data_20108 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Conformational Flexibility of SecA IRA1 Loop Region ; _BMRB_accession_number 20108 _BMRB_flat_file_name bmr20108.str _Entry_type original _Submission_date 2009-11-27 _Accession_date 2009-11-27 _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 Palladino Pasquale . . 2 Saviano Gabriella . . 3 Tancredi Teodorico . . 4 Ragone Raffaele . . 5 Benedetti Ettore . . 6 Rossi Filomena . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 structure_coordinate_set 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 114 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2012-06-28 update BMRB 'coordinate file not annotated' 2011-06-02 original author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 20111 SecA[788-804]Y794A stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Structural determinants of protein translocation in bacteria: conformational flexibility of SecA IRA1 loop region.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 21337475 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Palladino Pasquale . . 2 Saviano Gabriella . . 3 Tancredi Teodorico . . 4 Benedetti Ettore . . 5 Rossi Filomena . . 6 Ragone Raffaele . . stop_ _Journal_abbreviation 'J. Pept. Sci.' _Journal_name_full 'Journal of peptide science : an official publication of the European Peptide Society' _Journal_volume 17 _Journal_issue 4 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 263 _Page_last 269 _Year 2011 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'SecA fragment' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label SecA[788-804] $SecA_788-804 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_SecA_788-804 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common SecA[788-804] _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 17 _Mol_residue_sequence GIHLRGYAQKDPKQEYK loop_ _Residue_seq_code _Residue_label 1 GLY 2 ILE 3 HIS 4 LEU 5 ARG 6 GLY 7 TYR 8 ALA 9 GLN 10 LYS 11 ASP 12 PRO 13 LYS 14 GLN 15 GLU 16 TYR 17 LYS 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 PDB 2FSF "Escherichia Coli Seca, The Preprotein Translocase Dimeric Atpase" 100.00 853 100.00 100.00 7.45e-02 PDB 2FSG "Complex Seca:atp From Escherichia Coli" 100.00 853 100.00 100.00 6.59e-02 PDB 2FSH "Complex Seca:amp-Pnp From Escherichia Coli" 100.00 853 100.00 100.00 7.45e-02 PDB 2FSI "Complex Seca:adp From Escherichia Coli" 100.00 853 100.00 100.00 7.45e-02 PDB 2VDA "Solution Structure Of The Seca-Signal Peptide Complex" 100.00 828 100.00 100.00 5.90e-02 DBJ BAB12918 "preprotein translocase secA subunit [Buchnera aphidicola str. APS (Acyrthosiphon pisum)]" 100.00 875 100.00 100.00 2.49e-02 DBJ BAB33525 "preprotein translocase SecA [Escherichia coli O157:H7 str. Sakai]" 100.00 901 100.00 100.00 8.52e-02 DBJ BAB96666 "preprotein translocase subunit, ATPase that targets protein precursors to the SecYE core translocon [Escherichia coli str. K12 " 100.00 901 100.00 100.00 8.60e-02 DBJ BAC24346 "secA [Wigglesworthia glossinidia endosymbiont of Glossina brevipalpis]" 100.00 832 100.00 100.00 3.13e-02 DBJ BAE73732 "preprotein translocase SecA [Sodalis glossinidius str. 'morsitans']" 100.00 902 100.00 100.00 7.19e-02 EMBL CAA38875 "SecA protein [Escherichia coli str. K-12 substr. W3110]" 100.00 901 100.00 100.00 8.52e-02 EMBL CAD01293 "preprotein translocase SecA subunit [Salmonella enterica subsp. enterica serovar Typhi str. CT18]" 100.00 901 100.00 100.00 8.36e-02 EMBL CAD16541 "probable preprotein translocase seca subunit [Ralstonia solanacearum GMI1000]" 100.00 934 100.00 100.00 7.23e-02 EMBL CAD83669 "preprotein translocase SecA subunit [Candidatus Blochmannia floridanus]" 100.00 840 100.00 100.00 2.29e-02 EMBL CAE16018 "Preprotein translocase SecA subunit [Photorhabdus luminescens subsp. laumondii TTO1]" 100.00 903 100.00 100.00 7.19e-02 GB AAA24619 "secA protein [Escherichia coli]" 100.00 901 100.00 100.00 8.52e-02 GB AAC22566 "preprotein translocase SecA subunit (secA) [Haemophilus influenzae Rd KW20]" 100.00 901 100.00 100.00 6.23e-02 GB AAC73209 "preprotein translocase subunit, ATPase [Escherichia coli str. K-12 substr. MG1655]" 100.00 901 100.00 100.00 8.60e-02 GB AAD22450 "SecA homolog [Aggregatibacter actinomycetemcomitans]" 100.00 899 100.00 100.00 6.41e-02 GB AAG54402 "preprotein translocase; secretion protein [Escherichia coli O157:H7 str. EDL933]" 100.00 901 100.00 100.00 8.52e-02 PIR AE0519 "preprotein translocase SecA chain [imported] - Salmonella enterica subsp. enterica serovar Typhi (strain CT18)" 100.00 901 100.00 100.00 8.36e-02 PIR F84953 "preprotein translocase secA subunit [imported] - Buchnera sp. (strain APS)" 100.00 875 100.00 100.00 2.49e-02 REF NP_240032 "preprotein translocase subunit SecA [Buchnera aphidicola str. APS (Acyrthosiphon pisum)]" 100.00 875 100.00 100.00 2.49e-02 REF NP_308129 "preprotein translocase subunit SecA [Escherichia coli O157:H7 str. Sakai]" 100.00 901 100.00 100.00 8.52e-02 REF NP_414640 "preprotein translocase subunit, ATPase [Escherichia coli str. K-12 substr. MG1655]" 100.00 901 100.00 100.00 8.60e-02 REF NP_439069 "preprotein translocase subunit SecA [Haemophilus influenzae Rd KW20]" 100.00 901 100.00 100.00 6.23e-02 REF NP_454748 "preprotein translocase subunit SecA [Salmonella enterica subsp. enterica serovar Typhi str. CT18]" 100.00 901 100.00 100.00 8.36e-02 SP A1A7E3 "RecName: Full=Protein translocase subunit SecA" 100.00 901 100.00 100.00 8.52e-02 SP A1JJK2 "RecName: Full=Protein translocase subunit SecA" 100.00 904 100.00 100.00 5.06e-02 SP A1SU27 "RecName: Full=Protein translocase subunit SecA" 100.00 906 100.00 100.00 5.78e-02 SP A3MYW1 "RecName: Full=Protein translocase subunit SecA" 100.00 905 100.00 100.00 5.78e-02 SP A4TQ74 "RecName: Full=Protein translocase subunit SecA" 100.00 904 100.00 100.00 5.57e-02 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species _Details $SecA_788-804 . . . . . . 'syntethic peptide' 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 $SecA_788-804 'recombinant technology' . . . . . 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 $SecA_788-804 1 mM 'natural abundance' TFEd2-OH 50 '% v/v' '[U-100% 2H]' H2O 50 '% v/v' 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ 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_NMRView _Saveframe_category software _Name NMRView _Version . loop_ _Vendor _Address _Electronic_address 'Johnson, One Moon Scientific' . . stop_ loop_ _Task 'chemical shift assignment' 'peak picking' 'data analysis' stop_ _Details . save_ save_CYANA _Saveframe_category software _Name CYANA _Version . loop_ _Vendor _Address _Electronic_address 'Guntert, Mumenthaler and Wuthrich' . . stop_ loop_ _Task 'structure solution' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_DRX-600 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 600 _Details 'equipped with a cryoprobe' 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_ save_2D_1H-1H_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_DQF-COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _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 300 . K pH 5.1 . pH stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference_1 _Saveframe_category chemical_shift_reference _Details '4.7 ppm of H2O peak' 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 water H 1 protons ppm 4.7 internal indirect . . . 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_ _Software_label $NMRPipe stop_ loop_ _Experiment_label '2D 1H-15N HSQC' '2D 1H-1H TOCSY' '2D 1H-1H NOESY' 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 SecA[788-804] _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 8.006 0.000 1 2 1 1 GLY HA2 H 3.888 0.000 2 3 1 1 GLY HA3 H 3.754 0.000 2 4 2 2 ILE H H 7.731 0.000 1 5 2 2 ILE HA H 4.011 0.000 1 6 2 2 ILE HB H 1.747 0.000 1 7 2 2 ILE HD1 H 0.784 0.000 1 8 2 2 ILE HG12 H 1.274 0.000 2 9 2 2 ILE HG13 H 1.094 0.000 2 10 2 2 ILE HG2 H 0.777 0.000 1 11 3 3 HIS H H 8.208 0.000 1 12 3 3 HIS HA H 4.628 0.000 1 13 3 3 HIS HB2 H 3.154 0.000 2 14 3 3 HIS HB3 H 3.225 0.000 2 15 3 3 HIS HD2 H 7.235 0.000 1 16 3 3 HIS HE1 H 8.482 0.000 1 17 4 4 LEU H H 7.844 0.000 1 18 4 4 LEU HA H 4.320 0.000 1 19 4 4 LEU HB2 H 1.608 0.000 2 20 4 4 LEU HB3 H 1.559 0.000 2 21 4 4 LEU HD1 H 0.887 0.000 2 22 4 4 LEU HD2 H 0.828 0.000 2 23 5 5 ARG H H 7.924 0.000 1 24 5 5 ARG HA H 4.214 0.000 1 25 5 5 ARG HB2 H 1.792 0.000 2 26 5 5 ARG HB3 H 1.792 0.000 2 27 5 5 ARG HD2 H 3.147 0.000 2 28 5 5 ARG HD3 H 3.147 0.000 2 29 5 5 ARG HE H 7.102 0.000 1 30 5 5 ARG HG2 H 1.614 0.000 2 31 5 5 ARG HG3 H 1.614 0.000 2 32 6 6 GLY H H 8.121 0.000 1 33 6 6 GLY HA2 H 3.842 0.000 2 34 6 6 GLY HA3 H 3.842 0.000 2 35 7 7 TYR H H 7.734 0.000 1 36 7 7 TYR HA H 4.446 0.000 1 37 7 7 TYR HB2 H 2.935 0.000 2 38 7 7 TYR HB3 H 3.024 0.000 2 39 7 7 TYR HD1 H 7.056 0.000 3 40 7 7 TYR HD2 H 7.056 0.000 3 41 7 7 TYR HE1 H 6.770 0.000 3 42 7 7 TYR HE2 H 6.770 0.000 3 43 8 8 ALA H H 7.921 0.000 1 44 8 8 ALA HA H 4.200 0.000 1 45 8 8 ALA HB H 1.326 0.000 1 46 9 9 GLN H H 7.893 0.000 1 47 9 9 GLN HA H 4.230 0.000 1 48 9 9 GLN HB2 H 1.959 0.000 2 49 9 9 GLN HB3 H 2.074 0.000 2 50 9 9 GLN HE21 H 7.399 0.000 2 51 9 9 GLN HE22 H 6.620 0.000 2 52 9 9 GLN HG2 H 2.319 0.000 2 53 9 9 GLN HG3 H 2.319 0.000 2 54 10 10 LYS H H 7.991 0.000 1 55 10 10 LYS HA H 4.279 0.000 1 56 10 10 LYS HB2 H 1.726 0.000 2 57 10 10 LYS HB3 H 1.726 0.000 2 58 10 10 LYS HD2 H 1.635 0.000 2 59 10 10 LYS HD3 H 1.635 0.000 2 60 10 10 LYS HE2 H 2.935 0.000 2 61 10 10 LYS HE3 H 2.935 0.000 2 62 10 10 LYS HG2 H 1.372 0.000 2 63 10 10 LYS HG3 H 1.372 0.000 2 64 11 11 ASP H H 8.137 0.000 1 65 11 11 ASP HA H 4.905 0.000 1 66 11 11 ASP HB2 H 2.645 0.000 2 67 11 11 ASP HB3 H 2.846 0.000 2 68 12 12 PRO HA H 4.349 0.000 1 69 12 12 PRO HB3 H 2.295 0.000 2 70 12 12 PRO HD3 H 3.925 0.000 2 71 12 12 PRO HG3 H 1.987 0.000 2 72 13 13 LYS H H 8.155 0.000 1 73 13 13 LYS HA H 4.153 0.000 1 74 13 13 LYS HB2 H 1.823 0.000 2 75 13 13 LYS HB3 H 1.823 0.000 2 76 13 13 LYS HD2 H 1.703 0.000 2 77 13 13 LYS HD3 H 1.703 0.000 2 78 13 13 LYS HE2 H 2.975 0.000 2 79 13 13 LYS HE3 H 2.975 0.000 2 80 13 13 LYS HG2 H 1.440 0.000 2 81 13 13 LYS HG3 H 1.440 0.000 2 82 14 14 GLN H H 7.857 0.000 1 83 14 14 GLN HA H 4.217 0.000 1 84 14 14 GLN HB2 H 2.013 0.000 2 85 14 14 GLN HB3 H 2.116 0.000 2 86 14 14 GLN HE21 H 7.502 0.000 2 87 14 14 GLN HE22 H 6.654 0.000 2 88 14 14 GLN HG2 H 2.316 0.000 2 89 14 14 GLN HG3 H 2.316 0.000 2 90 15 15 GLU H H 7.943 0.000 1 91 15 15 GLU HA H 4.217 0.000 1 92 15 15 GLU HB2 H 1.905 0.000 2 93 15 15 GLU HB3 H 1.905 0.000 2 94 15 15 GLU HG2 H 2.264 0.000 2 95 15 15 GLU HG3 H 2.264 0.000 2 96 16 16 TYR H H 7.909 0.000 1 97 16 16 TYR HA H 4.486 0.000 1 98 16 16 TYR HB2 H 2.944 0.000 2 99 16 16 TYR HB3 H 3.026 0.000 2 100 16 16 TYR HD1 H 7.090 0.000 3 101 16 16 TYR HD2 H 7.090 0.000 3 102 16 16 TYR HE1 H 6.794 0.000 3 103 16 16 TYR HE2 H 6.794 0.000 3 104 17 17 LYS H H 7.798 0.000 1 105 17 17 LYS HA H 4.217 0.000 1 106 17 17 LYS HB2 H 1.808 0.000 2 107 17 17 LYS HB3 H 1.808 0.000 2 108 17 17 LYS HD2 H 1.653 0.000 2 109 17 17 LYS HD3 H 1.653 0.000 2 110 17 17 LYS HE2 H 2.927 0.000 2 111 17 17 LYS HE3 H 2.927 0.000 2 112 17 17 LYS HG2 H 1.362 0.000 2 113 17 17 LYS HG3 H 1.362 0.000 2 114 17 17 LYS HZ H 7.531 0.000 1 stop_ save_