data_20014 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; STRUCTURE OF ANTIBACTERIAL PEPTIDE CAPISTRUIN: A 19-RESIDUE LARIAT PROTOKNOT WITH A THREADED 9-MEMBER SIDECHAIN TO-BACKBONE RING ; _BMRB_accession_number 20014 _BMRB_flat_file_name bmr20014.str _Entry_type original _Submission_date 2008-04-08 _Accession_date 2008-04-08 _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 Knappe T. A. . 2 Linne U. . . 3 Zirah S. . . 4 Rebuffat S. . . 5 Xie X. . . 6 Marahi M. A. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 spectral_peak_list 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 96 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2009-05-28 update BMRB 'Add links to time domain data' 2008-08-28 original author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 20015 BI-32169 stop_ save_ ############################# # Citation for this entry # ############################# save_citations _Saveframe_category entry_citation _Citation_full . _Citation_title 'Isolation and structural characterization of capistruin, a lasso peptide predicted from the genome sequence of Burkholderia thailandensis E264' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 18671394 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Knappe T. A. . 2 Linne U. . . 3 Zirah S. . . 4 Rebuffat S. . . 5 Xie X. . . 6 Marahiel M. A. . stop_ _Journal_abbreviation 'J. Am. Chem. Soc.' _Journal_volume 130 _Journal_issue 34 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 11446 _Page_last 11454 _Year 2008 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name CAPISTRUIN _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label CAPISTRUIN $CAPISTRUIN 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_CAPISTRUIN _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common CAPISTRUIN _Molecular_mass 2051.26 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 19 _Mol_residue_sequence GTPGFQTPDARVISRFGFN loop_ _Residue_seq_code _Residue_label 1 GLY 2 THR 3 PRO 4 GLY 5 PHE 6 GLN 7 THR 8 PRO 9 ASP 10 ALA 11 ARG 12 VAL 13 ILE 14 SER 15 ARG 16 PHE 17 GLY 18 PHE 19 ASN stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-04-23 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 EMBL CFB48912 "lasso peptide precursor [Burkholderia pseudomallei]" 100.00 47 100.00 100.00 2.64e-04 EMBL CFD83320 "lasso peptide precursor [Burkholderia pseudomallei]" 100.00 47 100.00 100.00 2.64e-04 EMBL CFD86202 "lasso peptide precursor [Burkholderia pseudomallei]" 100.00 47 100.00 100.00 2.64e-04 EMBL CFK34393 "lasso peptide precursor [Burkholderia pseudomallei]" 100.00 47 100.00 100.00 2.64e-04 EMBL CFK38857 "lasso peptide precursor [Burkholderia pseudomallei]" 100.00 47 100.00 100.00 2.64e-04 GB ABN83845 "hypothetical protein BURPS668_1904 [Burkholderia pseudomallei 668]" 100.00 47 100.00 100.00 2.64e-04 GB ABN91987 "hypothetical protein BURPS1106A_1917 [Burkholderia pseudomallei 1106a]" 100.00 47 100.00 100.00 2.64e-04 GB ACQ98583 "conserved hypothetical protein [Burkholderia pseudomallei MSHR346]" 100.00 47 100.00 100.00 2.64e-04 GB AFI66377 "hypothetical protein BP1026B_I1752 [Burkholderia pseudomallei 1026b]" 100.00 47 100.00 100.00 2.64e-04 GB AGK46793 "hypothetical protein BTI_2078 [Burkholderia thailandensis MSMB121]" 100.00 47 100.00 100.00 2.26e-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 _Gene_mnemonic $CAPISTRUIN 'Burkholderia thailandensis' 57975 Bacteria . Burkholderia thailandensis MCJA stop_ save_ ######################### # Experimental source # ######################### save_experimental_source _Saveframe_category experimental_source loop_ _Mol_label _Production_method _Host_organism_name_common _Genus _Species _Strain _Vector_type _Vector_name $CAPISTRUIN 'recombinant technology' BACTERIA Burkholderia thailandensis E264 PLASMID M20 stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details '4.4 MG OF CAPISTRUIN IN 90% H2O 10% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $CAPISTRUIN 8.6 mM 'natural abundance' D2O 10 % . H2O 90 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_CYANA _Saveframe_category software _Name CYANA _Version 2.1 loop_ _Vendor _Address _Electronic_address 'G NTERT, P.' . . stop_ loop_ _Task 'geometry optimization' stop_ _Details . save_ save_TOPSPIN _Saveframe_category software _Name TOPSPIN _Version 2.1 loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task processing stop_ _Details . save_ save_SPARKY _Saveframe_category software _Name SPARKY _Version 2.1 loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'data analysis' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer BRUKER _Model AVANCE _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_DQF-COSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _Sample_label $sample_1 save_ save_NOESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name NOESY _Sample_label $sample_1 save_ save_2D_1H-1H_TOCSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_DQF-COSY _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NOESY _Saveframe_category NMR_applied_experiment _Experiment_name NOESY _BMRB_pulse_sequence_accession_number . _Details . save_ save_2D_1H-1H_TOCSY _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _BMRB_pulse_sequence_accession_number . _Details . save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 0 . mM pH . . pH pressure 1 . bar temperature 283 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_DSS _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 external direct cylindrical 'separate tube (no insert) similar to the experimental sample tube' parallel 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 DQF-COSY' NOESY '2D 1H-1H TOCSY' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $DSS _Mol_system_component_name CAPISTRUIN _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 8.509 0.002 . 2 1 1 GLY HA2 H 4.485 0.004 . 3 1 1 GLY HA3 H 3.816 0.002 . 4 2 2 THR H H 7.757 0.002 . 5 2 2 THR HA H 4.753 0.004 . 6 2 2 THR HB H 4.060 0.005 . 7 2 2 THR HG2 H 1.190 0.002 . 8 3 3 PRO HA H 4.270 0.004 . 9 3 3 PRO HB2 H 2.276 0.004 . 10 3 3 PRO HB3 H 1.882 0.008 . 11 3 3 PRO HD2 H 3.925 0.004 . 12 3 3 PRO HD3 H 3.699 0.001 . 13 3 3 PRO HG2 H 2.149 0.005 . 14 3 3 PRO HG3 H 1.906 0.005 . 15 4 4 GLY H H 8.035 0.001 . 16 4 4 GLY HA2 H 3.471 0.001 . 17 4 4 GLY HA3 H 3.662 0.001 . 18 5 5 PHE H H 8.721 0.001 . 19 5 5 PHE HA H 4.833 0.001 . 20 5 5 PHE HB2 H 2.741 0.001 . 21 5 5 PHE HB3 H 3.401 0.015 . 22 6 6 GLN H H 8.049 0.006 . 23 6 6 GLN HA H 4.484 0.004 . 24 6 6 GLN HB2 H 1.780 0.005 . 25 6 6 GLN HB3 H 2.085 0.016 . 26 6 6 GLN HE21 H 7.816 0.003 . 27 6 6 GLN HE22 H 7.816 0.003 . 28 6 6 GLN HG2 H 2.293 0.004 . 29 6 6 GLN HG3 H 2.293 0.004 . 30 7 7 THR H H 7.828 0.005 . 31 7 7 THR HA H 4.938 0.002 . 32 7 7 THR HB H 3.999 0.006 . 33 7 7 THR HG2 H 1.012 0.003 . 34 8 8 PRO HA H 4.735 0.001 . 35 8 8 PRO HB2 H 2.260 0.003 . 36 8 8 PRO HB3 H 1.950 0.004 . 37 8 8 PRO HD2 H 3.904 0.005 . 38 8 8 PRO HD3 H 3.801 0.004 . 39 8 8 PRO HG2 H 2.108 0.001 . 40 8 8 PRO HG3 H 1.870 0.005 . 41 9 9 ASP H H 8.596 0.002 . 42 9 9 ASP HA H 4.862 0.001 . 43 9 9 ASP HB2 H 3.044 0.017 . 44 9 9 ASP HB3 H 3.498 0.011 . 45 10 10 ALA H H 8.253 0.002 . 46 10 10 ALA HA H 4.114 0.008 . 47 10 10 ALA HB H 1.419 0.003 . 48 11 11 ARG H H 8.032 0.005 . 49 11 11 ARG HA H 4.629 0.001 . 50 11 11 ARG HB2 H 1.765 0.004 . 51 11 11 ARG HB3 H 1.952 0.004 . 52 11 11 ARG HD2 H 3.246 0.002 . 53 11 11 ARG HD3 H 3.246 0.002 . 54 11 11 ARG HE H 7.372 0.005 . 55 11 11 ARG HG2 H 1.620 0.008 . 56 11 11 ARG HG3 H 1.620 0.008 . 57 12 12 VAL H H 8.263 0.002 . 58 12 12 VAL HA H 4.742 0.003 . 59 12 12 VAL HB H 2.192 0.012 . 60 12 12 VAL HG1 H 0.831 0.003 . 61 12 12 VAL HG2 H 0.520 0.001 . 62 13 13 ILE H H 8.375 0.001 . 63 13 13 ILE HA H 3.469 0.003 . 64 13 13 ILE HB H 1.782 0.003 . 65 13 13 ILE HD1 H 0.760 0.012 . 66 13 13 ILE HG12 H 1.469 0.004 . 67 13 13 ILE HG13 H 1.202 0.001 . 68 13 13 ILE HG2 H 0.737 0.004 . 69 14 14 SER H H 8.011 0.011 . 70 14 14 SER HA H 5.215 0.001 . 71 14 14 SER HB2 H 3.845 0.003 . 72 14 14 SER HB3 H 3.752 0.002 . 73 15 15 ARG H H 8.170 0.005 . 74 15 15 ARG HA H 4.699 0.001 . 75 15 15 ARG HB2 H 1.713 0.002 . 76 15 15 ARG HB3 H 1.713 0.002 . 77 15 15 ARG HD2 H 3.060 0.008 . 78 15 15 ARG HD3 H 3.060 0.008 . 79 15 15 ARG HE H 7.088 0.001 . 80 15 15 ARG HG2 H 1.395 0.004 . 81 15 15 ARG HG3 H 1.395 0.004 . 82 16 16 PHE H H 8.286 0.002 . 83 16 16 PHE HA H 4.629 0.005 . 84 16 16 PHE HB2 H 3.095 0.012 . 85 16 16 PHE HB3 H 2.852 0.002 . 86 17 17 GLY H H 8.523 0.002 . 87 17 17 GLY HA2 H 3.730 0.001 . 88 17 17 GLY HA3 H 3.883 0.001 . 89 18 18 PHE H H 8.131 0.002 . 90 18 18 PHE HA H 4.629 0.001 . 91 18 18 PHE HB2 H 3.213 0.001 . 92 18 18 PHE HB3 H 3.013 0.011 . 93 19 19 ASN H H 8.479 0.004 . 94 19 19 ASN HA H 4.695 0.005 . 95 19 19 ASN HB2 H 2.779 0.005 . 96 19 19 ASN HB3 H 2.845 0.005 . stop_ save_ save_constraint_statistics _Saveframe_category constraint_statistics _Text_data_format . _Text_data . _NOE_interproton_distance_evaluation . _NOE_pseudoatom_corrections . _Details . save_ save_representative_conformer _Saveframe_category representative_structure _Details . _Rep_structure_derivation . _Rep_structure_file_name . _Structure_coordinate_set_label $conformer_family_coord_set _Rep_struction_original_file . save_