data_25092 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; truncated EcMazE-DNA complex ; _BMRB_accession_number 25092 _BMRB_flat_file_name bmr25092.str _Entry_type original _Submission_date 2014-07-15 _Accession_date 2014-07-15 _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 Zorzini Valentina . . 2 Buts Lieven . . 3 Loris Remy . . 4 'van Nuland' Nico . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 65 "15N chemical shifts" 61 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2015-02-02 original author . stop_ loop_ _Related_BMRB_accession_number _Relationship 25086 'truncated EcMazE' stop_ _Original_release_date 2015-02-02 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Escherichia coli antitoxin MazE as transcription factor: insights into MazE-DNA binding' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 25564525 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Zorzini Valentina . . 2 Buts Lieven . . 3 Schrank Evelyne . . 4 Sterckx Yann GJ . 5 Respondek Michal . . 6 Engelberg-Kulka Hanna . . 7 Loris Remy . . 8 Zangger Klaus . . 9 'van Nuland' Nico AJ . stop_ _Journal_abbreviation 'Nucleic Acids Res.' _Journal_volume 43 _Journal_issue 2 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 1241 _Page_last 1256 _Year 2015 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'MazE-DNA binding' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label entity_1_1 $entity_1 entity_1_2 $entity_1 'DNA (5'-D(*CP*GP*TP*GP*AP*TP*AP*TP*AP*TP*AP*GP*TP*GP*C)-3')' $DNA_(5'-D(*CP*GP*TP*GP*AP*TP*AP*TP*AP*TP*AP*GP*TP*GP*C)-3') 'DNA (5'-D(P*GP*CP*AP*CP*TP*AP*TP*AP*TP*AP*TP*CP*AP*CP*G)-3')' $DNA_(5'-D(P*GP*CP*AP*CP*TP*AP*TP*AP*TP*AP*TP*CP*AP*CP*G)-3') 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_1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common entity_1 _Molecular_mass 5558.510 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 67 _Mol_residue_sequence ; NHKVHHHHHHMSDDDDKGIH SSVKRWGNSPAVRIPATLMQ ALNLNIDDEVKIDLVDGKLI IEPVRKE ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 -16 ASN 2 -15 HIS 3 -14 LYS 4 -13 VAL 5 -12 HIS 6 -11 HIS 7 -10 HIS 8 -9 HIS 9 -8 HIS 10 -7 HIS 11 -6 MET 12 -5 SER 13 -4 ASP 14 -3 ASP 15 -2 ASP 16 -1 ASP 17 0 LYS 18 1 GLY 19 2 ILE 20 3 HIS 21 4 SER 22 5 SER 23 6 VAL 24 7 LYS 25 8 ARG 26 9 TRP 27 10 GLY 28 11 ASN 29 12 SER 30 13 PRO 31 14 ALA 32 15 VAL 33 16 ARG 34 17 ILE 35 18 PRO 36 19 ALA 37 20 THR 38 21 LEU 39 22 MET 40 23 GLN 41 24 ALA 42 25 LEU 43 26 ASN 44 27 LEU 45 28 ASN 46 29 ILE 47 30 ASP 48 31 ASP 49 32 GLU 50 33 VAL 51 34 LYS 52 35 ILE 53 36 ASP 54 37 LEU 55 38 VAL 56 39 ASP 57 40 GLY 58 41 LYS 59 42 LEU 60 43 ILE 61 44 ILE 62 45 GLU 63 46 PRO 64 47 VAL 65 48 ARG 66 49 LYS 67 50 GLU stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-11-25 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 25086 truncEcMazE 100.00 67 100.00 100.00 1.56e-38 BMRB 25093 full_EcMazE_free 73.13 82 100.00 100.00 8.88e-25 BMRB 25094 full_EcMazE-DNA 73.13 82 100.00 100.00 8.88e-25 PDB 1MVF "Maze Addiction Antidote" 73.13 82 100.00 100.00 8.88e-25 PDB 1UB4 "Crystal Structure Of Mazef Complex" 73.13 85 100.00 100.00 1.54e-24 PDB 2MRN "Structure Of Truncated Ecmaze" 100.00 67 100.00 100.00 1.56e-38 PDB 2MRU "Structure Of Truncated Ecmaze-dna Complex" 100.00 67 100.00 100.00 1.56e-38 DBJ BAA41177 "ChpAI [Escherichia coli]" 73.13 82 100.00 100.00 8.88e-25 DBJ BAB37066 "suppressor of ChpA inhibitory function [Escherichia coli O157:H7 str. Sakai]" 73.13 82 100.00 100.00 8.88e-25 DBJ BAE76857 "antitoxin of the ChpA-ChpR toxin-antitoxin system [Escherichia coli str. K12 substr. W3110]" 73.13 82 100.00 100.00 8.88e-25 DBJ BAG78565 "suppressor of inhibitor protein [Escherichia coli SE11]" 73.13 82 100.00 100.00 8.88e-25 DBJ BAI27044 "antitoxin ChpR of the ChpA-ChpR toxin-antitoxin system [Escherichia coli O26:H11 str. 11368]" 73.13 82 100.00 100.00 8.88e-25 EMBL CAP77216 "PemI-like protein 1 [Escherichia coli LF82]" 73.13 82 100.00 100.00 8.88e-25 EMBL CAQ33107 "MazE antitoxin of the MazF-MazE toxin-antitoxin system, subunit of MazE-MazF complex [Escherichia coli BL21(DE3)]" 73.13 82 100.00 100.00 8.88e-25 EMBL CAQ87849 "antitoxin of the ChpA-ChpR toxin-antitoxin system [Escherichia fergusonii ATCC 35469]" 73.13 82 100.00 100.00 8.88e-25 EMBL CAQ99711 "antitoxin of the ChpA-ChpR toxin-antitoxin system [Escherichia coli IAI1]" 73.13 82 100.00 100.00 8.88e-25 EMBL CAR04293 "antitoxin of the ChpA-ChpR toxin-antitoxin system [Escherichia coli S88]" 73.13 82 100.00 100.00 8.88e-25 GB AAA03238 "homologous to plasmid R100 pemI gene [Escherichia coli]" 73.13 82 100.00 100.00 8.88e-25 GB AAA69293 "pemI-like protein 1 [Escherichia coli str. K-12 substr. MG1655]" 73.13 82 100.00 100.00 8.88e-25 GB AAC75825 "antitoxin of the ChpA-ChpR toxin-antitoxin system [Escherichia coli str. K-12 substr. MG1655]" 73.13 82 100.00 100.00 8.88e-25 GB AAG57896 "suppressor of inhibitory function of ChpA, PemI-like, autoregulated [Escherichia coli O157:H7 str. EDL933]" 73.13 82 100.00 100.00 8.88e-25 GB AAZ89539 "suppressor of inhibitory function of ChpA, PemI-like, autoregulated [Shigella sonnei Ss046]" 73.13 82 100.00 100.00 8.88e-25 REF NP_311670 "antitoxin MazE [Escherichia coli O157:H7 str. Sakai]" 73.13 82 100.00 100.00 8.88e-25 REF NP_417263 "antitoxin of the ChpA-ChpR toxin-antitoxin system [Escherichia coli str. K-12 substr. MG1655]" 73.13 82 100.00 100.00 8.88e-25 REF WP_000581935 "antitoxin MazE [Escherichia coli]" 73.13 82 97.96 97.96 1.13e-23 REF WP_000581936 "antitoxin MazE [Escherichia coli]" 73.13 82 100.00 100.00 1.07e-24 REF WP_000581937 "MULTISPECIES: antitoxin MazE [Proteobacteria]" 73.13 82 100.00 100.00 8.88e-25 SP P0AE72 "RecName: Full=Antitoxin MazE" 73.13 82 100.00 100.00 8.88e-25 SP P0AE73 "RecName: Full=Antitoxin MazE" 73.13 82 100.00 100.00 8.88e-25 stop_ save_ save_DNA_(5'-D(*CP*GP*TP*GP*AP*TP*AP*TP*AP*TP*AP*GP*TP*GP*C)-3') _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common DNA_(5'-D(*CP*GP*TP*GP*AP*TP*AP*TP*AP*TP*AP*GP*TP*GP*C)-3') _Molecular_mass 4624.059 _Mol_thiol_state 'NOT PRESENT' _Details . _Residue_count 15 _Mol_residue_sequence CGTGATATATAGTGC loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 DC 2 2 DG 3 3 DT 4 4 DG 5 5 DA 6 6 DT 7 7 DA 8 8 DT 9 9 DA 10 10 DT 11 11 DA 12 12 DG 13 13 DT 14 14 DG 15 15 DC stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ save_DNA_(5'-D(P*GP*CP*AP*CP*TP*AP*TP*AP*TP*AP*TP*CP*AP*CP*G)-3') _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common DNA_(5'-D(P*GP*CP*AP*CP*TP*AP*TP*AP*TP*AP*TP*CP*AP*CP*G)-3') _Molecular_mass 4553.023 _Mol_thiol_state . _Details . _Residue_count 15 _Mol_residue_sequence GCACTATATATCACG loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 DG 2 2 DC 3 3 DA 4 4 DC 5 5 DT 6 6 DA 7 7 DT 8 8 DA 9 9 DT 10 10 DA 11 11 DT 12 12 DC 13 13 DA 14 14 DC 15 15 DG stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $entity_1 'E. coli' 562 Bacteria . Escherichia coli $DNA_(5'-D(*CP*GP*TP*GP*AP*TP*AP*TP*AP*TP*AP*GP*TP*GP*C)-3') 'E. coli' 562 Bacteria . Escherichia coli $DNA_(5'-D(P*GP*CP*AP*CP*TP*AP*TP*AP*TP*AP*TP*CP*AP*CP*G)-3') 'E. coli' 562 Bacteria . 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 _Vector_name $entity_1 'recombinant technology' . . . . pQE30-mazE $DNA_(5'-D(*CP*GP*TP*GP*AP*TP*AP*TP*AP*TP*AP*GP*TP*GP*C)-3') 'chemical synthesis' . . . . . $DNA_(5'-D(P*GP*CP*AP*CP*TP*AP*TP*AP*TP*AP*TP*CP*AP*CP*G)-3') '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 _Concentration_min_value _Concentration_max_value _Isotopic_labeling $entity_1 . mM 0.33 0.4 '[U-99% 13C; U-99% 15N]' $DNA_(5'-D(*CP*GP*TP*GP*AP*TP*AP*TP*AP*TP*AP*GP*TP*GP*C)-3') . mM 0 0.4 'natural abundance' $DNA_(5'-D(P*GP*CP*AP*CP*TP*AP*TP*AP*TP*AP*TP*CP*AP*CP*G)-3') . mM 0 0.4 'natural abundance' 'potassium phosphate' 50 mM . . 'natural abundance' 'sodium chloride' 50 mM . . 'natural abundance' H2O 90 % . . 'natural abundance' D2O 10 % . . 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_CcpNMR _Saveframe_category software _Name CcpNMR _Version . loop_ _Vendor _Address _Electronic_address CCPN . . stop_ loop_ _Task 'data analysis' stop_ _Details . save_ save_Haddock _Saveframe_category software _Name Haddock _Version . loop_ _Vendor _Address _Electronic_address 'Alexandre Bonvin' . . stop_ loop_ _Task 'structure solution' refinement stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model VNMRS _Field_strength 600 _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_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 298 . K pH 6.5 . pH pressure 1 . atm 'ionic strength' 50 . mM 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 H 1 'methyl protons' ppm 0.00 internal direct . . . 1.000000000 DSS N 15 'methyl protons' ppm 0.00 na 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_ _Experiment_label '2D 1H-15N HSQC' 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 entity_1_1 _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 -16 1 ASN HD21 H 7.661 0.000 1 2 -16 1 ASN HD22 H 6.981 0.000 1 3 -16 1 ASN ND2 N 112.972 0.001 1 4 -14 3 LYS H H 8.443 0.000 1 5 -14 3 LYS N N 122.627 0.000 1 6 -13 4 VAL H H 8.163 0.000 1 7 -13 4 VAL N N 121.597 0.000 1 8 -12 5 HIS H H 8.574 0.000 1 9 -12 5 HIS N N 123.067 0.000 1 10 -6 11 MET H H 8.629 0.000 1 11 -6 11 MET N N 122.783 0.000 1 12 -5 12 SER H H 8.457 0.000 1 13 -5 12 SER N N 116.739 0.000 1 14 -4 13 ASP H H 8.439 0.000 1 15 -4 13 ASP N N 122.175 0.000 1 16 -3 14 ASP H H 8.217 0.000 1 17 -3 14 ASP N N 119.766 0.000 1 18 -2 15 ASP H H 8.199 0.000 1 19 -2 15 ASP N N 120.048 0.000 1 20 -1 16 ASP H H 8.220 0.000 1 21 -1 16 ASP N N 120.110 0.000 1 22 0 17 LYS H H 8.288 0.000 1 23 0 17 LYS N N 121.485 0.000 1 24 1 18 GLY H H 8.358 0.000 1 25 1 18 GLY N N 109.058 0.000 1 26 2 19 ILE H H 8.707 0.000 1 27 2 19 ILE N N 121.346 0.000 1 28 3 20 HIS H H 9.080 0.000 1 29 3 20 HIS N N 125.254 0.000 1 30 4 21 SER H H 8.946 0.000 1 31 4 21 SER N N 118.107 0.000 1 32 5 22 SER H H 8.753 0.000 1 33 5 22 SER N N 114.278 0.000 1 34 6 23 VAL H H 8.270 0.000 1 35 6 23 VAL N N 120.995 0.000 1 36 7 24 LYS H H 9.202 0.000 1 37 7 24 LYS N N 128.801 0.000 1 38 8 25 ARG H H 8.446 0.000 1 39 8 25 ARG HE H 7.322 0.000 1 40 8 25 ARG N N 120.582 0.000 1 41 8 25 ARG NE N 84.060 0.000 1 42 9 26 TRP H H 8.969 0.000 1 43 9 26 TRP HE1 H 9.929 0.000 1 44 9 26 TRP N N 131.711 0.000 1 45 9 26 TRP NE1 N 126.525 0.000 1 46 11 28 ASN HD21 H 7.725 0.000 1 47 11 28 ASN HD22 H 7.036 0.000 1 48 11 28 ASN ND2 N 112.411 0.005 1 49 14 31 ALA H H 9.341 0.000 1 50 14 31 ALA N N 124.141 0.000 1 51 15 32 VAL H H 8.516 0.000 1 52 15 32 VAL N N 115.416 0.000 1 53 17 34 ILE H H 8.069 0.000 1 54 17 34 ILE N N 122.124 0.000 1 55 19 36 ALA H H 9.513 0.000 1 56 19 36 ALA N N 130.051 0.000 1 57 20 37 THR H H 8.576 0.000 1 58 20 37 THR N N 108.945 0.000 1 59 21 38 LEU H H 7.105 0.000 1 60 21 38 LEU N N 121.150 0.000 1 61 22 39 MET H H 7.601 0.000 1 62 22 39 MET N N 117.925 0.000 1 63 23 40 GLN H H 7.997 0.000 1 64 23 40 GLN HE22 H 6.830 0.000 1 65 23 40 GLN N N 116.324 0.000 1 66 23 40 GLN NE2 N 111.558 0.006 1 67 24 41 ALA H H 7.711 0.000 1 68 24 41 ALA N N 122.090 0.000 1 69 25 42 LEU H H 7.493 0.000 1 70 25 42 LEU N N 115.349 0.000 1 71 26 43 ASN H H 7.967 0.000 1 72 26 43 ASN HD21 H 6.775 0.000 1 73 26 43 ASN HD22 H 7.518 0.000 1 74 26 43 ASN N N 118.502 0.000 1 75 26 43 ASN ND2 N 111.989 0.001 1 76 27 44 LEU H H 8.216 0.000 1 77 27 44 LEU N N 119.031 0.000 1 78 28 45 ASN H H 8.767 0.000 1 79 28 45 ASN HD21 H 6.831 0.000 1 80 28 45 ASN HD22 H 8.038 0.000 1 81 28 45 ASN N N 120.652 0.000 1 82 28 45 ASN ND2 N 116.253 0.007 1 83 29 46 ILE H H 8.518 0.000 1 84 29 46 ILE N N 120.521 0.000 1 85 30 47 ASP H H 9.108 0.000 1 86 30 47 ASP N N 121.678 0.000 1 87 31 48 ASP H H 8.091 0.000 1 88 31 48 ASP N N 121.847 0.000 1 89 32 49 GLU H H 8.664 0.000 1 90 32 49 GLU N N 121.021 0.000 1 91 33 50 VAL H H 8.483 0.000 1 92 33 50 VAL N N 115.250 0.000 1 93 34 51 LYS H H 8.962 0.000 1 94 34 51 LYS N N 122.218 0.000 1 95 35 52 ILE H H 8.821 0.000 1 96 35 52 ILE N N 124.281 0.000 1 97 36 53 ASP H H 9.002 0.000 1 98 36 53 ASP N N 126.160 0.000 1 99 37 54 LEU H H 8.642 0.000 1 100 37 54 LEU N N 123.524 0.000 1 101 38 55 VAL H H 8.773 0.000 1 102 38 55 VAL N N 126.792 0.000 1 103 39 56 ASP H H 9.168 0.000 1 104 39 56 ASP N N 127.349 0.000 1 105 40 57 GLY H H 8.431 0.000 1 106 40 57 GLY N N 103.109 0.000 1 107 41 58 LYS H H 7.687 0.000 1 108 41 58 LYS N N 117.131 0.000 1 109 42 59 LEU H H 8.598 0.000 1 110 42 59 LEU N N 119.995 0.000 1 111 43 60 ILE H H 9.096 0.000 1 112 43 60 ILE N N 123.912 0.000 1 113 44 61 ILE H H 9.445 0.000 1 114 44 61 ILE N N 126.851 0.000 1 115 45 62 GLU H H 8.975 0.000 1 116 45 62 GLU N N 127.013 0.000 1 117 47 64 VAL H H 7.924 0.000 1 118 47 64 VAL N N 124.329 0.000 1 119 48 65 ARG H H 8.675 0.000 1 120 48 65 ARG HE H 7.286 0.000 1 121 48 65 ARG N N 126.777 0.000 1 122 48 65 ARG NE N 85.000 0.000 1 123 49 66 LYS H H 8.574 0.000 1 124 49 66 LYS N N 124.091 0.000 1 125 50 67 GLU H H 8.024 0.000 1 126 50 67 GLU N N 127.081 0.000 1 stop_ save_