data_25235 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; The solution structure of the FtsH periplasmic N-domain ; _BMRB_accession_number 25235 _BMRB_flat_file_name bmr25235.str _Entry_type original _Submission_date 2014-09-18 _Accession_date 2014-09-18 _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 Scharfenberg Franka . . 2 Serek-Heuberger Justyna . . 3 Martin Joerg . . 4 Lupas Andrei N. . 5 Coles Murray . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 19 "13C chemical shifts" 12 "15N chemical shifts" 3 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2016-09-22 update BMRB 'update entry citation' 2015-01-27 original author 'original release' stop_ _Original_release_date 2016-09-22 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Structure and Evolution of N-domains in AAA Metalloproteases ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 25576874 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Scharfenberg Franka . . 2 Serek-Heuberger Justyna . . 3 Coles Murray . . 4 Hartmann Marcus D. . 5 Habeck Michael . . 6 Martin Joerg . . 7 Lupas Andrei N. . 8 Alva Vikram . . stop_ _Journal_abbreviation 'J. Mol. Biol.' _Journal_volume 427 _Journal_issue 4 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 910 _Page_last 923 _Year 2015 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'FtsH periplasmic N-domain' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'FtsH periplasmic N-domain' $FtsH-N 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_FtsH-N _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common FtsH-N _Molecular_mass 9545.674 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 82 _Mol_residue_sequence ; MASESNGRKVDYSTFLQEVN NDQVREARINGREINVTKKD SNRYTTYIPVQDPKLLDNLL TKNVKVVGEPPEEPLEHHHH HH ; loop_ _Residue_seq_code _Residue_label 1 MET 2 ALA 3 SER 4 GLU 5 SER 6 ASN 7 GLY 8 ARG 9 LYS 10 VAL 11 ASP 12 TYR 13 SER 14 THR 15 PHE 16 LEU 17 GLN 18 GLU 19 VAL 20 ASN 21 ASN 22 ASP 23 GLN 24 VAL 25 ARG 26 GLU 27 ALA 28 ARG 29 ILE 30 ASN 31 GLY 32 ARG 33 GLU 34 ILE 35 ASN 36 VAL 37 THR 38 LYS 39 LYS 40 ASP 41 SER 42 ASN 43 ARG 44 TYR 45 THR 46 THR 47 TYR 48 ILE 49 PRO 50 VAL 51 GLN 52 ASP 53 PRO 54 LYS 55 LEU 56 LEU 57 ASP 58 ASN 59 LEU 60 LEU 61 THR 62 LYS 63 ASN 64 VAL 65 LYS 66 VAL 67 VAL 68 GLY 69 GLU 70 PRO 71 PRO 72 GLU 73 GLU 74 PRO 75 LEU 76 GLU 77 HIS 78 HIS 79 HIS 80 HIS 81 HIS 82 HIS stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . 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 GB CDL26129.1 FtsH . . . . . stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $FtsH-N '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 $FtsH-N 'recombinant technology' . Escherichia coli 'C41 (DE3)' pET28b stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_15N-labelled _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $FtsH-N 0.7 mM '[U-100% 15N]' 'sodium phosphate' 15 mM 'natural abundance' 'sodium chloride' 75 mM 'natural abundance' stop_ save_ save_13C-15N-labelled _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $FtsH-N 0.7 mM '[U-100% 13C; U-100% 15N]' 'sodium phosphate' 15 mM 'natural abundance' 'sodium chloride' 75 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_TOPSPIN _Saveframe_category software _Name TOPSPIN _Version . loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task collection processing stop_ _Details . save_ save_SPARKY _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' 'data analysis' stop_ _Details . save_ save_X-PLOR_NIH _Saveframe_category software _Name X-PLOR_NIH _Version 2.9.4 loop_ _Vendor _Address _Electronic_address 'Schwieters, Kuszewski, Tjandra and Clore' . . stop_ loop_ _Task refinement 'structure solution' stop_ _Details . save_ save_NMR-SPIRIT _Saveframe_category software _Name NMR-SPIRIT _Version 1.1 loop_ _Vendor _Address _Electronic_address 'In house' . . stop_ loop_ _Task refinement stop_ _Details '3D-NOESY back-calculation suite' save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_600 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 600 _Details . save_ save_750 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DMX _Field_strength 750 _Details . save_ save_900 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 900 _Details . save_ ############################# # NMR applied experiments # ############################# save_3D_CBCA(CO)NH_1 _Saveframe_category NMR_applied_experiment _Experiment_name '3D CBCA(CO)NH' _Sample_label $13C-15N-labelled save_ save_3D_HNCACB_2 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HNCACB' _Sample_label $13C-15N-labelled save_ save_3D_HNCO_3 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HNCO' _Sample_label $13C-15N-labelled save_ save_3D_HN(CA)CO_4 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HN(CA)CO' _Sample_label $13C-15N-labelled save_ save_3D_C(CO)NH_5 _Saveframe_category NMR_applied_experiment _Experiment_name '3D C(CO)NH' _Sample_label $13C-15N-labelled save_ save_3D_HCCH-TOCSY_6 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HCCH-TOCSY' _Sample_label $13C-15N-labelled save_ save_3D_CCH_NOESY_7 _Saveframe_category NMR_applied_experiment _Experiment_name '3D CCH NOESY' _Sample_label $13C-15N-labelled save_ save_3D_CNH_NOESY_8 _Saveframe_category NMR_applied_experiment _Experiment_name '3D CNH NOESY' _Sample_label $13C-15N-labelled save_ save_3D_1H-15N_NOESY_9 _Saveframe_category NMR_applied_experiment _Experiment_name '3D 1H-15N NOESY' _Sample_label $15N-labelled save_ save_3D_1H-13C_NOESY_10 _Saveframe_category NMR_applied_experiment _Experiment_name '3D 1H-13C NOESY' _Sample_label $13C-15N-labelled save_ save_3D_HNHA_11 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HNHA' _Sample_label $15N-labelled save_ save_3D_HNHB_12 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HNHB' _Sample_label $15N-labelled 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' 0.105 . M pH 7.2 . pH pressure 1 . atm temperature 298 . 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 2.60 . 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 $TOPSPIN $SPARKY stop_ loop_ _Experiment_label '3D CBCA(CO)NH' '3D HNCACB' '3D HNCO' '3D HN(CA)CO' '3D C(CO)NH' '3D HCCH-TOCSY' '3D HNHA' '3D HNHB' stop_ loop_ _Sample_label $13C-15N-labelled $15N-labelled stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'FtsH periplasmic N-domain' _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 26 26 GLU H H 8.20 0.02 1 2 26 26 GLU HA H 5.30 0.02 1 3 26 26 GLU HB2 H 1.88 0.02 1 4 26 26 GLU HB3 H 1.81 0.02 1 5 26 26 GLU HG2 H 2.04 0.02 2 6 26 26 GLU HG3 H 1.93 0.02 2 7 26 26 GLU C C 172.42 0.05 1 8 26 26 GLU CA C 54.62 0.05 1 9 26 26 GLU CB C 34.81 0.05 1 10 26 26 GLU CG C 37.28 0.05 1 11 26 26 GLU N N 119.26 0.05 1 12 42 42 ASN H H 8.42 0.02 1 13 42 42 ASN HA H 4.64 0.02 1 14 42 42 ASN HB2 H 3.08 0.02 1 15 42 42 ASN HB3 H 2.71 0.02 1 16 42 42 ASN HD21 H 7.56 0.02 1 17 42 42 ASN HD22 H 6.98 0.02 1 18 42 42 ASN C C 174.04 0.05 1 19 42 42 ASN CA C 54.91 0.05 1 20 42 42 ASN CB C 39.42 0.05 1 21 42 42 ASN N N 121.32 0.05 1 22 42 42 ASN ND2 N 114.62 0.05 1 23 71 71 PRO HA H 4.37 0.02 1 24 71 71 PRO HB2 H 1.84 0.02 1 25 71 71 PRO HB3 H 2.19 0.02 1 26 71 71 PRO HG2 H 1.95 0.02 1 27 71 71 PRO HG3 H 1.95 0.02 1 28 71 71 PRO HD2 H 3.72 0.02 1 29 71 71 PRO HD3 H 3.72 0.02 1 30 71 71 PRO C C 176.52 0.05 1 31 71 71 PRO CA C 62.76 0.05 1 32 71 71 PRO CB C 31.72 0.05 1 33 71 71 PRO CG C 27.45 0.05 1 34 71 71 PRO CD C 50.69 0.05 1 stop_ save_