data_5859 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Structure of Antibacterial Peptide Microcin J25: A 21-Residue Lariat Protoknot ; _BMRB_accession_number 5859 _BMRB_flat_file_name bmr5859.str _Entry_type original _Submission_date 2003-07-04 _Accession_date 2003-07-07 _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 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_ 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 "13C chemical shifts" 72 "15N chemical shifts" 19 "coupling constants" 13 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2009-07-09 update BMRB 'added time domain data' 2003-10-17 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Structure of Antibacterial Peptide Microcin J25: A 21-Residue Lariat Protoknot' _Citation_status published _Citation_type journal _CAS_abstract_code . _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 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 12382 _Page_last 12383 _Year 2003 _Details . save_ ####################################### # Cited references within the entry # ####################################### save_ref_1 _Saveframe_category citation _Citation_full 'Kawarabayasi et al. (1998) DNA Res. 5, 55-76' _Citation_title 'Complete sequence and gene organization of the genome of a hyper-thermophilic archaebacterium, Pyrococcus horikoshii OT3.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 9679194 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Kawarabayasi Y. . . 2 Sawada M. . . 3 Horikawa H. . . 4 Haikawa Y. . . 5 Hino Y. . . 6 Yamamoto S. . . 7 Sekine M. . . 8 Baba S. . . 9 Kosugi H. . . 10 Hosoyama A. . . 11 Nagai Y. . . 12 Sakai M. . . 13 Ogura K. . . 14 Otsuka R. . . 15 Nakazawa H. . . 16 Takamiya M. . . 17 Ohfuku Y. . . 18 Funahashi T. . . 19 Tanaka T. . . 20 Kudoh Y. . . 21 Yamazaki J. . . 22 Kushida N. . . 23 Oguchi A. . . 24 Aoki K. . . 25 Kikuchi H. . . stop_ _Journal_abbreviation 'DNA Res.' _Journal_name_full 'DNA research : an international journal for rapid publication of reports on genes and genomes' _Journal_volume 5 _Journal_issue 2 _Journal_CSD . _Book_title . _Book_chapter_title . _Book_volume . _Book_series . _Book_publisher . _Book_publisher_city . _Book_ISBN . _Conference_title . _Conference_site . _Conference_state_province . _Conference_country . _Conference_start_date . _Conference_end_date . _Conference_abstract_number . _Thesis_institution . _Thesis_institution_city . _Thesis_institution_country . _Page_first 55 _Page_last 76 _Year 1998 _Details ; The complete sequence of the genome of a hyper-thermophilic archaebacterium, Pyrococcus horikoshii OT3, has been determined by assembling the sequences of the physical map-based contigs of fosmid clones and of long polymerase chain reaction (PCR) products which were used for gap-filling. The entire length of the genome was 1,738,505 bp. The authenticity of the entire genome sequence was supported by restriction analysis of long PCR products, which were directly amplified from the genomic DNA. As the potential protein-coding regions, a total of 2061 open reading frames (ORFs) were assigned, and by similarity search against public databases, 406 (19.7%) were related to genes with putative function and 453 (22.0%) to the sequences registered but with unknown function. The remaining 1202 ORFs (58.3%) did not show any significant similarity to the sequences in the databases. Sequence comparison among the assigned ORFs in the genome provided evidence that a considerable number of ORFs were generated by sequence duplication. By similarity search, 11 ORFs were assumed to contain the intein elements. The RNA genes identified were a single 16S-23S rRNA operon, two 5S rRNA genes and 46 tRNA genes including two with the intron structure. All the assigned ORFs and RNA coding regions occupied 91.25% of the whole genome. The data presented in this paper are available on the internet at http:@www.nite.go.jp. ; save_ save_ref_2 _Saveframe_category citation _Citation_full ; Delaglio F., Grzesiek S., Vuister G.W., Zhu G., Pfeifer J., Bax A. J. Biomol. NMR. (1995) 6, 277-293. ; _Citation_title 'NMRPipe: a multidimensional spectral processing system based on UNIX pipes.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 8520220 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Delaglio F. . . 2 Grzesiek S. . . 3 Vuister 'G. W.' W. . 4 Zhu G. . . 5 Pfeifer J. . . 6 Bax A. . . stop_ _Journal_abbreviation 'J. Biomol. NMR' _Journal_name_full 'Journal of biomolecular NMR' _Journal_volume 6 _Journal_issue 3 _Journal_CSD . _Book_title . _Book_chapter_title . _Book_volume . _Book_series . _Book_publisher . _Book_publisher_city . _Book_ISBN . _Conference_title . _Conference_site . _Conference_state_province . _Conference_country . _Conference_start_date . _Conference_end_date . _Conference_abstract_number . _Thesis_institution . _Thesis_institution_city . _Thesis_institution_country . _Page_first 277 _Page_last 293 _Year 1995 _Details ; The NMRPipe system is a UNIX software environment of processing, graphics, and analysis tools designed to meet current routine and research-oriented multidimensional processing requirements, and to anticipate and accommodate future demands and developments. The system is based on UNIX pipes, which allow programs running simultaneously to exchange streams of data under user control. In an NMRPipe processing scheme, a stream of spectral data flows through a pipeline of processing programs, each of which performs one component of the overall scheme, such as Fourier transformation or linear prediction. Complete multidimensional processing schemes are constructed as simple UNIX shell scripts. The processing modules themselves maintain and exploit accurate records of data sizes, detection modes, and calibration information in all dimensions, so that schemes can be constructed without the need to explicitly define or anticipate data sizes or storage details of real and imaginary channels during processing. The asynchronous pipeline scheme provides other substantial advantages, including high flexibility, favorable processing speeds, choice of both all-in-memory and disk-bound processing, easy adaptation to different data formats, simpler software development and maintenance, and the ability to distribute processing tasks on multi-CPU computers and computer networks. ; save_ save_ref_3 _Saveframe_category citation _Citation_full ; T. D. Goddard and D. G. Kneller, SPARKY 3, University of California, San Francisco. ; _Citation_title . _Citation_status . _Citation_type . _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID ? _Journal_abbreviation . _Journal_name_full . _Journal_volume . _Journal_issue . _Journal_CSD . _Book_title . _Book_chapter_title . _Book_volume . _Book_series . _Book_publisher . _Book_publisher_city . _Book_ISBN . _Conference_title . _Conference_site . _Conference_state_province . _Conference_country . _Conference_start_date . _Conference_end_date . _Conference_abstract_number . _Thesis_institution . _Thesis_institution_city . _Thesis_institution_country . _Page_first . _Page_last . _Year . _Details . save_ save_ref_4 _Saveframe_category citation _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. ; _Citation_title . _Citation_status . _Citation_type . _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID ? _Journal_abbreviation . _Journal_name_full . _Journal_volume . _Journal_issue . _Journal_CSD . _Book_title . _Book_chapter_title . _Book_volume . _Book_series . _Book_publisher . _Book_publisher_city . _Book_ISBN . _Conference_title . _Conference_site . _Conference_state_province . _Conference_country . _Conference_start_date . _Conference_end_date . _Conference_abstract_number . _Thesis_institution . _Thesis_institution_city . _Thesis_institution_country . _Page_first . _Page_last . _Year . _Details . save_ save_ref_5 _Saveframe_category citation _Citation_full 'see: www-nmr.cabm.rutgers.edu/NMRsoftware/nmr_software.html' _Citation_title . _Citation_status . _Citation_type . _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID ? _Journal_abbreviation . _Journal_name_full . _Journal_volume . _Journal_issue . _Journal_CSD . _Book_title . _Book_chapter_title . _Book_volume . _Book_series . _Book_publisher . _Book_publisher_city . _Book_ISBN . _Conference_title . _Conference_site . _Conference_state_province . _Conference_country . _Conference_start_date . _Conference_end_date . _Conference_abstract_number . _Thesis_institution . _Thesis_institution_city . _Thesis_institution_country . _Page_first . _Page_last . _Year . _Details . save_ save_ref_6 _Saveframe_category citation _Citation_full ; Guntert P, Mumenthaler C, Wuthrich K. (1997) J. Mol. Biol. 273, 283-98. ; _Citation_title 'Torsion angle dynamics for NMR structure calculation with the new program DYANA.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 9367762 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Guntert P. . . 2 Mumenthaler C. . . 3 Wuthrich K. . . stop_ _Journal_abbreviation 'J. Mol. Biol.' _Journal_name_full 'Journal of molecular biology' _Journal_volume 273 _Journal_issue 1 _Journal_CSD . _Book_title . _Book_chapter_title . _Book_volume . _Book_series . _Book_publisher . _Book_publisher_city . _Book_ISBN . _Conference_title . _Conference_site . _Conference_state_province . _Conference_country . _Conference_start_date . _Conference_end_date . _Conference_abstract_number . _Thesis_institution . _Thesis_institution_city . _Thesis_institution_country . _Page_first 283 _Page_last 298 _Year 1997 _Details ; The new program DYANA (DYnamics Algorithm for Nmr Applications) for efficient calculation of three-dimensional protein and nucleic acid structures from distance constraints and torsion angle constraints collected by nuclear magnetic resonance (NMR) experiments performs simulated annealing by molecular dynamics in torsion angle space and uses a fast recursive algorithm to integrate the equations of motions. Torsion angle dynamics can be more efficient than molecular dynamics in Cartesian coordinate space because of the reduced number of degrees of freedom and the concomitant absence of high-frequency bond and angle vibrations, which allows for the use of longer time-steps and/or higher temperatures in the structure calculation. It also represents a significant advance over the variable target function method in torsion angle space with the REDAC strategy used by the predecessor program DIANA. DYANA computation times per accepted conformer in the "bundle" used to represent the NMR structure compare favorably with those of other presently available structure calculation algorithms, and are of the order of 160 seconds for a protein of 165 amino acid residues when using a DEC Alpha 8400 5/300 computer. Test calculations starting from conformers with random torsion angle values further showed that DYANA is capable of efficient calculation of high-quality protein structures with up to 400 amino acid residues, and of nucleic acid structures. ; 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_molecular_weight . _System_physical_state native _System_oligomer_state monomer _System_paramagnetic no _System_thiol_state 'not present' loop_ _Biological_function 'transcription inhibitor' stop_ _Database_query_date . _Details . 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' _Details . ############################## # 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 . _Sequence_homology_query_revised_last_date 2015-01-28 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 1PP5 "Structure Of Antibacterial Peptide Microcin J25: A 21-Residue Lariat Protoknot" 95.24 21 100.00 100.00 9.09e-04 PDB 1Q71 "The Structure Of Microcin J25 Is A Threaded Sidechain-To-Backbone Ring Structure And Not A Head-To-Tail Cyclized Backbone" 100.00 21 100.00 100.00 2.78e-04 PDB 4CU4 "Fhua From E. Coli In Complex With The Lasso Peptide Microcin J25 (mccj25)" 100.00 21 100.00 100.00 2.78e-04 GB AAD28494 "microcin J25 precursor [Escherichia coli]" 100.00 58 100.00 100.00 5.00e-05 GB AGC14267 "McjA [Escherichia coli O25b:H4-ST131 str. EC958]" 100.00 58 100.00 100.00 5.00e-05 GB AIF78688 "hypothetical protein [Escherichia coli]" 100.00 58 100.00 100.00 5.00e-05 GB ELC03738 "microcin J25 [Escherichia coli KTE4]" 100.00 58 100.00 100.00 5.00e-05 GB ELC41113 "microcin J25 [Escherichia coli KTE25]" 100.00 58 100.00 100.00 5.00e-05 REF WP_001513516 "microcin J25 [Escherichia coli]" 100.00 58 100.00 100.00 5.00e-05 REF YP_007443296 "McjA [Escherichia coli O25b:H4-ST131 str. EC958]" 100.00 58 100.00 100.00 5.00e-05 REF YP_009071192 "hypothetical protein [Escherichia coli]" 100.00 58 100.00 100.00 5.00e-05 REF YP_009075876 "microcin J25 precursor [Escherichia coli]" 100.00 58 100.00 100.00 5.00e-05 SP Q9X2V7 "RecName: Full=Microcin J25; Short=MccJ25; Flags: Precursor [Escherichia coli]" 100.00 58 100.00 100.00 5.00e-05 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 $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 _Details . 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 _Details . 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 _Version . loop_ _Task 'data collection' stop_ _Details . _Citation_label $ref_1 save_ save_software_2 _Saveframe_category software _Name nmrPipe _Version . loop_ _Task 'raw spectral data processing' stop_ _Details . _Citation_label $ref_2 save_ save_software_3 _Saveframe_category software _Name Sparky _Version . loop_ _Task 'spectral visualization' stop_ _Details . _Citation_label $ref_3 save_ save_software_4 _Saveframe_category software _Name AutoStructure _Version . loop_ _Task 'automated structural determination' stop_ _Details . _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 _Details . save_ save_NMR_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer varian _Model 'UNITY Inova' _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_NH_HSQC_1 _Saveframe_category NMR_applied_experiment _Experiment_name 'NH HSQC' _Sample_label . save_ save_HNCACB_2 _Saveframe_category NMR_applied_experiment _Experiment_name HNCACB _Sample_label . save_ save_CBCAcoNH_3 _Saveframe_category NMR_applied_experiment _Experiment_name CBCAcoNH _Sample_label . save_ save_CH_HSQC_4 _Saveframe_category NMR_applied_experiment _Experiment_name 'CH HSQC' _Sample_label . save_ save_HCCH-COSY_5 _Saveframe_category NMR_applied_experiment _Experiment_name HCCH-COSY _Sample_label . save_ save_15N-edited_NOESY_6 _Saveframe_category NMR_applied_experiment _Experiment_name '15N-edited NOESY' _Sample_label . save_ save_13C_edited_NOESY_7 _Saveframe_category NMR_applied_experiment _Experiment_name '13C edited NOESY' _Sample_label . save_ save_HNHA_8 _Saveframe_category NMR_applied_experiment _Experiment_name HNHA _Sample_label . save_ save_HBCBcgcdHD_9 _Saveframe_category NMR_applied_experiment _Experiment_name HBCBcgcdHD _Sample_label . save_ save_aromatic_TOCSY_RD_10 _Saveframe_category NMR_applied_experiment _Experiment_name 'aromatic TOCSY RD' _Sample_label . save_ save_hetNOE_11 _Saveframe_category NMR_applied_experiment _Experiment_name hetNOE _Sample_label . save_ save_15N_HSQC_TOCSY_12 _Saveframe_category NMR_applied_experiment _Experiment_name '15N HSQC TOCSY' _Sample_label . save_ save_NMR_spectrometer_expt_1 _Saveframe_category NMR_applied_experiment _Experiment_name 'NH HSQC' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spectrometer_expt_2 _Saveframe_category NMR_applied_experiment _Experiment_name HNCACB _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spectrometer_expt_3 _Saveframe_category NMR_applied_experiment _Experiment_name CBCAcoNH _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spectrometer_expt_4 _Saveframe_category NMR_applied_experiment _Experiment_name 'CH HSQC' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spectrometer_expt_5 _Saveframe_category NMR_applied_experiment _Experiment_name HCCH-COSY _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spectrometer_expt_6 _Saveframe_category NMR_applied_experiment _Experiment_name '15N-edited NOESY' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spectrometer_expt_7 _Saveframe_category NMR_applied_experiment _Experiment_name '13C edited NOESY' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spectrometer_expt_8 _Saveframe_category NMR_applied_experiment _Experiment_name HNHA _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spectrometer_expt_9 _Saveframe_category NMR_applied_experiment _Experiment_name HBCBcgcdHD _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spectrometer_expt_10 _Saveframe_category NMR_applied_experiment _Experiment_name 'aromatic TOCSY RD' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spectrometer_expt_11 _Saveframe_category NMR_applied_experiment _Experiment_name hetNOE _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spectrometer_expt_12 _Saveframe_category NMR_applied_experiment _Experiment_name '15N HSQC TOCSY' _BMRB_pulse_sequence_accession_number . _Details . 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 _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 _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 # # # # 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_MCCJ25 _Saveframe_category assigned_chemical_shifts _Details . 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' _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 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 _Details . loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $Ex-cond_1 _Spectrometer_frequency_1H 500 _Mol_system_component_name 'Microcin J25' _Text_data_format . _Text_data . loop_ _Coupling_constant_ID _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_min_value _Coupling_constant_max_value _Coupling_constant_value_error 1 3JHNHA 3 ALA H 3 ALA HA 8.1837 . . 1.0 2 3JHNHA 5 HIS H 5 HIS HA 10.0325 . . 1.0 3 3JHNHA 6 VAL H 6 VAL HA 9.0839 . . 1.0 4 3JHNHA 8 GLU H 8 GLU HA 8.6937 . . 1.0 5 3JHNHA 9 TYR H 9 TYR HA 8.0515 . . 1.0 6 3JHNHA 10 PHE H 10 PHE HA 8.5932 . . 1.0 7 3JHNHA 11 VAL H 11 VAL HA 7.8373 . . 1.0 8 3JHNHA 13 ILE H 13 ILE HA 7.7360 . . 1.0 9 3JHNHA 15 THR H 15 THR HA 7.9909 . . 1.0 10 3JHNHA 17 ILE H 17 ILE HA 9.0353 . . 1.0 11 3JHNHA 18 SER H 18 SER HA 6.7196 . . 1.0 12 3JHNHA 19 PHE H 19 PHE HA 10.0942 . . 1.0 13 3JHNHA 20 TYR H 20 TYR HA 7.8812 . . 1.0 stop_ save_