PHE HB3 H 3.102 0.003 1 59 . 12 PHE HD1 H 7.442 0.003 1 60 . 12 PHE HD2 H 7.442 0.003 1 61 . 12 PHE HE1 H 7.367 0.014 1 62 . 12 PHE HE2 H 7.367 0.014 1 63 . 12 PHE HZ H 7.265 0.003 1 64 . 13 THR H H 9.174 0.001 1 65 . 13 THR HA H 3.953 0.001 1 66 . 13 THR HB H 4.536 0.000 1 67 . 13 THR HG1 H 4.796 0.001 1 68 . 13 THR HG2 H 1.271 0.004 1 69 . 14 GLU H H 8.023 0.001 1 70 . 14 GLU HA H 4.686 0.002 1 71 . 14 GLU HB2 H 2.066 0.002 1 72 . 14 GLU HB3 H 2.066 0.002 1 73 . 14 GLU HG2 H 2.295 0.002 1 74 . 14 GLU HG3 H 2.572 0.003 1 75 . 15 VAL H H 7.220 0.002 1 76 . 15 VAL HA H 3.971 0.004 1 77 . 15 VAL HB H 2.188 0.002 1 78 . 15 VAL HG1 H 1.018 0.003 1 79 . 15 VAL HG2 H 1.018 0.003 1 80 . 16 ILE H H 7.185 0.003 1 81 . 16 ILE HA H 4.518 0.002 1 82 . 16 ILE HB H 2.187 0.003 1 83 . 16 ILE HG12 H 1.561 0.006 1 84 . 16 ILE HG13 H 1.561 0.006 1 85 . 16 ILE HG2 H 0.974 0.005 1 86 . 16 ILE HD1 H 0.855 0.003 1 87 . 17 GLY H H 7.629 0.002 1 88 . 17 GLY HA2 H 4.280 0.019 1 89 . 17 GLY HA3 H 3.566 0.004 1 90 . 18 CYS H H 7.498 0.003 1 91 . 18 CYS HA H 4.691 0.002 1 92 . 18 CYS HB2 H 3.278 0.002 1 93 . 18 CYS HB3 H 2.189 0.002 1 94 . 19 SER H H 9.004 0.002 1 95 . 19 SER HA H 4.485 0.001 1 96 . 19 SER HB2 H 3.699 0.007 1 97 . 19 SER HB3 H 3.699 0.007 1 98 . 20 CYS H H 8.608 0.005 1 99 . 20 CYS HA H 4.415 0.006 1 100 . 20 CYS HB2 H 2.710 0.004 1 101 . 20 CYS HB3 H 2.880 0.003 1 102 . 21 LYS H H 9.533 0.002 1 103 . 21 LYS HA H 4.480 0.003 1 104 . 21 LYS HB2 H 1.702 0.018 1 105 . 21 LYS HB3 H 1.766 0.008 1 106 . 21 LYS HG2 H 1.220 0.003 1 107 . 21 LYS HG3 H 1.341 0.011 1 108 . 21 LYS HD2 H 1.455 0.007 1 109 . 21 LYS HD3 H 1.455 0.007 1 110 . 21 LYS HE2 H 2.751 0.000 1 111 . 21 LYS HE3 H 2.751 0.000 1 112 . 22 ASN H H 9.043 0.002 1 113 . 22 ASN HA H 4.204 0.004 1 114 . 22 ASN HB2 H 2.885 0.107 1 115 . 22 ASN HB3 H 2.671 0.005 1 116 . 22 ASN HD21 H 6.731 0.000 1 117 . 22 ASN HD22 H 7.344 0.002 1 118 . 23 LYS H H 8.118 0.003 1 119 . 23 LYS HA H 3.392 0.001 1 120 . 23 LYS HB2 H 1.760 0.006 1 121 . 23 LYS HB3 H 2.252 0.003 1 122 . 23 LYS HG2 H 1.255 0.009 1 123 . 23 LYS HG3 H 1.255 0.009 1 124 . 23 LYS HD2 H 1.604 0.005 1 125 . 23 LYS HD3 H 1.604 0.005 1 126 . 23 LYS HE2 H 2.941 0.004 1 127 . 23 LYS HE3 H 2.941 0.004 1 128 . 24 VAL H H 7.935 0.003 1 129 . 24 VAL HA H 4.164 0.006 1 130 . 24 VAL HB H 1.884 0.002 1 131 . 24 VAL HG1 H 0.865 0.003 1 132 . 24 VAL HG2 H 0.412 0.001 1 133 . 25 CYS H H 7.890 0.001 1 134 . 25 CYS HA H 4.710 0.009 1 135 . 25 CYS HB2 H 2.441 0.005 1 136 . 25 CYS HB3 H 2.913 0.007 1 137 . 26 TYR H H 9.264 0.002 1 138 . 26 TYR HA H 5.071 0.001 1 139 . 26 TYR HB2 H 2.609 0.005 1 140 . 26 TYR HB3 H 2.842 0.004 1 141 . 26 TYR HD1 H 6.842 0.001 1 142 . 26 TYR HD2 H 6.842 0.001 1 143 . 26 TYR HE1 H 6.777 0.003 1 144 . 26 TYR HE2 H 6.777 0.003 1 145 . 27 LEU H H 9.113 0.002 1 146 . 27 LEU HA H 4.505 0.004 1 147 . 27 LEU HB2 H 1.735 0.002 1 148 . 27 LEU HB3 H 1.473 0.009 1 149 . 27 LEU HG H 1.412 0.000 1 150 . 27 LEU HD1 H 0.818 0.003 1 151 . 27 LEU HD2 H 0.818 0.003 1 152 . 28 ASN H H 9.251 0.006 1 153 . 28 ASN HA H 4.105 0.006 1 154 . 28 ASN HB2 H 2.969 0.012 1 155 . 28 ASN HB3 H 2.905 0.015 1 156 . 28 ASN HD21 H 6.864 0.002 1 157 . 28 ASN HD22 H 7.439 0.005 1 158 . 29 SER H H 8.141 0.003 1 159 . 29 SER HA H 4.056 0.001 1 160 . 29 SER HB2 H 3.994 0.004 1 161 . 29 SER HB3 H 3.822 0.003 1 162 . 30 ILE H H 8.191 0.003 1 163 . 30 ILE HA H 4.243 0.007 1 164 . 30 ILE HB H 2.052 0.002 1 165 . 30 ILE HG12 H 1.174 0.004 1 166 . 30 ILE HG13 H 1.544 0.003 1 167 . 30 ILE HG2 H 0.907 0.002 1 168 . 30 ILE HD1 H 0.814 0.002 1 169 . 31 SER H H 8.619 0.004 1 170 . 31 SER HA H 3.683 0.006 1 171 . 31 SER HB2 H 3.630 0.012 1 172 . 31 SER HB3 H 3.630 0.012 1 stop_ save_