data_2488 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Assignment of hyperfine-shifted resonances in yeast ferricytochrome c isozyme 2 using the proton pre-steady-state nuclear Overhauser effect ; _BMRB_accession_number 2488 _BMRB_flat_file_name bmr2488.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 Satterlee James D. . 2 Avizonis Daina Z. . 3 Moench Susan J. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 10 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-06-17 revision BMRB 'Complete natural source information' 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 ; Satterlee, James D., Avizonis, Daina Z., Moench, Susan J., "Assignment of hyperfine-shifted resonances in yeast ferricytochrome c isozyme 2 using the proton pre-steady-state nuclear Overhauser effect," Biochim. Biophys. Acta 952, 317-324 (1988). ; _Citation_title ; Assignment of hyperfine-shifted resonances in yeast ferricytochrome c isozyme 2 using the proton pre-steady-state nuclear Overhauser effect ; _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 Satterlee James D. . 2 Avizonis Daina Z. . 3 Moench Susan J. . stop_ _Journal_abbreviation 'Biochim. Biophys. Acta' _Journal_volume 952 _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 317 _Page_last 324 _Year 1988 _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' _Name_variant 'isozyme 2' _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 112 _Mol_residue_sequence ; AKESTGFKPGSAKKGATLFK KRCQQCHTIEEGGPNKVGPN LHGIFGRHSGQVKGYSYYTA NINKNVKWDEDSMSEYLTNP KKYIPGTKMAFAGLKKEKDR NDLITYMTKAAK ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 -8 ALA 2 -7 LYS 3 -6 GLU 4 -5 SER 5 -4 THR 6 -3 GLY 7 -2 PHE 8 -1 LYS 9 0 PRO 10 1 GLY 11 2 SER 12 3 ALA 13 4 LYS 14 5 LYS 15 6 GLY 16 7 ALA 17 8 THR 18 9 LEU 19 10 PHE 20 11 LYS 21 12 LYS 22 13 ARG 23 14 CYS 24 15 GLN 25 16 GLN 26 17 CYS 27 18 HIS 28 19 THR 29 20 ILE 30 21 GLU 31 22 GLU 32 23 GLY 33 24 GLY 34 25 PRO 35 26 ASN 36 27 LYS 37 28 VAL 38 29 GLY 39 30 PRO 40 31 ASN 41 32 LEU 42 33 HIS 43 34 GLY 44 35 ILE 45 36 PHE 46 37 GLY 47 38 ARG 48 39 HIS 49 40 SER 50 41 GLY 51 42 GLN 52 43 VAL 53 44 LYS 54 45 GLY 55 46 TYR 56 47 SER 57 48 TYR 58 49 TYR 59 50 THR 60 51 ALA 61 52 ASN 62 53 ILE 63 54 ASN 64 55 LYS 65 56 ASN 66 57 VAL 67 58 LYS 68 59 TRP 69 60 ASP 70 61 GLU 71 62 ASP 72 63 SER 73 64 MET 74 65 SER 75 66 GLU 76 67 TYR 77 68 LEU 78 69 THR 79 70 ASN 80 71 PRO 81 72 LYS 82 73 LYS 83 74 TYR 84 75 ILE 85 76 PRO 86 77 GLY 87 78 THR 88 79 LYS 89 80 MET 90 81 ALA 91 82 PHE 92 83 ALA 93 84 GLY 94 85 LEU 95 86 LYS 96 87 LYS 97 88 GLU 98 89 LYS 99 90 ASP 100 91 ARG 101 92 ASN 102 93 ASP 103 94 LEU 104 95 ILE 105 96 THR 106 97 TYR 107 98 MET 108 99 THR 109 100 LYS 110 101 ALA 111 102 ALA 112 103 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 1416 "cytochrome c" 100.00 112 98.21 98.21 1.09e-73 BMRB 228 "cytochrome c" 100.00 112 100.00 100.00 2.03e-76 BMRB 234 "cytochrome c" 100.00 112 100.00 100.00 2.03e-76 BMRB 2489 "cytochrome c" 100.00 112 98.21 98.21 1.09e-73 DBJ GAA22787 "K7_Cyc7p [Saccharomyces cerevisiae Kyokai no. 7]" 100.00 113 97.32 97.32 1.36e-73 EMBL CAA24606 "unnamed protein product [Saccharomyces cerevisiae]" 100.00 113 97.32 97.32 1.36e-73 EMBL CAY79121 "Cyc7p [Saccharomyces cerevisiae EC1118]" 100.00 113 97.32 97.32 1.36e-73 GB AAA34940 "cytochrome c isozyme [Saccharomyces cerevisiae]" 100.00 113 97.32 97.32 1.36e-73 GB AAB59339 "iso-2-cytochrome c [Saccharomyces cerevisiae]" 100.00 113 97.32 97.32 1.36e-73 GB AAB65003 "Cyc7p: cytochrome c, isoform-2 [Saccharomyces cerevisiae]" 100.00 113 97.32 97.32 1.36e-73 GB AAD13974 "Unknown [Saccharomyces cerevisiae]" 100.00 113 97.32 97.32 1.36e-73 GB AAT93051 "YEL039C [Saccharomyces cerevisiae]" 100.00 113 97.32 97.32 1.36e-73 REF NP_010875 "cytochrome c isoform 2 [Saccharomyces cerevisiae S288c]" 100.00 113 97.32 97.32 1.36e-73 SP P00045 "RecName: Full=Cytochrome c iso-2" 100.00 113 97.32 97.32 1.36e-73 TPG DAA07614 "TPA: cytochrome c isoform 2 [Saccharomyces cerevisiae S288c]" 100.00 113 97.32 97.32 1.36e-73 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 'not present' _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 4932 Eukaryota Fungi Saccharomyces cerevisiae 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_ ############################# # 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 6.9 . na temperature 297 . 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 HOD H . . ppm 4.63 . . . . . $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 . 27 HIS HA H 9 . 1 2 . 27 HIS HB2 H 14.1 . 2 3 . 27 HIS HB3 H 9 . 2 4 . 89 MET HB2 H 1.65 . 2 5 . 89 MET HB3 H 4.96 . 2 6 . 89 MET HG2 H 26.1 . 2 7 . 89 MET HG3 H 31.6 . 2 8 . 89 MET HE H -22.5 . 1 9 . 89 MET HE H -22.5 . 1 10 . 89 MET HE H -22.5 . 1 stop_ save_