data_5859 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Structure of Antibacterial Peptide Microcin J25: A 21-Residue Lariat Protoknot ; loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Bayro Marvin J. . 2 Swapna Gurla V.T. . 3 Huang Yuangpeng J. . 4 Ma Li-chung . . 5 Mukhopadhyay Jayanta . . 6 Sineva Elena . . 7 Ebright Richard H. . 8 Montelione Gaetano T. . stop_ _BMRB_accession_number 5859 _BMRB_flat_file_name bmr5859.str _Entry_type new _Submission_date 2003-07-04 _Accession_date 2003-07-07 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 coupling_constants 1 stop_ loop_ _Data_type _Data_type_count '1H chemical shifts' 113 '15N chemical shifts' 19 '13C chemical shifts' 72 'coupling constants' 13 stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_title ; Structure of Antibacterial Peptide Microcin J25: A 21-Residue Lariat Protoknot ; _Citation_status published _Citation_type journal _MEDLINE_UI_code . _PubMed_ID 14531661 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Bayro Marvin J. . 2 Mukhopadhyay Jayanta . . 3 Swapna G. V.T. . 4 Huang Yuangpeng J. . 5 Ma Li-chung . . 6 Sineva Elena . . 7 Dawson Philip . . 8 Montelione Gaetano T. . 9 Ebright Richard H. . stop_ _Journal_abbreviation "J. Am. Chem. Soc." _Journal_volume 125 _Journal_issue 41 _Page_first 12382 _Page_last 12383 _Year 2003 save_ ################################## # Molecular system description # ################################## save_system_MCCJ25 _Saveframe_category molecular_system _Mol_system_name 'Microcin J25' _Abbreviation_common 'Microcin J25' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'Microcin J25' $MCCJ25 stop_ _System_physical_state native _System_oligomer_state monomer _System_paramagnetic no _System_thiol_state 'not present' loop_ _Biological_function 'transcription inhibitor' stop_ loop_ _Database_name _Database_accession_code _Database_entry_mol_name _Database_entry_relation_type _Database_entry_details PDB 1PP5 'Microcin J25' . . stop_ save_ ######################## # Monomeric polymers # ######################## save_MCCJ25 _Saveframe_category monomeric_polymer _Mol_type 'polymer' _Mol_polymer_class protein _Name_common 'Microcin J25' _Name_variant 'Microcin J25' _Abbreviation_common 'Microcin J25' _Molecular_mass 2107.3 _Mol_thiol_state 'not present' ############################## # Polymer residue sequence # ############################## _Residue_count 21 _Mol_residue_sequence ; GGAGHVPEYFVGIGTPISFY G ; loop_ _Residue_seq_code _Residue_label 1 GLY 2 GLY 3 ALA 4 GLY 5 HIS 6 VAL 7 PRO 8 GLU 9 TYR 10 PHE 11 VAL 12 GLY 13 ILE 14 GLY 15 THR 16 PRO 17 ILE 18 SER 19 PHE 20 TYR 21 GLY stop_ _Sequence_homology_query_date 2003-11-27 _Sequence_homology_query_revised_last_date 2003-10-24 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 $MCCJ25 'Escherichia coli' 562 Bacteria . Escherichia coli 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_name $MCCJ25 'recombinate technology' 'Eschericia coli' Escherichia coli 'DH5alpha' 'plasmid pTUC202' stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $MCCJ25 2.0 mM "[U-94% 13C; U-94% 15N]" CD3OH 100 % . stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $MCCJ25 2.0 mM "[U-100% 15N]" CD3OH 100 % . stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name VNMR6.1C loop_ _Task "data collection" stop_ _Citation_label $ref_1 save_ save_software_2 _Saveframe_category software _Name nmrPipe loop_ _Task "raw spectral data processing" stop_ _Citation_label $ref_2 save_ save_software_3 _Saveframe_category software _Name Sparky loop_ _Task "spectral visualization" stop_ _Citation_label $ref_3 save_ save_software_4 _Saveframe_category software _Name AutoStructure loop_ _Task "automated structural determination" stop_ _Citation_label $ref_4 save_ save_software_5 _Saveframe_category software _Name HYPER _Version 3.2 loop_ _Task "data analysis" stop_ _Details ; In-house developed software for the determination of dihedral angle restraints from NMR data. ; _Citation_label $ref_5 save_ save_software_6 _Saveframe_category software _Name DYANA _Version 1.5 loop_ _Task "structure refinement" stop_ _Details ; Structure refinement using torsion angle dynamics. ; _Citation_label $ref_6 save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer varian _Model 'UNITY Inova' _Field_strength 500 save_ save_NMR_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer varian _Model 'UNITY Inova' _Field_strength 600 save_ ############################# # NMR applied experiments # ############################# save_NMR_applied_experiment_1 _Saveframe_category NMR_applied_experiment _Experiment_name ; NH HSQC HNCACB CBCAcoNH CH HSQC HCCH-COSY 15N-edited NOESY 13C edited NOESY HNHA HBCBcgcdHD aromatic TOCSY RD hetNOE 15N HSQC TOCSY ; save_ ####################### # Sample conditions # ####################### save_Ex-cond_1 _Saveframe_category sample_conditions _Details ; The sample is in CD3OH and the pH was therefore not measured. ; loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH ? . n/a temperature 298 0.1 K 'ionic strength' 0.1 . M stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference _Saveframe_category chemical_shift_reference 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 _Indirect_shift_ratio_citation_label CD3OH H 1 "methyl protons" ppm 3.313 internal direct cylindrical external parallel 1.0 $ref_2 DSS C 13 "methyl protons" ppm 0.00 external indirect cylindrical external parallel 0.101329118 $ref_2 DSS N 15 "methyl protons" ppm 0.00 external indirect cylindrical external parallel 0.251449530 $ref_2 stop_ save_ ################################### # Assigned chemical shift lists # ################################### ################################################################### # Chemical Shift Ambiguity Index Value Definitions # # # # Index Value Definition # # # # 1 Unique # # 2 Ambiguity of geminal atoms or geminal methyl # # proton groups # # 3 Aromatic atoms on opposite sides of the ring # # (e.g. Tyr HE1 and HE2 protons) # # 4 Intraresidue ambiguities (e.g. Lys HG and # # HD protons) # # 5 Interresidue ambiguities (Lys 12 vs. Lys 27) # # 9 Ambiguous, specific ambiguity not defined # # # ################################################################### save_chemical_shift_MCCJ25 _Saveframe_category assigned_chemical_shifts loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $Ex-cond_1 _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name 'Microcin J25' loop_ _Atom_shift_assign_ID _Residue_seq_code _Residue_label _Atom_name _Atom_type _Chem_shift_value _Chem_shift_value_error _Chem_shift_ambiguity_code 1 1 GLY CA C 45.7 0.25 1 2 1 GLY H H 8.01 0.025 1 3 1 GLY HA2 H 3.63 0.025 2 4 1 GLY HA3 H 4.38 0.025 2 5 1 GLY N N 108.0 0.25 1 6 2 GLY CA C 47.0 0.25 1 7 2 GLY H H 9.05 0.025 1 8 2 GLY HA2 H 3.96 0.025 2 9 2 GLY HA3 H 4.32 0.025 2 10 2 GLY N N 108.8 0.25 1 11 3 ALA CA C 50.9 0.25 1 12 3 ALA CB C 19.9 0.25 1 13 3 ALA H H 8.59 0.025 1 14 3 ALA HA H 4.75 0.025 1 15 3 ALA HB H 1.39 0.025 1 16 3 ALA N N 128.3 0.25 1 17 4 GLY CA C 45.1 0.25 1 18 4 GLY H H 7.82 0.025 1 19 4 GLY HA2 H 3.58 0.025 2 20 4 GLY HA3 H 4.14 0.025 2 21 4 GLY N N 103.4 0.25 1 22 5 HIS CA C 55.5 0.25 1 23 5 HIS CB C 31.4 0.25 1 24 5 HIS CD2 C 120.3 0.25 1 25 5 HIS CE1 C 136.9 0.25 1 26 5 HIS H H 7.51 0.025 1 27 5 HIS HA H 4.79 0.025 1 28 5 HIS HB2 H 3.01 0.025 2 29 5 HIS HB3 H 3.34 0.025 2 30 5 HIS HD2 H 7.42 0.025 1 31 5 HIS HE1 H 8.79 0.025 1 32 5 HIS N N 112.6 0.25 1 33 6 VAL CA C 59.7 0.25 1 34 6 VAL CB C 33.6 0.25 1 35 6 VAL CG1 C 20.8 0.25 1 36 6 VAL CG2 C 21.2 0.25 1 37 6 VAL H H 8.74 0.025 1 38 6 VAL HA H 4.77 0.025 1 39 6 VAL HB H 1.87 0.025 1 40 6 VAL HG1 H 0.95 0.025 2 41 6 VAL HG2 H 1.18 0.025 2 42 6 VAL N N 120.6 0.25 1 43 7 PRO CA C 63.8 0.25 1 44 7 PRO CB C 32.8 0.25 1 45 7 PRO CG C 28.1 0.25 1 46 7 PRO CD C 50.9 0.25 1 47 7 PRO HA H 4.31 0.025 1 48 7 PRO HB2 H 1.78 0.025 2 49 7 PRO HB3 H 1.89 0.025 2 50 7 PRO HG2 H 2.06 0.025 2 51 7 PRO HG3 H 2.33 0.025 2 52 7 PRO HD2 H 3.91 0.025 2 53 7 PRO HD3 H 4.22 0.025 2 54 8 GLU CA C 55.4 0.25 1 55 8 GLU CB C 29.8 0.25 1 56 8 GLU CG C 34.9 0.25 1 57 8 GLU H H 8.41 0.025 1 58 8 GLU HA H 4.48 0.025 1 59 8 GLU HB2 H 1.76 0.025 1 60 8 GLU HB3 H 1.76 0.025 1 61 8 GLU HG2 H 1.90 0.025 2 62 8 GLU HG3 H 2.01 0.025 2 63 8 GLU N N 117.9 0.25 1 64 9 TYR CA C 57.5 0.25 1 65 9 TYR CB C 40.6 0.25 1 66 9 TYR CD1 C 132.9 0.25 1 67 9 TYR CD2 C 132.9 0.25 1 68 9 TYR CE1 C 118.0 0.25 1 69 9 TYR CE2 C 118.0 0.25 1 70 9 TYR H H 7.40 0.025 1 71 9 TYR HA H 4.65 0.025 1 72 9 TYR HB2 H 2.73 0.025 2 73 9 TYR HB3 H 2.95 0.025 2 74 9 TYR HD1 H 7.02 0.025 1 75 9 TYR HD2 H 7.02 0.025 1 76 9 TYR HE1 H 6.78 0.025 1 77 9 TYR HE2 H 6.78 0.025 1 78 9 TYR N N 116.6 0.25 1 79 10 PHE CA C 57.2 0.25 1 80 10 PHE CB C 41.6 0.25 1 81 10 PHE CD1 C 131.6 0.25 1 82 10 PHE CD2 C 131.6 0.25 1 83 10 PHE CE1 C 129.0 0.25 1 84 10 PHE CE2 C 129.0 0.25 1 85 10 PHE CZ C 131.1 0.25 1 86 10 PHE H H 8.39 0.025 1 87 10 PHE HA H 4.95 0.025 1 88 10 PHE HB2 H 2.84 0.025 2 89 10 PHE HB3 H 3.03 0.025 2 90 10 PHE HD1 H 7.15 0.025 1 91 10 PHE HD2 H 7.15 0.025 1 92 10 PHE HE1 H 7.15 0.025 1 93 10 PHE HE2 H 7.15 0.025 1 94 10 PHE HZ H 7.25 0.025 2 95 10 PHE N N 120.7 0.25 1 96 11 VAL CA C 61.4 0.25 1 97 11 VAL CB C 33.9 0.25 1 98 11 VAL CG1 C 20.1 0.25 1 99 11 VAL CG2 C 21.2 0.25 1 100 11 VAL H H 8.35 0.025 1 101 11 VAL HA H 4.37 0.025 1 102 11 VAL HB H 2.21 0.025 1 103 11 VAL HG1 H 1.00 0.025 2 104 11 VAL HG2 H 1.02 0.025 2 105 11 VAL N N 115.9 0.25 1 106 12 GLY CA C 45.3 0.25 1 107 12 GLY H H 8.25 0.025 1 108 12 GLY HA2 H 3.84 0.025 2 109 12 GLY HA3 H 4.07 0.025 2 110 12 GLY N N 108.6 0.25 1 111 13 ILE CA C 61.3 0.25 1 112 13 ILE CB C 38.1 0.25 1 113 13 ILE CG1 C 27.4 0.25 1 114 13 ILE CG2 C 17.4 0.25 1 115 13 ILE CD1 C 12.7 0.25 1 116 13 ILE H H 8.40 0.025 1 117 13 ILE HA H 4.25 0.025 1 118 13 ILE HB H 2.01 0.025 1 119 13 ILE HG2 H 1.01 0.025 1 120 13 ILE HG12 H 1.28 0.025 1 121 13 ILE HG13 H 1.62 0.025 1 122 13 ILE HD1 H 0.97 0.025 1 123 13 ILE N N 119.4 0.25 1 124 14 GLY CA C 45.8 0.25 1 125 14 GLY H H 8.52 0.025 1 126 14 GLY HA2 H 3.72 0.025 2 127 14 GLY HA3 H 4.15 0.025 2 128 14 GLY N N 109.4 0.25 1 129 15 THR CA C 59.9 0.25 1 130 15 THR CB C 70.1 0.25 1 131 15 THR CG2 C 21.3 0.25 1 132 15 THR H H 8.00 0.025 1 133 15 THR HA H 4.82 0.025 1 134 15 THR HB H 4.19 0.025 1 135 15 THR HG2 H 1.29 0.025 1 136 15 THR N N 114.6 0.25 1 137 16 PRO CA C 62.9 0.25 1 138 16 PRO CB C 32.3 0.25 1 139 16 PRO CG C 27.4 0.25 1 140 16 PRO CD C 50.7 0.25 1 141 16 PRO HA H 4.58 0.025 1 142 16 PRO HB2 H 1.80 0.025 2 143 16 PRO HB3 H 1.91 0.025 2 144 16 PRO HG2 H 2.05 0.025 2 145 16 PRO HG3 H 2.24 0.025 2 146 16 PRO HD2 H 3.94 0.025 2 147 16 PRO HD3 H 4.09 0.025 2 148 17 ILE CA C 60.3 0.25 1 149 17 ILE CB C 40.2 0.25 1 150 17 ILE CG1 C 27.5 0.25 1 151 17 ILE CG2 C 17.8 0.25 1 152 17 ILE CD1 C 13.4 0.25 1 153 17 ILE H H 8.06 0.025 1 154 17 ILE HA H 4.51 0.025 1 155 17 ILE HB H 1.95 0.025 1 156 17 ILE HG2 H 0.93 0.025 1 157 17 ILE HG12 H 1.50 0.025 1 158 17 ILE HG13 H 1.16 0.025 1 159 17 ILE HD1 H 1.03 0.025 1 160 17 ILE N N 114.9 0.25 1 161 18 SER CA C 58.3 0.25 1 162 18 SER CB C 63.8 0.25 1 163 18 SER H H 7.44 0.025 1 164 18 SER HA H 4.46 0.025 1 165 18 SER HB2 H 3.93 0.025 2 166 18 SER HB3 H 4.14 0.025 2 167 18 SER N N 113.5 0.25 1 168 19 PHE CA C 58.6 0.25 1 169 19 PHE CB C 44.7 0.25 1 170 19 PHE CD1 C 132.1 0.25 1 171 19 PHE CD2 C 132.1 0.25 1 172 19 PHE CE1 C 130.5 0.25 1 173 19 PHE CE2 C 130.5 0.25 1 174 19 PHE CZ C 129.3 0.25 2 175 19 PHE H H 8.92 0.025 1 176 19 PHE HA H 5.49 0.025 1 177 19 PHE HB2 H 2.64 0.025 2 178 19 PHE HB3 H 2.67 0.025 2 179 19 PHE HD1 H 6.95 0.025 1 180 19 PHE HD2 H 6.95 0.025 1 181 19 PHE HE1 H 7.15 0.025 1 182 19 PHE HE2 H 7.15 0.025 1 183 19 PHE HZ H 7.21 0.025 2 184 19 PHE N N 118.9 0.25 1 185 20 TYR CA C 57.5 0.25 1 186 20 TYR CB C 40.9 0.25 1 187 20 TYR CD1 C 133.2 0.25 1 188 20 TYR CD2 C 133.2 0.25 1 189 20 TYR CE1 C 117.6 0.25 1 190 20 TYR CE2 C 117.6 0.25 1 191 20 TYR H H 9.58 0.025 1 192 20 TYR HA H 4.95 0.025 1 193 20 TYR HB2 H 3.07 0.025 1 194 20 TYR HB3 H 3.07 0.025 1 195 20 TYR HD1 H 7.04 0.025 1 196 20 TYR HD2 H 7.04 0.025 1 197 20 TYR HE1 H 6.67 0.025 1 198 20 TYR HE2 H 6.67 0.025 1 199 20 TYR N N 117.4 0.25 1 200 21 GLY CA C 44.4 0.25 1 201 21 GLY H H 8.66 0.025 1 202 21 GLY HA2 H 3.95 0.025 1 203 21 GLY HA3 H 3.95 0.025 1 204 21 GLY N N 109.2 0.25 1 stop_ save_ ######################## # Coupling constants # ######################## save_MCCJ25_JNH_1 _Saveframe_category coupling_constants loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $Ex-cond_1 _Spectrometer_frequency_1H 500 _Mol_system_component_name 'Microcin J25' loop_ _Coupling_constant_code _Atom_one_residue_seq_code _Atom_one_residue_label _Atom_one_name _Atom_two_residue_seq_code _Atom_two_residue_label _Atom_two_name _Coupling_constant_value _Coupling_constant_value_error 3JHNHA 3 ALA H 3 ALA HA 8.1837 1.0 3JHNHA 5 HIS H 5 HIS HA 10.0325 1.0 3JHNHA 6 VAL H 6 VAL HA 9.0839 1.0 3JHNHA 8 GLU H 8 GLU HA 8.6937 1.0 3JHNHA 9 TYR H 9 TYR HA 8.0515 1.0 3JHNHA 10 PHE H 10 PHE HA 8.5932 1.0 3JHNHA 11 VAL H 11 VAL HA 7.8373 1.0 3JHNHA 13 ILE H 13 ILE HA 7.7360 1.0 3JHNHA 15 THR H 15 THR HA 7.9909 1.0 3JHNHA 17 ILE H 17 ILE HA 9.0353 1.0 3JHNHA 18 SER H 18 SER HA 6.7196 1.0 3JHNHA 19 PHE H 19 PHE HA 10.0942 1.0 3JHNHA 20 TYR H 20 TYR HA 7.8812 1.0 stop_ save_ ####################################### # Cited references within the entry # ####################################### save_ref_1 _Saveframe_category citation _PubMed_ID 98344137 _Citation_full ; Kawarabayasi et al. (1998) DNA Res. 5, 55-76 ; save_ save_ref_2 _Saveframe_category citation _PubMed_ID 8520220 _Citation_full ; Delaglio F., Grzesiek S., Vuister G.W., Zhu G., Pfeifer J., Bax A. J. Biomol. NMR. (1995) 6, 277-293. ; save_ save_ref_3 _Saveframe_category citation _PubMed_ID . _Citation_full ; T. D. Goddard and D. G. Kneller, SPARKY 3, University of California, San Francisco. ; save_ save_ref_4 _Saveframe_category citation _PubMed_ID . _Citation_full ; Huang, Y.J. (2001). Automated determination of protein structures from NMR data by iterative analysis of self-consistent contact patterns, PhD thesis, Rutgers University, New Brunswick, NJ. ; save_ save_ref_5 _Saveframe_category citation _PubMed_ID . _Citation_full ; see: www-nmr.cabm.rutgers.edu/NMRsoftware/nmr_software.html ; save_ save_ref_6 _Saveframe_category citation _PubMed_ID 9367762 _Citation_full ; Guntert P, Mumenthaler C, Wuthrich K. (1997) J. Mol. Biol. 273, 283-98. ; save_