data_235 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Determination of the Coordination Geometry at the Heme Iron in Three Cytochromes c from Saccharomyces cerevisiae and from Candida krusei Based on Individual 1H-NMR Assignments for Heme c and the Axially Coordinated Amino Acids ; _BMRB_accession_number 235 _BMRB_flat_file_name bmr235.str _Entry_type update _Submission_date 1995-07-31 _Accession_date 1996-04-12 _Entry_origination BMRB _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 Senn Hans . . 2 Eugster Albert . . 3 Wuthrich Kurt . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 4 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-06-10 revision BMRB 'Complete natural source information' 2008-09-24 revision BMRB 'Updating non-standard residue' 1999-06-14 revision BMRB 'Converted to BMRB NMR-STAR V 2.1 format' 1996-04-12 revision BMRB 'Error corrected in abrreviations given to non-polymers' 1996-03-25 reformat BMRB 'Converted to the BMRB 1996-03-01 STAR flat-file format' 1995-07-31 original BMRB 'Last release in original BMRB flat-file format' stop_ _Original_release_date 2015-07-28 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full ; Senn, Hans, Eugster, Albert, Wuthrich, Kurt, "Determination of the Coordination Geometry at the Heme Iron in Three Cytochromes c from Saccharomyces cerevisiae and from Candida krusei Based on Individual 1H-NMR Assignments for Heme c and the Axially Coordinated Amino Acids," Biochim. Biophys. Acta 743, 58-68 (1983). ; _Citation_title ; Determination of the Coordination Geometry at the Heme Iron in Three Cytochromes c from Saccharomyces cerevisiae and from Candida krusei Based on Individual 1H-NMR Assignments for Heme c and the Axially Coordinated Amino Acids ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID ? loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Senn Hans . . 2 Eugster Albert . . 3 Wuthrich Kurt . . stop_ _Journal_abbreviation 'Biochim. Biophys. Acta' _Journal_volume 743 _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 58 _Page_last 68 _Year 1983 _Details . save_ ################################## # Molecular system description # ################################## save_system_cytochrome_c _Saveframe_category molecular_system _Mol_system_name 'cytochrome c' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'cytochrome c' $cytochrome_c 'Heme C' $entity_HEC stop_ _System_molecular_weight . _System_oligomer_state ? _System_paramagnetic ? _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_cytochrome_c _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common 'cytochrome c' _Molecular_mass . _Mol_thiol_state . _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 109 _Mol_residue_sequence ; PAPFEQGSAKKGATLFKTRC AQCHTIEAGGPHKVGPNLHG IFSRHSGQAEGYSYTDANKR AGVEWAEPTMSDYLENPXKY IPGTKMAFGGLKKAKDRNDL VTYMLEASK ; loop_ _Residue_seq_code _Residue_label 1 PRO 2 ALA 3 PRO 4 PHE 5 GLU 6 GLN 7 GLY 8 SER 9 ALA 10 LYS 11 LYS 12 GLY 13 ALA 14 THR 15 LEU 16 PHE 17 LYS 18 THR 19 ARG 20 CYS 21 ALA 22 GLN 23 CYS 24 HIS 25 THR 26 ILE 27 GLU 28 ALA 29 GLY 30 GLY 31 PRO 32 HIS 33 LYS 34 VAL 35 GLY 36 PRO 37 ASN 38 LEU 39 HIS 40 GLY 41 ILE 42 PHE 43 SER 44 ARG 45 HIS 46 SER 47 GLY 48 GLN 49 ALA 50 GLU 51 GLY 52 TYR 53 SER 54 TYR 55 THR 56 ASP 57 ALA 58 ASN 59 LYS 60 ARG 61 ALA 62 GLY 63 VAL 64 GLU 65 TRP 66 ALA 67 GLU 68 PRO 69 THR 70 MET 71 SER 72 ASP 73 TYR 74 LEU 75 GLU 76 ASN 77 PRO 78 M3L 79 LYS 80 TYR 81 ILE 82 PRO 83 GLY 84 THR 85 LYS 86 MET 87 ALA 88 PHE 89 GLY 90 GLY 91 LEU 92 LYS 93 LYS 94 ALA 95 LYS 96 ASP 97 ARG 98 ASN 99 ASP 100 LEU 101 VAL 102 THR 103 TYR 104 MET 105 LEU 106 GLU 107 ALA 108 SER 109 LYS stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-08-05 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 1115 "cytochrome c" 100.00 109 100.00 100.00 5.57e-74 BMRB 1117 "cytochrome c" 100.00 109 100.00 100.00 5.57e-74 BMRB 219 "cytochrome c" 100.00 109 98.17 98.17 2.96e-71 BMRB 223 "cytochrome c" 100.00 109 98.17 98.17 2.96e-71 BMRB 226 "cytochrome c" 100.00 109 98.17 98.17 2.96e-71 BMRB 229 "cytochrome c" 100.00 109 100.00 100.00 5.57e-74 GB KGK39453 "hypothetical protein JL09_g1383 [Pichia kudriavzevii]" 100.00 110 97.25 97.25 8.61e-72 SP P00041 "RecName: Full=Cytochrome c" 100.00 109 99.08 99.08 5.45e-74 stop_ save_ ###################### # Polymer residues # ###################### save_chem_comp_M3L _Saveframe_category polymer_residue _Mol_type 'L-PEPTIDE LINKING' _Name_common N-TRIMETHYLLYSINE _BMRB_code M3L _PDB_code M3L _Standard_residue_derivative . _Molecular_mass 189.275 _Mol_paramagnetic . _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons N N N . 0 . ? CA CA C . 0 . ? CB CB C . 0 . ? CG CG C . 0 . ? CD CD C . 0 . ? CE CE C . 0 . ? NZ NZ N . 1 . ? C C C . 0 . ? O O O . 0 . ? OXT OXT O . 0 . ? CM1 CM1 C . 0 . ? CM2 CM2 C . 0 . ? CM3 CM3 C . 0 . ? H H H . 0 . ? H2 H2 H . 0 . ? HA HA H . 0 . ? HB2 HB2 H . 0 . ? HB3 HB3 H . 0 . ? HG2 HG2 H . 0 . ? HG3 HG3 H . 0 . ? HD2 HD2 H . 0 . ? HD3 HD3 H . 0 . ? HE2 HE2 H . 0 . ? HE3 HE3 H . 0 . ? HXT HXT H . 0 . ? HM11 HM11 H . 0 . ? HM12 HM12 H . 0 . ? HM13 HM13 H . 0 . ? HM21 HM21 H . 0 . ? HM22 HM22 H . 0 . ? HM23 HM23 H . 0 . ? HM31 HM31 H . 0 . ? HM32 HM32 H . 0 . ? HM33 HM33 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 N CA ? ? SING N H ? ? SING N H2 ? ? SING CA CB ? ? SING CA C ? ? SING CA HA ? ? SING CB CG ? ? SING CB HB2 ? ? SING CB HB3 ? ? SING CG CD ? ? SING CG HG2 ? ? SING CG HG3 ? ? SING CD CE ? ? SING CD HD2 ? ? SING CD HD3 ? ? SING CE NZ ? ? SING CE HE2 ? ? SING CE HE3 ? ? SING NZ CM1 ? ? SING NZ CM2 ? ? SING NZ CM3 ? ? DOUB C O ? ? SING C OXT ? ? SING OXT HXT ? ? SING CM1 HM11 ? ? SING CM1 HM12 ? ? SING CM1 HM13 ? ? SING CM2 HM21 ? ? SING CM2 HM22 ? ? SING CM2 HM23 ? ? SING CM3 HM31 ? ? SING CM3 HM32 ? ? SING CM3 HM33 ? ? stop_ save_ ############# # Ligands # ############# save_HEC _Saveframe_category ligand _Mol_type "non-polymer (NON-POLYMER)" _Name_common 'HEME C' _BMRB_code HEC _PDB_code HEC _Molecular_mass 618.503 _Mol_charge 0 _Mol_paramagnetic . _Mol_aromatic yes _Details . 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 $cytochrome_c yeast 4909 Eukaryota Fungi Candida krusei 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 $cytochrome_c 'not available' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_one _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling . . mM . stop_ save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_list _Saveframe_category NMR_spectrometer _Manufacturer unknown _Model unknown _Field_strength 0 _Details 'spectrometer information not available' save_ ############################# # NMR applied experiments # ############################# save__1 _Saveframe_category NMR_applied_experiment _Sample_label $sample_one save_ ####################### # Sample conditions # ####################### save_sample_condition_set_one _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 7.2 . na temperature 293 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chem_shift_reference_par_set_one _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_citation_label _Correction_value_citation_label TSP H . . ppm 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_assignment_data_set_one _Saveframe_category assigned_chemical_shifts _Details . loop_ _Sample_label $sample_one stop_ _Sample_conditions_label $sample_condition_set_one _Chem_shift_reference_set_label $chem_shift_reference_par_set_one _Mol_system_component_name 'cytochrome c' _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 . 24 HIS HD2 H 25.5 . 1 2 . 86 MET HG2 H 32.7 . 2 3 . 86 MET HG3 H 25.1 . 2 4 . 86 MET HE H -23.9 . 1 stop_ save_