data_16067 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Backbone assignment of RelB antitoxin C-terminal peptide (RelBc) in the RelE-free state ; _BMRB_accession_number 16067 _BMRB_flat_file_name bmr16067.str _Entry_type original _Submission_date 2008-12-17 _Accession_date 2008-12-17 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details 'There is a related deposition of this peptide in complex with its cognate toxin RelE.' loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Li Guang-Yao . . 2 Zhang Yonglong . . 3 Inouye Masayori . . 4 Ikura Mitsuhiko . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 31 "13C chemical shifts" 66 "15N chemical shifts" 31 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2009-05-18 update BMRB 'complete entry citation' 2009-04-22 original author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 16065 'RelE:RelBc complex' 16066 RelE stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Inhibitory mechanism of E. coli RelE/RelB toxin/antitoxin module involves a helix displacement near a mRNA interferase active site ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 19297318 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Li Guang-Yao . . 2 Zhang Yonglong . . 3 Inouye Masayori . . 4 Ikura Mitsuhiko . . stop_ _Journal_abbreviation 'J. Biol. Chem.' _Journal_volume 284 _Journal_issue 21 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 14628 _Page_last 14636 _Year 2009 _Details . loop_ _Keyword Antitoxin RelB stop_ save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name RelBc _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'chain A' $RelBc stop_ _System_molecular_weight 4128.7 _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . loop_ _Biological_function 'Antitoxin, which countacts the toxicity of RelE.' stop_ _Database_query_date . _Details 'E. coli antitoxin C-terminal peptide (RelBc, K47-L79)' save_ ######################## # Monomeric polymers # ######################## save_RelBc _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common RelBc _Molecular_mass 4128.7 _Mol_thiol_state 'not present' loop_ _Biological_function Antitoxin 'Transcriptional repressor' stop_ _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 36 _Mol_residue_sequence ; GSHKQTLLSDEDAELVEIVK ERLRNPKPVRVTLDEL ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 -2 GLY 2 -1 SER 3 0 HIS 4 47 LYS 5 48 GLN 6 49 THR 7 50 LEU 8 51 LEU 9 52 SER 10 53 ASP 11 54 GLU 12 55 ASP 13 56 ALA 14 57 GLU 15 58 LEU 16 59 VAL 17 60 GLU 18 61 ILE 19 62 VAL 20 63 LYS 21 64 GLU 22 65 ARG 23 66 LEU 24 67 ARG 25 68 ASN 26 69 PRO 27 70 LYS 28 71 PRO 29 72 VAL 30 73 ARG 31 74 VAL 32 75 THR 33 76 LEU 34 77 ASP 35 78 GLU 36 79 LEU stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-10-21 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 2KC8 "Structure Of E. Coli Toxin Rele (R81aR83A) MUTANT IN Complex With Antitoxin Relbc (K47-L79) Peptide" 100.00 36 100.00 100.00 4.83e-15 PDB 4FXE "Crystal Structure Of The Intact E. Coli Relbe Toxin-Antitoxin Complex" 94.44 79 97.06 97.06 3.46e-12 DBJ BAA15263 "bifunctional antitoxin of the RelE-RelB toxin-antitoxin system and transcriptional repressor [Escherichia coli str. K12 substr." 94.44 79 97.06 97.06 3.46e-12 DBJ BAI25453 "bifunctional antitoxin of the RelE-RelB toxin-antitoxin system/transcriptional repressor [Escherichia coli O26:H11 str. 11368]" 94.44 79 97.06 97.06 3.46e-12 DBJ BAJ43364 "bifunctional antitoxin/transcriptional repressorRelB [Escherichia coli DH1]" 94.44 79 97.06 97.06 3.46e-12 EMBL CAA26250 "unnamed protein product [Escherichia coli]" 94.44 79 97.06 97.06 3.46e-12 EMBL CAQ98463 "bifunctional antitoxin of the RelE-RelB toxin-antitoxin system and transcriptional repressor; Qin prophage [Escherichia coli IA" 94.44 79 97.06 97.06 3.46e-12 EMBL CBG34538 "antitoxin of the RelE-RelB toxin-antitoxin system and transcriptional repressor of relBEF [Escherichia coli 042]" 94.44 79 97.06 97.06 3.46e-12 EMBL CBK86917 "addiction module antitoxin, RelB/DinJ family [Enterobacter cloacae subsp. cloacae NCTC 9394]" 94.44 79 97.06 97.06 3.46e-12 EMBL CCF87937 "Negative regulator of translation [Salmonella enterica subsp. enterica serovar Senftenberg str. SS209]" 94.44 79 97.06 97.06 3.46e-12 GB AAC74637 "antitoxin of the RelE-RelB toxin-antitoxin syste; transcriptional repressor [Escherichia coli str. K-12 substr. MG1655]" 94.44 79 97.06 97.06 3.46e-12 GB AAN43138 "negative regulator of translation [Shigella flexneri 2a str. 301]" 94.44 79 97.06 97.06 3.46e-12 GB AAP17029 "negative regulator of translation [Shigella flexneri 2a str. 2457T]" 94.44 79 97.06 97.06 3.46e-12 GB ABF03723 "negative regulator of translation [Shigella flexneri 5 str. 8401]" 94.44 79 97.06 97.06 3.46e-12 GB ABP62831 "addiction module antitoxin, RelB/DinJ family [Enterobacter sp. 638]" 94.44 79 97.06 97.06 3.46e-12 REF NP_416082 "antitoxin of the RelE-RelB toxin-antitoxin syste; transcriptional repressor [Escherichia coli str. K-12 substr. MG1655]" 94.44 79 97.06 97.06 3.46e-12 REF NP_707431 "bifunctional antitoxin/transcriptional repressor RelB [Shigella flexneri 2a str. 301]" 94.44 79 97.06 97.06 3.46e-12 REF WP_000534858 "MULTISPECIES: antitoxin RelB [Proteobacteria]" 94.44 79 97.06 97.06 3.46e-12 REF WP_001413280 "antitoxin RelB [Escherichia coli]" 94.44 79 97.06 97.06 3.57e-12 REF WP_001625283 "antitoxin RelB [Escherichia coli]" 94.44 83 97.06 97.06 4.39e-12 SP P0C079 "RecName: Full=Antitoxin RelB" 94.44 79 97.06 97.06 3.46e-12 SP P0C080 "RecName: Full=Antitoxin RelB" 94.44 79 97.06 97.06 3.46e-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 $RelBc 'E. coli' 562 Eubacteria . Escherichia coli stop_ save_ ######################### # Experimental source # ######################### save_experimental_source _Saveframe_category experimental_source loop_ _Mol_label _Production_method _Host_organism_name_common _Genus _Species _Strain _Variant _Vector_name _Details $RelBc 'recombinant technology' . Escherichia coli BL21 DE3 PGEX2T 'RelBc (K47-L79) is expressed with GST-tag fusion. The GST-tag is removed by thrombin afterward.' stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_h2o _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $RelBc 1 mM '[U-13C; U-15N]' 'sodium phosphate' 25 mM 'natural abundance' 'sodium chloride' 300 mM 'natural abundance' DTT 1 mM 'natural abundance' 'sodium azide' 0.5 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_VNMR _Saveframe_category software _Name VNMR _Version . loop_ _Vendor _Address _Electronic_address Varian . . stop_ loop_ _Task collection stop_ _Details . save_ save_NMRPipe _Saveframe_category software _Name NMRPipe _Version . loop_ _Vendor _Address _Electronic_address 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' . . stop_ loop_ _Task processing stop_ _Details . save_ save_XEASY _Saveframe_category software _Name XEASY _Version . loop_ _Vendor _Address _Electronic_address 'Bartels et al.' . . stop_ loop_ _Task 'chemical shift assignment' 'data analysis' 'peak picking' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 500 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-15N_HSQC_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N HSQC' _Sample_label $sample_h2o save_ save_3D_HNCACB_2 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HNCACB' _Sample_label $sample_h2o save_ save_3D_C(CO)NH_3 _Saveframe_category NMR_applied_experiment _Experiment_name '3D C(CO)NH' _Sample_label $sample_h2o 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' 0.5 0.05 M pH 6.5 0.05 pH pressure 1 . atm temperature 296.5 0.1 K 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 DSS C 13 'methyl protons' ppm 0.00 . indirect . . . 0.251449530 DSS H 1 'methyl protons' ppm 0.00 internal direct . . . 1.000000000 DSS N 15 'methyl protons' ppm 0.00 . indirect . . . 0.101329118 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_ _Software_label $XEASY stop_ loop_ _Experiment_label '2D 1H-15N HSQC' '3D HNCACB' stop_ loop_ _Sample_label $sample_h2o stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'chain A' _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 47 4 LYS H H 8.509 0.001 1 2 47 4 LYS CA C 56.225 0 1 3 47 4 LYS CB C 32.873 0 1 4 47 4 LYS N N 121.949 0 1 5 48 5 GLN H H 8.508 0 1 6 48 5 GLN CA C 55.746 0 1 7 48 5 GLN CB C 29.54 0 1 8 48 5 GLN N N 121.949 0 1 9 49 6 THR H H 8.245 0.002 1 10 49 6 THR CA C 61.784 0 1 11 49 6 THR CB C 69.534 0 1 12 49 6 THR N N 116.347 0 1 13 50 7 LEU H H 8.322 0 1 14 50 7 LEU CA C 54.935 0 1 15 50 7 LEU CB C 42.296 0 1 16 50 7 LEU N N 124.968 0 1 17 51 8 LEU H H 8.306 0 1 18 51 8 LEU CA C 54.908 0 1 19 51 8 LEU CB C 42.296 0 1 20 51 8 LEU N N 123.239 0 1 21 52 9 SER H H 8.375 0 1 22 52 9 SER CA C 57.866 0.016 1 23 52 9 SER CB C 63.889 0 1 24 52 9 SER N N 116.347 0 1 25 53 10 ASP H H 8.434 0.002 1 26 53 10 ASP CA C 54.825 0 1 27 53 10 ASP CB C 40.825 0 1 28 53 10 ASP N N 122.469 0 1 29 54 11 GLU H H 8.384 0 1 30 54 11 GLU CA C 57.149 0.019 1 31 54 11 GLU CB C 30.127 0.015 1 32 54 11 GLU N N 120.496 0 1 33 55 12 ASP H H 8.222 0 1 34 55 12 ASP CA C 54.679 0 1 35 55 12 ASP CB C 41.028 0 1 36 55 12 ASP N N 121.015 0 1 37 56 13 ALA H H 8.137 0 1 38 56 13 ALA CA C 53.158 0.012 1 39 56 13 ALA CB C 19.134 0.007 1 40 56 13 ALA N N 124.104 0 1 41 57 14 GLU H H 8.275 0 1 42 57 14 GLU CA C 56.973 0.009 1 43 57 14 GLU CB C 29.882 0.005 1 44 57 14 GLU N N 118.808 0 1 45 58 15 LEU H H 8.025 0 1 46 58 15 LEU CA C 55.578 0.012 1 47 58 15 LEU CB C 41.884 0 1 48 58 15 LEU N N 122.227 0 1 49 59 16 VAL H H 7.949 0 1 50 59 16 VAL CA C 63.178 0.016 1 51 59 16 VAL CB C 32.422 0 1 52 59 16 VAL N N 120.225 0 1 53 60 17 GLU H H 8.259 0 1 54 60 17 GLU CA C 56.876 0.005 1 55 60 17 GLU CB C 29.896 0 1 56 60 17 GLU N N 122.595 0 1 57 61 18 ILE H H 8.066 0.001 1 58 61 18 ILE CA C 61.857 0.014 1 59 61 18 ILE CB C 38.266 0.005 1 60 61 18 ILE N N 122.128 0 1 61 62 19 VAL H H 8.111 0.002 1 62 62 19 VAL CA C 63.616 0.008 1 63 62 19 VAL CB C 32.098 0.022 1 64 62 19 VAL N N 123.554 0 1 65 63 20 LYS H H 8.235 0 1 66 63 20 LYS CA C 57.431 0.008 1 67 63 20 LYS CB C 32.617 0 1 68 63 20 LYS N N 123.314 0 1 69 64 21 GLU H H 8.257 0 1 70 64 21 GLU CA C 57.31 0 1 71 64 21 GLU CB C 29.885 0 1 72 64 21 GLU N N 120.622 0.019 1 73 65 22 ARG H H 8.179 0 1 74 65 22 ARG CA C 56.674 0 1 75 65 22 ARG CB C 30.52 0 1 76 65 22 ARG N N 120.784 0 1 77 66 23 LEU H H 8.042 0 1 78 66 23 LEU CA C 55.297 0 1 79 66 23 LEU CB C 42.087 0 1 80 66 23 LEU N N 121.246 0 1 81 67 24 ARG H H 8.073 0 1 82 67 24 ARG CA C 56.102 0 1 83 67 24 ARG CB C 30.732 0 1 84 67 24 ARG N N 120.656 0 1 85 68 25 ASN H H 8.191 0 1 86 68 25 ASN CA C 56.384 0 1 87 68 25 ASN CB C 41.056 0 1 88 68 25 ASN N N 120.784 0 1 89 69 26 PRO CA C 62.979 0 1 90 69 26 PRO CB C 32.101 0 1 91 70 27 LYS H H 8.322 0 1 92 70 27 LYS CA C 53.847 0 1 93 70 27 LYS CB C 32.33 0 1 94 70 27 LYS N N 122.519 0 1 95 71 28 PRO CA C 62.803 0 1 96 71 28 PRO CB C 32.09 0 1 97 72 29 VAL H H 8.25 0 1 98 72 29 VAL CA C 62.281 0 1 99 72 29 VAL CB C 32.706 0.029 1 100 72 29 VAL N N 120.957 0 1 101 73 30 ARG H H 8.386 0 1 102 73 30 ARG CA C 55.613 0 1 103 73 30 ARG CB C 30.903 0 1 104 73 30 ARG N N 125.259 0 1 105 74 31 VAL H H 8.338 0 1 106 74 31 VAL CA C 62.185 0 1 107 74 31 VAL CB C 32.821 0.01 1 108 74 31 VAL N N 122.368 0 1 109 75 32 THR H H 8.228 0 1 110 75 32 THR CA C 61.337 0 1 111 75 32 THR CB C 69.63 0 1 112 75 32 THR N N 118.303 0 1 113 76 33 LEU H H 8.361 0.001 1 114 76 33 LEU CA C 55.083 0.014 1 115 76 33 LEU CB C 42.167 0.027 1 116 76 33 LEU N N 124.501 0 1 117 77 34 ASP H H 8.252 0.001 1 118 77 34 ASP CA C 54.463 0.025 1 119 77 34 ASP CB C 41.065 0 1 120 77 34 ASP N N 120.225 0 1 121 78 35 GLU H H 8.18 0 1 122 78 35 GLU CA C 56.262 0.011 1 123 78 35 GLU CB C 30.411 0 1 124 78 35 GLU N N 120.656 0 1 125 79 36 LEU H H 7.847 0 1 126 79 36 LEU CA C 56.561 0 1 127 79 36 LEU CB C 43.189 0 1 128 79 36 LEU N N 128.921 0 1 stop_ save_