data_5087 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Characterization of Hydrogenobacter thermophilus Cytochromes c(552) Expressed in the Cytoplasm and Periplasm of Escherichia coli ; _BMRB_accession_number 5087 _BMRB_flat_file_name bmr5087.str _Entry_type original _Submission_date 2001-07-23 _Accession_date 2001-07-24 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details ; Ht p-cyt c-552 is Ht cyt c-552 expressed in the periplasm of E. coli, and has a native-like fold. Ht c-cyt c-552 is Ht cyt c-552 expressed in the cytoplasm of E. coli. Ht c-cyt c-552 retains the N-terminal Met and is less stable than native. The protein reported in the PDB (1AYG) was isolated from the native organism, and these are recombinant samples. ; loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Karan Elizabeth F. . 2 Russell Brandy S. . 3 Bren Kara L. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 24 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2002-08-22 original author . stop_ loop_ _Related_BMRB_accession_number _Relationship 5086 'reduced periplasmic Hydrogenobacter thermophilus cytochrome c-552' 5088 'reduced cytosolic Hydrogenobacter thermophilus cytochrome c-552' 5089 'oxidized cytosolic Hydrogenobacter thermophilus cytochrome c-552' stop_ _Original_release_date 2002-08-22 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Characterization of Hydrogenobacter thermophilus Cytochromes c(552) Expressed in the Cytoplasm and Periplasm of Escherichia coli ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code 21932593 _PubMed_ID 11935350 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Karan Elizabeth F. . 2 Russell Brandy S. . 3 Bren Kara L. . stop_ _Journal_abbreviation 'J. Biol. Inorg. Chem.' _Journal_volume 7 _Journal_issue 3 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 260 _Page_last 272 _Year 2002 _Details . loop_ _Keyword cytochrome thermophilic 'Hydrogenobacter thermophilus' stop_ save_ ################################## # Molecular system description # ################################## save_system_Ht_cyt_c-552 _Saveframe_category molecular_system _Mol_system_name 'Hydrogenobacter thermophilus cytochrome c-552' _Abbreviation_common 'Ht cyt c-552' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'Ht p-cyt c-552' $c-552 heme $HEC stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state monomer _System_paramagnetic yes _System_thiol_state 'all other bound' loop_ _Biological_function 'putative electron transfer' stop_ _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_c-552 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common 'cytochrome c-552' _Abbreviation_common 'cyt c-552' _Molecular_mass 9187 _Mol_thiol_state 'all other bound' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 80 _Mol_residue_sequence ; NEQLAKQKGCMACHDLKAKK VGPAYADVAKKYAGRKDAVD YLAGKIKKGGSGVWGSVPMP PQNVTDAEAKQLAQWILSIK ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 3 ASN 2 4 GLU 3 5 GLN 4 6 LEU 5 7 ALA 6 8 LYS 7 9 GLN 8 10 LYS 9 11 GLY 10 12 CYS 11 13 MET 12 14 ALA 13 15 CYS 14 16 HIS 15 17 ASP 16 18 LEU 17 19 LYS 18 20 ALA 19 21 LYS 20 22 LYS 21 23 VAL 22 24 GLY 23 25 PRO 24 26 ALA 25 27 TYR 26 28 ALA 27 29 ASP 28 30 VAL 29 31 ALA 30 32 LYS 31 33 LYS 32 34 TYR 33 35 ALA 34 36 GLY 35 37 ARG 36 38 LYS 37 39 ASP 38 40 ALA 39 41 VAL 40 42 ASP 41 43 TYR 42 44 LEU 43 45 ALA 44 46 GLY 45 47 LYS 46 48 ILE 47 49 LYS 48 50 LYS 49 51 GLY 50 52 GLY 51 53 SER 52 54 GLY 53 55 VAL 54 56 TRP 55 57 GLY 56 58 SER 57 59 VAL 58 60 PRO 59 61 MET 60 62 PRO 61 63 PRO 62 64 GLN 63 65 ASN 64 66 VAL 65 67 THR 66 68 ASP 67 69 ALA 68 70 GLU 69 71 ALA 70 72 LYS 71 73 GLN 72 74 LEU 73 75 ALA 74 76 GLN 75 77 TRP 76 78 ILE 77 79 LEU 78 80 SER 79 81 ILE 80 82 LYS stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2014-10-26 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 10134 cytc 100.00 80 100.00 100.00 4.89e-49 BMRB 10135 cytc 100.00 80 100.00 100.00 4.89e-49 BMRB 17053 Cc6 100.00 80 100.00 100.00 4.89e-49 BMRB 5086 c-552 100.00 80 100.00 100.00 4.89e-49 BMRB 5088 c-552 100.00 81 100.00 100.00 4.04e-49 BMRB 5089 c-552 100.00 81 100.00 100.00 4.04e-49 BMRB 6033 HT-c552 100.00 80 97.50 97.50 4.34e-47 PDB 1AYG "Solution Structure Of Cytochrome C-552, Nmr, 20 Structures" 98.75 80 100.00 100.00 5.25e-48 PDB 1YNR "Crystal Structure Of The Cytochrome C-552 From Hydrogenobacter Thermophilus At 2.0 Resolution" 100.00 80 100.00 100.00 4.89e-49 PDB 2AI5 "Solution Structure Of Cytochrome C552, Determined By Distributed Computing Implementation For Nmr Data" 98.75 80 100.00 100.00 5.25e-48 PDB 3VYM "Dimeric Hydrogenobacter Thermophilus Cytochrome C552" 100.00 80 100.00 100.00 4.89e-49 DBJ BAI69446 "cytochrome c-552 [Hydrogenobacter thermophilus TK-6]" 100.00 98 100.00 100.00 2.01e-49 EMBL CAA40902 "cytochrome c-552 [Hydrogenobacter thermophilus TK-6]" 100.00 98 100.00 100.00 2.01e-49 GB ADO45379 "cytochrome c class I [Hydrogenobacter thermophilus TK-6]" 100.00 98 100.00 100.00 2.01e-49 REF WP_012963626 "cytochrome C' [Hydrogenobacter thermophilus]" 100.00 98 100.00 100.00 2.01e-49 REF YP_003432647 "cytochrome c-552 [Hydrogenobacter thermophilus TK-6]" 100.00 98 100.00 100.00 2.01e-49 REF YP_005511672 "cytochrome c class I [Hydrogenobacter thermophilus TK-6]" 100.00 98 100.00 100.00 2.01e-49 SP P15452 "RecName: Full=Cytochrome c-552; AltName: Full=Cytochrome c552; Flags: Precursor [Hydrogenobacter thermophilus TK-6]" 100.00 98 100.00 100.00 2.01e-49 stop_ save_ ############# # Ligands # ############# save_HEC _Saveframe_category ligand _Mol_type non-polymer _Name_common "HEC (HEME C)" _BMRB_code . _PDB_code HEC _Molecular_mass 618.503 _Mol_charge 0 _Mol_paramagnetic . _Mol_aromatic yes _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Thu Jun 9 14:10:39 2011 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons FE FE FE . 0 . ? CHA CHA C . 0 . ? CHB CHB C . 0 . ? CHC CHC C . 0 . ? CHD CHD C . 0 . ? NA NA N . 0 . ? C1A C1A C . 0 . ? C2A C2A C . 0 . ? C3A C3A C . 0 . ? C4A C4A C . 0 . ? CMA CMA C . 0 . ? CAA CAA C . 0 . ? CBA CBA C . 0 . ? CGA CGA C . 0 . ? O1A O1A O . 0 . ? O2A O2A O . 0 . ? NB NB N . 0 . ? C1B C1B C . 0 . ? C2B C2B C . 0 . ? C3B C3B C . 0 . ? C4B C4B C . 0 . ? CMB CMB C . 0 . ? CAB CAB C . 0 . ? CBB CBB C . 0 . ? NC NC N . 0 . ? C1C C1C C . 0 . ? C2C C2C C . 0 . ? C3C C3C C . 0 . ? C4C C4C C . 0 . ? CMC CMC C . 0 . ? CAC CAC C . 0 . ? CBC CBC C . 0 . ? ND ND N . 0 . ? C1D C1D C . 0 . ? C2D C2D C . 0 . ? C3D C3D C . 0 . ? C4D C4D C . 0 . ? CMD CMD C . 0 . ? CAD CAD C . 0 . ? CBD CBD C . 0 . ? CGD CGD C . 0 . ? O1D O1D O . 0 . ? O2D O2D O . 0 . ? HHA HHA H . 0 . ? HHB HHB H . 0 . ? HHC HHC H . 0 . ? HHD HHD H . 0 . ? HMA1 HMA1 H . 0 . ? HMA2 HMA2 H . 0 . ? HMA3 HMA3 H . 0 . ? HAA1 HAA1 H . 0 . ? HAA2 HAA2 H . 0 . ? HBA1 HBA1 H . 0 . ? HBA2 HBA2 H . 0 . ? H2A H2A H . 0 . ? HMB1 HMB1 H . 0 . ? HMB2 HMB2 H . 0 . ? HMB3 HMB3 H . 0 . ? HAB HAB H . 0 . ? HBB1 HBB1 H . 0 . ? HBB2 HBB2 H . 0 . ? HBB3 HBB3 H . 0 . ? HMC1 HMC1 H . 0 . ? HMC2 HMC2 H . 0 . ? HMC3 HMC3 H . 0 . ? HAC HAC H . 0 . ? HBC1 HBC1 H . 0 . ? HBC2 HBC2 H . 0 . ? HBC3 HBC3 H . 0 . ? HMD1 HMD1 H . 0 . ? HMD2 HMD2 H . 0 . ? HMD3 HMD3 H . 0 . ? HAD1 HAD1 H . 0 . ? HAD2 HAD2 H . 0 . ? HBD1 HBD1 H . 0 . ? HBD2 HBD2 H . 0 . ? H2D H2D H . 0 . ? stop_ loop_ _Bond_order _Bond_atom_one_atom_name _Bond_atom_two_atom_name _PDB_bond_atom_one_atom_name _PDB_bond_atom_two_atom_name SING FE NA ? ? SING FE NB ? ? SING FE NC ? ? SING FE ND ? ? DOUB CHA C1A ? ? SING CHA C4D ? ? SING CHA HHA ? ? DOUB CHB C4A ? ? SING CHB C1B ? ? SING CHB HHB ? ? DOUB CHC C4B ? ? SING CHC C1C ? ? SING CHC HHC ? ? DOUB CHD C4C ? ? SING CHD C1D ? ? SING CHD HHD ? ? SING NA C1A ? ? SING NA C4A ? ? SING C1A C2A ? ? DOUB C2A C3A ? ? SING C2A CAA ? ? SING C3A C4A ? ? SING C3A CMA ? ? SING CMA HMA1 ? ? SING CMA HMA2 ? ? SING CMA HMA3 ? ? SING CAA CBA ? ? SING CAA HAA1 ? ? SING CAA HAA2 ? ? SING CBA CGA ? ? SING CBA HBA1 ? ? SING CBA HBA2 ? ? DOUB CGA O1A ? ? SING CGA O2A ? ? SING O2A H2A ? ? SING NB C1B ? ? SING NB C4B ? ? DOUB C1B C2B ? ? SING C2B C3B ? ? SING C2B CMB ? ? SING C3B C4B ? ? DOUB C3B CAB ? ? SING CMB HMB1 ? ? SING CMB HMB2 ? ? SING CMB HMB3 ? ? SING CAB CBB ? ? SING CAB HAB ? ? SING CBB HBB1 ? ? SING CBB HBB2 ? ? SING CBB HBB3 ? ? SING NC C1C ? ? SING NC C4C ? ? DOUB C1C C2C ? ? SING C2C C3C ? ? SING C2C CMC ? ? SING C3C C4C ? ? DOUB C3C CAC ? ? SING CMC HMC1 ? ? SING CMC HMC2 ? ? SING CMC HMC3 ? ? SING CAC CBC ? ? SING CAC HAC ? ? SING CBC HBC1 ? ? SING CBC HBC2 ? ? SING CBC HBC3 ? ? SING ND C1D ? ? SING ND C4D ? ? DOUB C1D C2D ? ? SING C2D C3D ? ? SING C2D CMD ? ? DOUB C3D C4D ? ? SING C3D CAD ? ? SING CMD HMD1 ? ? SING CMD HMD2 ? ? SING CMD HMD3 ? ? SING CAD CBD ? ? SING CAD HAD1 ? ? SING CAD HAD2 ? ? SING CBD CGD ? ? SING CBD HBD1 ? ? SING CBD HBD2 ? ? DOUB CGD O1D ? ? SING CGD O2D ? ? SING O2D H2D ? ? 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 $c-552 . 940 Bacteria . Hydrogenobacter thermophilus 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 _Details $c-552 'recombinant technology' 'E. coli' . . . . 'Expressed in the periplasm of E. coli.' stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details 'Samples were oxidized with a 5-fold molar excess of potassium ferricyanide.' loop_ _Mol_label _Concentration_value _Concentration_value_units _Concentration_min_value _Isotopic_labeling $c-552 2.13 mM . . $HEC 2.13 mM . . 'sodium acetate' 120 mM . [U-2H] 'potassium ferricyanide' . mM 11 . stop_ save_ ############################ # Computer software used # ############################ save_FELIX _Saveframe_category software _Name FELIX _Version 97 _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 500 _Details . save_ ############################# # NMR applied experiments # ############################# save_1H_TOCSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '1H TOCSY' _Sample_label $sample_1 save_ save_1H_NOESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '1H NOESY' _Sample_label $sample_1 save_ save_NMR_spec_expt__0_1 _Saveframe_category NMR_applied_experiment _Experiment_name '1H TOCSY' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_2 _Saveframe_category NMR_applied_experiment _Experiment_name '1H NOESY' _BMRB_pulse_sequence_accession_number . _Details . save_ ####################### # Sample conditions # ####################### save_condition_1 _Saveframe_category sample_conditions _Details 'Samples were oxidized with a 5-fold molar excess of potassium ferricyanide.' loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 5 0.1 na temperature 298 0.2 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 _Indirect_shift_ratio_citation_label _Correction_value_citation_label DSS H 1 'methyl protons' ppm 0.0 internal direct . . . 1.0 $entry_citation $entry_citation 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_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '1H TOCSY' '1H NOESY' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $condition_1 _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name heme _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 HEC HMB1 H 18.16 0.05 1 2 . 1 HEC HMB2 H 18.16 0.05 1 3 . 1 HEC HMB3 H 18.16 0.05 1 4 . 1 HEC HMC1 H 22.29 0.05 1 5 . 1 HEC HMC2 H 22.29 0.05 1 6 . 1 HEC HMC3 H 22.29 0.05 1 7 . 1 HEC HAC H 0.25 0.05 1 8 . 1 HEC HBC1 H 1.20 0.05 1 9 . 1 HEC HBC2 H 1.20 0.05 1 10 . 1 HEC HBC3 H 1.20 0.05 1 11 . 1 HEC HMD1 H 22.89 0.05 1 12 . 1 HEC HMD2 H 22.89 0.05 1 13 . 1 HEC HMD3 H 22.89 0.05 1 14 . 1 HEC HAD1 H 3.60 0.05 2 15 . 1 HEC HAA1 H 12.98 0.05 2 16 . 1 HEC HAA2 H 2.20 0.05 2 17 . 1 HEC HBA1 H -1.13 0.05 2 18 . 1 HEC HBA2 H -1.13 0.05 2 19 . 1 HEC HMA1 H 24.28 0.05 1 20 . 1 HEC HMA2 H 24.28 0.05 1 21 . 1 HEC HMA3 H 24.28 0.05 1 22 . 1 HEC HHC H -0.42 0.05 1 23 . 1 HEC HHD H 9.07 0.05 1 24 . 1 HEC HHA H -1.17 0.05 1 stop_ save_