data_16235 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution structure of linear kalata B1 (loop 6) ; _BMRB_accession_number 16235 _BMRB_flat_file_name bmr16235.str _Entry_type new _Submission_date 2009-04-01 _Accession_date 2009-04-01 _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" 140 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-05-28 update BMRB 'edit entity/assembly name' 2010-01-12 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'The biological activity of the prototypic cyclotide kalata b1 is modulated by the formation of multimeric pores.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 19491108 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Huang Yen-Hua . . 2 Colgrave Michelle L. . 3 Daly Norelle L. . 4 Keleshian Asbed . . 5 Martinac Boris . . 6 Craik David J. . stop_ _Journal_abbreviation 'J. Biol. Chem.' _Journal_name_full 'The Journal of biological chemistry' _Journal_volume 284 _Journal_issue 31 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 20699 _Page_last 20707 _Year 2009 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'linear kalata B1' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'loop 6' $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 'loop 6' _Molecular_mass 2917.343 _Mol_thiol_state 'all disulfide bound' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 29 _Mol_residue_sequence ; GLPVCGETCVGGTCNTPGCT CSWPVCTRN ; loop_ _Residue_seq_code _Residue_label 1 GLY 2 LEU 3 PRO 4 VAL 5 CYS 6 GLY 7 GLU 8 THR 9 CYS 10 VAL 11 GLY 12 GLY 13 THR 14 CYS 15 ASN 16 THR 17 PRO 18 GLY 19 CYS 20 THR 21 CYS 22 SER 23 TRP 24 PRO 25 VAL 26 CYS 27 THR 28 ARG 29 ASN stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-07-08 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 BMRB 18506 Tg_Micronemal_Protein_5 75.86 29 100.00 100.00 7.40e-05 BMRB 18536 entity 75.86 29 100.00 100.00 7.40e-05 BMRB 19611 entity 86.21 33 100.00 100.00 5.33e-07 PDB 1JJZ "Refined Structure And Disulfide Pairing Of The Kalata B1 Peptide" 96.55 29 100.00 100.00 4.74e-09 PDB 1K48 "Refined Structure And Disulfide Pairing Of The Kalata B1 Peptide" 96.55 29 100.00 100.00 4.74e-09 PDB 1KAL "Elucidation Of The Primary And Three-Dimensional Structure Of The Uterotonic Polypeptide Kalata B1" 72.41 29 100.00 100.00 1.65e-03 PDB 1NB1 "High Resolution Solution Structure Of Kalata B1" 86.21 29 100.00 100.00 4.65e-07 PDB 1ORX "Solution Structure Of The Acyclic Permutant Des-(24-28)- Kalata B1" 79.31 24 100.00 100.00 2.75e-05 PDB 1ZNU "Structure Of Cyclotide Kalata B1 In Dpc Micelles Solution" 82.76 29 100.00 100.00 2.07e-06 PDB 2KHB "Solution Structure Of Linear Kalata B1 (Loop 6)" 100.00 29 100.00 100.00 7.00e-10 PDB 2LUR "Nmr Solution Structure Of Kb1[ghrw;23-28]" 75.86 29 100.00 100.00 7.40e-05 PDB 2MH1 "Enzymatic Cyclisation Of Kalata B1 Using Sortase A" 86.21 33 100.00 100.00 5.33e-07 PDB 4TTM "Racemic Structure Of Kalata B1 (kb1)" 100.00 29 100.00 100.00 7.00e-10 GB AAL05477 "kalata B1 precursor [Oldenlandia affinis]" 100.00 124 100.00 100.00 7.44e-12 GB ACI29319 "kalata B1 precursor protein, partial [Oldenlandia affinis]" 100.00 121 100.00 100.00 8.49e-12 GB ADJ17473 "cyclotide precursor Oak10, partial [Oldenlandia affinis]" 100.00 106 100.00 100.00 1.10e-11 PIR A56283 "kalata B1 [validated] - Oldenlandia affinis" 72.41 29 100.00 100.00 1.40e-03 SP P56254 "RecName: Full=Kalata-B1; Flags: Precursor" 100.00 124 100.00 100.00 7.44e-12 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 . . . . . . 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 '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 $entity 1 mM 'natural abundance' H20 90 % 'natural abundance' D20 10 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_CNS _Saveframe_category software _Name CNS _Version 1.2 loop_ _Vendor _Address _Electronic_address 'Brunger, Adams, Clore, Gros, Nilges and Read' . . stop_ loop_ _Task 'structure solution' refinement stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model ARX _Field_strength 500 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_TOCSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_2 _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 temperature 303 . K pH 5 . pH pressure 1.0 . atm 'ionic strength' 0 . M 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 . . . 1.000000000 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 TOCSY' 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 'loop 6' _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 8.500 . . 2 1 1 GLY HA2 H 3.790 . . 3 2 2 LEU H H 8.500 . . 4 2 2 LEU HA H 4.584 . . 5 2 2 LEU HB2 H 1.646 . . 6 2 2 LEU HB3 H 1.539 . . 7 2 2 LEU HD1 H 0.872 . . 8 2 2 LEU HD2 H 0.872 . . 9 2 2 LEU HG H 1.444 . . 10 3 3 PRO HA H 4.446 . . 11 3 3 PRO HB2 H 2.218 . . 12 3 3 PRO HB3 H 2.031 . . 13 3 3 PRO HD2 H 3.808 . . 14 3 3 PRO HD3 H 3.595 . . 15 3 3 PRO HG2 H 1.851 . . 16 3 3 PRO HG3 H 1.851 . . 17 4 4 VAL H H 8.124 . . 18 4 4 VAL HA H 4.111 . . 19 4 4 VAL HB H 2.116 . . 20 4 4 VAL HG1 H 0.914 . . 21 4 4 VAL HG2 H 0.914 . . 22 5 5 CYS H H 8.439 . . 23 5 5 CYS HA H 4.716 . . 24 5 5 CYS HB2 H 2.929 . . 25 5 5 CYS HB3 H 2.799 . . 26 6 6 GLY H H 8.104 . . 27 6 6 GLY HA2 H 3.985 . . 28 6 6 GLY HA3 H 3.747 . . 29 7 7 GLU H H 8.329 . . 30 7 7 GLU HA H 4.414 . . 31 7 7 GLU HB2 H 1.999 . . 32 7 7 GLU HB3 H 1.944 . . 33 7 7 GLU HG2 H 2.368 . . 34 7 7 GLU HG3 H 2.286 . . 35 8 8 THR H H 8.276 . . 36 8 8 THR HA H 4.490 . . 37 8 8 THR HB H 4.196 . . 38 8 8 THR HG2 H 1.168 . . 39 9 9 CYS H H 8.166 . . 40 9 9 CYS HA H 4.761 . . 41 9 9 CYS HB2 H 3.079 . . 42 9 9 CYS HB3 H 3.030 . . 43 10 10 VAL H H 8.397 . . 44 10 10 VAL HA H 3.946 . . 45 10 10 VAL HB H 1.978 . . 46 10 10 VAL HG1 H 0.926 . . 47 10 10 VAL HG2 H 0.926 . . 48 11 11 GLY H H 8.839 . . 49 11 11 GLY HA2 H 4.097 . . 50 11 11 GLY HA3 H 3.835 . . 51 12 12 GLY H H 8.304 . . 52 12 12 GLY HA2 H 4.321 . . 53 12 12 GLY HA3 H 3.970 . . 54 13 13 THR H H 7.758 . . 55 13 13 THR HA H 4.721 . . 56 13 13 THR HB H 4.091 . . 57 13 13 THR HG2 H 1.107 . . 58 14 14 CYS H H 8.579 . . 59 14 14 CYS HA H 4.710 . . 60 14 14 CYS HB2 H 3.190 . . 61 14 14 CYS HB3 H 2.732 . . 62 15 15 ASN H H 9.548 . . 63 15 15 ASN HA H 4.640 . . 64 15 15 ASN HB2 H 2.739 . . 65 15 15 ASN HB3 H 2.739 . . 66 15 15 ASN HD21 H 7.574 . . 67 15 15 ASN HD22 H 6.795 . . 68 16 16 THR H H 8.439 . . 69 16 16 THR HA H 4.436 . . 70 16 16 THR HB H 4.065 . . 71 16 16 THR HG2 H 1.211 . . 72 17 17 PRO HA H 4.255 . . 73 17 17 PRO HB2 H 2.277 . . 74 17 17 PRO HB3 H 2.082 . . 75 17 17 PRO HD2 H 4.094 . . 76 17 17 PRO HD3 H 3.650 . . 77 17 17 PRO HG2 H 1.946 . . 78 17 17 PRO HG3 H 1.838 . . 79 18 18 GLY H H 8.677 . . 80 18 18 GLY HA2 H 4.206 . . 81 18 18 GLY HA3 H 3.662 . . 82 19 19 CYS H H 7.625 . . 83 19 19 CYS HA H 5.274 . . 84 19 19 CYS HB2 H 3.129 . . 85 19 19 CYS HB3 H 2.662 . . 86 20 20 THR H H 9.486 . . 87 20 20 THR HA H 4.500 . . 88 20 20 THR HB H 3.938 . . 89 20 20 THR HG2 H 1.050 . . 90 21 21 CYS H H 8.867 . . 91 21 21 CYS HA H 4.509 . . 92 21 21 CYS HB2 H 3.078 . . 93 21 21 CYS HB3 H 2.811 . . 94 22 22 SER H H 8.963 . . 95 22 22 SER HA H 4.698 . . 96 22 22 SER HB2 H 3.790 . . 97 22 22 SER HB3 H 3.790 . . 98 23 23 TRP H H 8.136 . . 99 23 23 TRP HA H 4.069 . . 100 23 23 TRP HB2 H 3.233 . . 101 23 23 TRP HB3 H 3.233 . . 102 23 23 TRP HD1 H 7.224 . . 103 23 23 TRP HE1 H 10.288 . . 104 23 23 TRP HE3 H 7.414 . . 105 23 23 TRP HH2 H 7.206 . . 106 23 23 TRP HZ2 H 7.491 . . 107 23 23 TRP HZ3 H 7.110 . . 108 24 24 PRO HA H 3.345 . . 109 24 24 PRO HB2 H -0.092 . . 110 24 24 PRO HB3 H 1.673 . . 111 24 24 PRO HD2 H 3.237 . . 112 24 24 PRO HD3 H 3.184 . . 113 24 24 PRO HG2 H 1.398 . . 114 24 24 PRO HG3 H 1.305 . . 115 25 25 VAL H H 8.169 . . 116 25 25 VAL HA H 4.397 . . 117 25 25 VAL HB H 1.934 . . 118 25 25 VAL HG1 H 0.756 . . 119 25 25 VAL HG2 H 0.756 . . 120 26 26 CYS H H 8.291 . . 121 26 26 CYS HA H 5.064 . . 122 26 26 CYS HB2 H 3.295 . . 123 26 26 CYS HB3 H 2.642 . . 124 27 27 THR H H 9.668 . . 125 27 27 THR HA H 4.731 . . 126 27 27 THR HB H 4.106 . . 127 27 27 THR HG2 H 1.110 . . 128 28 28 ARG H H 8.416 . . 129 28 28 ARG HA H 4.661 . . 130 28 28 ARG HB2 H 1.841 . . 131 28 28 ARG HB3 H 1.841 . . 132 28 28 ARG HD2 H 3.173 . . 133 28 28 ARG HD3 H 3.173 . . 134 28 28 ARG HE H 7.162 . . 135 28 28 ARG HG2 H 1.656 . . 136 28 28 ARG HG3 H 1.656 . . 137 29 29 ASN H H 8.164 . . 138 29 29 ASN HA H 4.396 . . 139 29 29 ASN HB2 H 2.638 . . 140 29 29 ASN HB3 H 2.564 . . stop_ save_