data_6191 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Structure of the C-Terminal Domain of the SecA ATPase ; _BMRB_accession_number 6191 _BMRB_flat_file_name bmr6191.str _Entry_type original _Submission_date 2004-04-22 _Accession_date 2004-04-22 _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 Dempsey B. R. . 2 Wrona M. . . 3 Moulin J. M. . 4 Gloor G. B. . 5 Jalilehvand F. . . 6 Lajoie G. . . 7 Shaw G. S. . 8 Shilton B. H. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 113 "13C chemical shifts" 25 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2004-09-07 original author . stop_ _Original_release_date 2004-09-07 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Solution NMR structure and X-ray absorption analysis of the C-terminal zinc-binding domain of the SecA ATPase' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 15260479 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Dempsey B. R. . 2 Wrona M. . . 3 Moulin J. M. . 4 Gloor G. B. . 5 Jalilehvand F. . . 6 Lajoie G. . . 7 Shaw G. S. . 8 Shilton B. H. . stop_ _Journal_abbreviation Biochemistry _Journal_volume 43 _Journal_issue 29 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 9361 _Page_last 9371 _Year 2004 _Details . loop_ _Keyword 'metal ion' 'no secondary structure' 'structural zinc coordination' 'tetrahedral coordination' zinc stop_ save_ ################################## # Molecular system description # ################################## save_system_SecA _Saveframe_category molecular_system _Mol_system_name SecA _Abbreviation_common SecA _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label SecA $SecA 'ZINC (II) ION' $ZN stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state monomer _System_paramagnetic no _System_thiol_state 'all other bound' _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_SecA _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common SecA _Abbreviation_common SecA _Molecular_mass . _Mol_thiol_state 'all other bound' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 22 _Mol_residue_sequence ; KVGRNDPCPCGSGKKYKQCH GR ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 LYS 2 2 VAL 3 3 GLY 4 4 ARG 5 5 ASN 6 6 ASP 7 7 PRO 8 8 CYS 9 9 PRO 10 10 CYS 11 11 GLY 12 12 SER 13 13 GLY 14 14 LYS 15 15 LYS 16 16 TYR 17 17 LYS 18 18 GLN 19 19 CYS 20 20 HIS 21 21 GLY 22 22 ARG stop_ _Sequence_homology_query_date 2008-08-19 _Sequence_homology_query_revised_last_date 2008-08-19 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 SWISS-PROT A4TQ74 'Protein translocase subunit secA' 100.00 904 100.00 100.00 1.49e-07 SWISS-PROT A6T2E8 'Protein translocase subunit secA' 100.00 920 100.00 100.00 1.49e-07 SWISS-PROT A1JJK2 'Protein translocase subunit secA' 100.00 904 100.00 100.00 1.49e-07 SWISS-PROT A4G8S7 'Protein translocase subunit secA' 100.00 921 100.00 100.00 1.49e-07 REF NP_414640 'preprotein translocase subunit, ATPase [Escherichia coli str. K-12 substr. MG1655]' 100.00 901 100.00 100.00 1.49e-07 SWISS-PROT A1A7E3 'Protein translocase subunit secA' 100.00 901 100.00 100.00 1.49e-07 REF NP_308129 'preprotein translocase subunit SecA [Escherichia coli O157:H7 str. Sakai]' 100.00 901 100.00 100.00 1.49e-07 REF NP_404205 'preprotein translocase subunit SecA [Yersinia pestis CO92]' 100.00 904 100.00 100.00 1.49e-07 REF AP_000761 'preprotein translocase subunit, ATPase that targets protein precursors to the SecYE core translocon [Escherichia coli W3110]' 100.00 901 100.00 100.00 1.49e-07 REF NP_285794 'preprotein translocase subunit SecA [Escherichia coli O157:H7 EDL933]' 100.00 901 100.00 100.00 1.49e-07 GenBank AAM87165 'preprotein translocase; secretion protein [Yersinia pestis KIM]' 100.00 904 100.00 100.00 1.49e-07 GenBank AAN41760 'preprotein translocase; secretion protein [Shigella flexneri 2a str. 301]' 100.00 901 100.00 100.00 1.49e-07 GenBank AAC73209 'preprotein translocase subunit, ATPase [Escherichia coli str. K-12 substr. MG1655]' 100.00 901 100.00 100.00 1.49e-07 GenBank AAG54402 'preprotein translocase; secretion protein [Escherichia coli O157:H7 EDL933]' 100.00 901 100.00 100.00 1.49e-07 EMBL CAL62914 'Preprotein translocase subunit SecA [Herminiimonas arsenicoxydans]' 100.00 921 100.00 100.00 1.49e-07 GenBank AAA24619 'secA protein' 100.00 901 100.00 100.00 1.49e-07 EMBL CAL10790 'preprotein translocase SecA [Yersinia enterocolitica subsp. enterocolitica 8081]' 100.00 904 100.00 100.00 1.49e-07 EMBL CAL19243 'preprotein translocase SecA [Yersinia pestis CO92]' 100.00 904 100.00 100.00 1.49e-07 EMBL CAA38875 'SecA protein [Escherichia coli]' 100.00 901 100.00 100.00 1.49e-07 EMBL CAH19937 'Type II general secretory pathway preprotein translocase ATPase subunit secA [Yersinia pseudotuberculosis IP 32953]' 100.00 904 100.00 100.00 1.49e-07 DBJ BAB33525 'preprotein translocase SecA [Escherichia coli O157:H7 str. Sakai]' 100.00 901 100.00 100.00 1.49e-07 DBJ BAB96666 'preprotein translocase subunit, ATPase that targets protein precursors to the SecYE core translocon [Escherichia coli W3110]' 100.00 901 100.00 100.00 1.49e-07 stop_ save_ ############# # Ligands # ############# save_ZN _Saveframe_category ligand _Mol_type non-polymer _Name_common "ZN (ZINC ION)" _BMRB_code . _PDB_code ZN _Molecular_mass 65.409 _Mol_charge 2 _Mol_paramagnetic . _Mol_aromatic no _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Mon Jun 20 15:04:17 2011 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons ZN ZN ZN . 2 . ? stop_ _Mol_thiol_state . _Sequence_homology_query_date . save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $SecA 'Escherichia 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 $SecA '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 _Isotopic_labeling $SecA 1.7 mM . 'deuterated Pipes buffer' 20 mM . NaCl 50 mM . TCEP 0.5 mM . ZnCl2 3.4 mM . H2O 90 % . D2O 10 % . stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $SecA 3.5 mM . 'deuterated Pipes buffer' 20 mM . NaCl 50 mM . NaN3 5 mM . TCEP 0.5 mM . ZnCl2 7 mM . H2O 90 % . D2O 10 % . stop_ save_ save_sample_3 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $SecA 1.7 mM . 'deuterated Pipes buffer' 20 mM . NaCl 50 mM . NaN3 5 mM . TCEP 0.5 mM . ZnCl2 3.4 mM . D2O 100 % . stop_ save_ save_sample_4 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $SecA 3.5 mM . 'deuterated Pipes buffer' 20 mM . NaCl 50 mM . NaN3 5 mM . TCEP 0.5 mM . ZnCl2 7 mM . D2O 100 % . stop_ save_ ############################ # Computer software used # ############################ save_CNS _Saveframe_category software _Name CNS _Version 1.1 loop_ _Task refinement 'structure solution' stop_ _Details 'Brunger et al.' save_ save_NMRPipe _Saveframe_category software _Name NMRPipe _Version 2.1 loop_ _Task processing stop_ _Details 'Delaglio et al.' save_ save_VNMR _Saveframe_category software _Name VNMR _Version 6.1c loop_ _Task processing stop_ _Details Varian save_ save_PIPP _Saveframe_category software _Name PIPP _Version 4.3.3 loop_ _Task 'data analysis' stop_ _Details 'Garrett et al.' save_ save_STAPP _Saveframe_category software _Name STAPP _Version 4.3.3 loop_ _Task 'data analysis' stop_ _Details 'Garrett et al.' save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_DQF-COSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name DQF-COSY _Sample_label . save_ save_2D_NOESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _Sample_label . save_ ####################### # Sample conditions # ####################### save_sample_cond_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 58.4 . mM pH 7.0 . pH pressure 1 . atm temperature 298 . K stop_ save_ save_sample_cond_2 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 62 . mM pH 7.0 . pH pressure 1 . atm temperature 298 . K 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 DSS C 13 'methyl protons' ppm 0.0 . indirect . . . 0.251449530 DSS H 1 'methyl protons' ppm 0.0 internal direct . . . 1.0 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_set_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_cond_1 _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name SecA _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 LYS H H 8.24 0.01 1 2 1 1 LYS CA C 56.41 0.30 1 3 1 1 LYS HA H 4.22 0.01 1 4 1 1 LYS HB2 H 1.76 0.01 2 5 1 1 LYS HB3 H 1.67 0.01 2 6 1 1 LYS HE2 H 3.00 0.01 2 7 2 2 VAL H H 7.62 0.01 1 8 2 2 VAL CA C 61.06 0.30 1 9 2 2 VAL HA H 4.07 0.01 1 10 2 2 VAL HB H 1.62 0.01 2 11 2 2 VAL HG2 H 0.57 0.01 2 12 3 3 GLY H H 8.75 0.01 1 13 3 3 GLY CA C 44.77 0.30 1 14 3 3 GLY HA2 H 4.21 0.01 2 15 3 3 GLY HA3 H 3.73 0.01 2 16 4 4 ARG H H 8.49 0.01 1 17 4 4 ARG CA C 59.74 0.30 1 18 4 4 ARG HA H 4.12 0.01 1 19 4 4 ARG HB3 H 1.85 0.01 2 20 4 4 ARG HG2 H 1.92 0.01 2 21 4 4 ARG HG3 H 1.83 0.01 2 22 4 4 ARG HD2 H 3.36 0.01 2 23 4 4 ARG HD3 H 3.26 0.01 2 24 5 5 ASN H H 8.56 0.01 1 25 5 5 ASN CA C 52.51 0.30 1 26 5 5 ASN HA H 4.95 0.01 1 27 5 5 ASN HB2 H 3.02 0.01 1 28 5 5 ASN HB3 H 2.68 0.01 1 29 6 6 ASP H H 7.54 0.01 1 30 6 6 ASP CA C 53.13 0.30 1 31 6 6 ASP HA H 4.85 0.01 1 32 6 6 ASP HB2 H 2.74 0.01 1 33 6 6 ASP HB3 H 2.65 0.01 1 34 7 7 PRO CA C 62.80 0.30 1 35 7 7 PRO HA H 4.31 0.01 1 36 7 7 PRO HB2 H 2.24 0.01 2 37 7 7 PRO HB3 H 1.73 0.01 2 38 7 7 PRO HG2 H 2.11 0.01 2 39 7 7 PRO HG3 H 1.95 0.01 2 40 7 7 PRO CD C 50.05 0.30 1 41 7 7 PRO HD2 H 3.88 0.01 2 42 7 7 PRO HD3 H 3.54 0.01 2 43 8 8 CYS H H 9.18 0.01 1 44 8 8 CYS CA C 59.36 0.30 1 45 8 8 CYS HA H 4.56 0.01 1 46 8 8 CYS HB2 H 3.21 0.01 1 47 8 8 CYS HB3 H 2.85 0.01 1 48 9 9 PRO CA C 64.59 0.30 1 49 9 9 PRO HA H 4.41 0.01 1 50 9 9 PRO HB2 H 2.39 0.01 2 51 9 9 PRO HB3 H 2.00 0.01 2 52 9 9 PRO HG2 H 2.00 0.01 2 53 9 9 PRO HG3 H 1.90 0.01 2 54 9 9 PRO CD C 53.35 0.30 1 55 9 9 PRO HD2 H 4.46 0.01 1 56 9 9 PRO HD3 H 3.97 0.01 1 57 10 10 CYS H H 7.67 0.01 1 58 10 10 CYS CA C 59.55 0.30 1 59 10 10 CYS HA H 4.46 0.01 1 60 10 10 CYS HB2 H 3.26 0.01 1 61 10 10 CYS HB3 H 2.43 0.01 1 62 11 11 GLY H H 7.94 0.01 1 63 11 11 GLY CA C 45.96 0.30 1 64 11 11 GLY HA2 H 4.34 0.01 1 65 11 11 GLY HA3 H 3.92 0.01 1 66 12 12 SER H H 8.93 0.01 1 67 12 12 SER CA C 57.16 0.30 1 68 12 12 SER HA H 4.18 0.01 1 69 12 12 SER CB C 63.30 0.30 1 70 12 12 SER HB2 H 4.22 0.01 2 71 12 12 SER HB3 H 3.90 0.01 2 72 13 13 GLY H H 9.43 0.01 1 73 13 13 GLY CA C 44.95 0.30 1 74 13 13 GLY HA2 H 4.35 0.01 1 75 13 13 GLY HA3 H 3.60 0.01 1 76 14 14 LYS H H 7.86 0.01 1 77 14 14 LYS CA C 54.90 0.30 1 78 14 14 LYS HA H 4.45 0.01 1 79 14 14 LYS HB2 H 1.88 0.01 2 80 14 14 LYS HB3 H 1.53 0.01 2 81 14 14 LYS HG2 H 1.40 0.01 2 82 14 14 LYS HD2 H 1.67 0.01 2 83 14 14 LYS HE2 H 2.99 0.01 2 84 15 15 LYS H H 8.50 0.01 1 85 15 15 LYS CA C 56.34 0.30 1 86 15 15 LYS HA H 4.32 0.01 1 87 15 15 LYS HB2 H 1.70 0.01 2 88 15 15 LYS HB3 H 1.57 0.01 2 89 15 15 LYS HG2 H 2.05 0.01 2 90 15 15 LYS HD2 H 1.41 0.01 2 91 15 15 LYS HE2 H 3.04 0.01 2 92 16 16 TYR H H 9.56 0.01 1 93 16 16 TYR CA C 61.69 0.30 1 94 16 16 TYR HA H 4.53 0.01 1 95 16 16 TYR HB2 H 3.26 0.01 1 96 16 16 TYR HB3 H 3.10 0.01 1 97 16 16 TYR HD1 H 7.54 0.01 2 98 16 16 TYR HE1 H 6.80 0.01 2 99 17 17 LYS H H 8.73 0.01 1 100 17 17 LYS CA C 57.66 0.30 1 101 17 17 LYS HA H 3.82 0.01 1 102 17 17 LYS HB2 H 2.02 0.01 2 103 17 17 LYS HB3 H 1.75 0.01 2 104 17 17 LYS HG2 H 1.35 0.01 2 105 17 17 LYS HG3 H 1.16 0.01 2 106 17 17 LYS HD2 H 1.58 0.01 2 107 17 17 LYS HE2 H 2.95 0.01 2 108 17 17 LYS HE3 H 2.81 0.01 2 109 18 18 GLN H H 7.61 0.01 1 110 18 18 GLN CA C 54.52 0.30 1 111 18 18 GLN HA H 4.46 0.01 1 112 18 18 GLN HB2 H 2.32 0.01 2 113 18 18 GLN HB3 H 2.03 0.01 2 114 18 18 GLN HG2 H 2.43 0.01 2 115 18 18 GLN HG3 H 2.18 0.01 2 116 19 19 CYS H H 7.81 0.01 1 117 19 19 CYS CA C 60.50 0.30 1 118 19 19 CYS HA H 4.50 0.01 1 119 19 19 CYS HB2 H 3.05 0.01 1 120 19 19 CYS HB3 H 2.50 0.01 1 121 20 20 HIS H H 8.89 0.01 1 122 20 20 HIS CA C 61.15 0.30 1 123 20 20 HIS HA H 4.34 0.01 1 124 20 20 HIS HB2 H 3.52 0.01 2 125 20 20 HIS HB3 H 3.11 0.01 2 126 20 20 HIS HD2 H 7.35 0.01 2 127 20 20 HIS HE1 H 7.97 0.01 2 128 21 21 GLY H H 7.95 0.01 1 129 21 21 GLY CA C 44.07 0.30 1 130 21 21 GLY HA2 H 3.79 0.01 1 131 21 21 GLY HA3 H 1.71 0.01 1 132 22 22 ARG H H 6.67 0.01 1 133 22 22 ARG CA C 57.85 0.30 1 134 22 22 ARG HA H 3.99 0.01 1 135 22 22 ARG HB2 H 1.60 0.01 2 136 22 22 ARG HG2 H 1.54 0.01 2 137 22 22 ARG HG3 H 1.44 0.01 2 138 22 22 ARG HD2 H 3.11 0.01 2 stop_ save_