data_5660 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Partial proton resonance assignements for the different conformers of ferricytochrome c produced in 30% acetonitrile and 70% water solution ; _BMRB_accession_number 5660 _BMRB_flat_file_name bmr5660.str _Entry_type original _Submission_date 2003-01-14 _Accession_date 2003-01-14 _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 Sivakolundu Sivashankar G. . 2 Mabrouk Patricia A. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 5 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 39 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2003-02-25 original author . stop_ loop_ _Related_BMRB_accession_number _Relationship 5372 'chemical shifts and coupling constants of reduced cytochrome c.' stop_ _Original_release_date 2003-02-25 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Insights into the Alkaline Transformation of Ferricyt c from 1H NMR Study in 30% Acetonitrile-Water ; _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 Sivakolundu Sivashankar G. . 2 Mabrouk Patricia A. . stop_ _Journal_abbreviation 'Protein Sci.' _Journal_volume 10 _Journal_issue 11 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 2291 _Page_last 2300 _Year 2001 _Details ; The V* form described in the citation is a histidine-ligated conformer of ferricyt c and not hydroxide-ligated cyt c. This was proved later and submitted for publication by the same authors in Journal of Inorganic Biochemistry in 2003. ; loop_ _Keyword 'alkaline transition' 'non-aqueous enzymology' stop_ save_ ####################################### # Cited references within the entry # ####################################### save_ref_1 _Saveframe_category citation _Citation_full ; Wilson MT, Greenwood C (1996) In: Scott RA, Mauk AG (eds) Cytochrome c: A Multidisciplinary Approach. University Science Books, Sausalito, California p 738. ; _Citation_title . _Citation_status . _Citation_type . _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID ? _Journal_abbreviation . _Journal_name_full . _Journal_volume . _Journal_issue . _Journal_CSD . _Book_title . _Book_chapter_title . _Book_volume . _Book_series . _Book_publisher . _Book_publisher_city . _Book_ISBN . _Conference_title . _Conference_site . _Conference_state_province . _Conference_country . _Conference_start_date . _Conference_end_date . _Conference_abstract_number . _Thesis_institution . _Thesis_institution_city . _Thesis_institution_country . _Page_first . _Page_last . _Year . _Details . save_ save_ref_2 _Saveframe_category citation _Citation_full ; Pollock WBR, Rosell FI, Twitchett MB, Dumont ME, Mauk AG (1998) Biochemistry 37: 6124-6131. ; _Citation_title 'Bacterial expression of a mitochondrial cytochrome c. Trimethylation of lys72 in yeast iso-1-cytochrome c and the alkaline conformational transition.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 9558351 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Pollock 'W. B.' B. . 2 Rosell 'F. I.' I. . 3 Twitchett 'M. B.' B. . 4 Dumont 'M. E.' E. . 5 Mauk 'A. G.' G. . stop_ _Journal_abbreviation Biochemistry _Journal_name_full Biochemistry _Journal_volume 37 _Journal_issue 17 _Journal_CSD . _Book_title . _Book_chapter_title . _Book_volume . _Book_series . _Book_publisher . _Book_publisher_city . _Book_ISBN . _Conference_title . _Conference_site . _Conference_state_province . _Conference_country . _Conference_start_date . _Conference_end_date . _Conference_abstract_number . _Thesis_institution . _Thesis_institution_city . _Thesis_institution_country . _Page_first 6124 _Page_last 6131 _Year 1998 _Details ; Saccharomyces cerevisiae iso-1-cytochrome c has been expressed in Escherichia coli by coexpression of the genes encoding the cytochrome (CYC1) and yeast cytochrome c heme lyase (CYC3). Construction of this expression system involved cloning the two genes in parallel into the vector pUC18 to give the plasmid pBPCYC1(wt)/3. Transcription was directed by two promoters, Lac and Trc, that were located upstream from CYC1. Both proteins were expressed in the cytoplasm of E. coli cells harboring the plasmid. Semianaerobic cultures grown in a fermentor produced 15 mg of recombinant iso-1-cytochrome c per liter of culture. Attempts to increase production by addition of IPTG suppressed the number of copies of the CYC1 gene within the population. Wild-type iso-1-cytochrome c expressed with pBPCYC1(wt)/3 in E. coli was compared to the same protein expressed in yeast. At neutral pH, the two proteins exhibit indistinguishable spectroscopic and physical (Tm, Em') characteristics. However, electrospray mass spectrometry revealed that the lysyl residue at position 72 is not trimethylated by E. coli as it is by S. cerevisiae. Interestingly, the pKa of the alkaline transition of the protein expressed in E. coli is approximately 0.6 pKa unit lower than that observed for the cytochrome expressed in yeast (8.5-8.7). 1H NMR spectroscopy of the bacterially expressed cytochrome collected at high pH revealed the presence of a third alkaline conformer that is not observed in the corresponding spectrum of the cytochrome expressed in yeast. These observations suggest that Lys72 can serve as an axial ligand to the heme iron of alkaline iso-1-ferricytochrome c if it is not modified posttranscriptionally to trimethyllysine. ; save_ save_ref_3 _Saveframe_category citation _Citation_full ; Russell BS, Melenkivitz R, Bren KL (2000) Proc. Natl. Acad. Sci. U.S.A. 97: 8312-8317. ; _Citation_title 'NMR investigation of ferricytochrome c unfolding: detection of an equilibrium unfolding intermediate and residual structure in the denatured state.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 10880578 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Russell 'B. S.' S. . 2 Melenkivitz R. . . 3 Bren 'K. L.' L. . stop_ _Journal_abbreviation 'Proc. Natl. Acad. Sci. U.S.A.' _Journal_name_full 'Proceedings of the National Academy of Sciences of the United States of America' _Journal_volume 97 _Journal_issue 15 _Journal_CSD . _Book_title . _Book_chapter_title . _Book_volume . _Book_series . _Book_publisher . _Book_publisher_city . _Book_ISBN . _Conference_title . _Conference_site . _Conference_state_province . _Conference_country . _Conference_start_date . _Conference_end_date . _Conference_abstract_number . _Thesis_institution . _Thesis_institution_city . _Thesis_institution_country . _Page_first 8312 _Page_last 8317 _Year 2000 _Details ; Horse ferricytochrome c (cyt c) undergoes exchange of one of its axial heme ligands (Met-80) for one or more non-native ligands under denaturing conditions. We have used (1)H NMR spectroscopy to detect two conformations of paramagnetic cyt c with non-native heme ligation through a range of urea concentrations. One non-native form is an equilibrium unfolding intermediate observed under partially denaturing conditions and is attributed to replacement of Met-80 with one or more Lys side chains. The second non-native form, in which the native Met ligand is replaced by a His, is observed under strongly denaturing conditions. Thermodynamic analysis of these data indicates a relatively small DeltaG (17 kJ/mol) for the transition from native to the Lys-ligated intermediate and a significantly larger DeltaG (47 kJ/mol) for the transition from native to the His-ligated species. Although CD and fluorescence data indicate that the equilibrium unfolding of cyt c is a two-state process, these NMR results implicate an intermediate with His-Lys ligation. ; save_ ################################## # Molecular system description # ################################## save_system_cyt_c _Saveframe_category molecular_system _Mol_system_name 'oxidized cytochrome c' _Abbreviation_common 'cyt c' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'cytochrome c' $cyt_c 'HEME C' $HEM stop_ _System_molecular_weight . _System_physical_state denatured _System_oligomer_state monomer _System_paramagnetic yes _System_thiol_state 'all other bound' loop_ _Biological_function 'electron transfer' 'cell apoptosis' stop_ _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_cyt_c _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common 'oxidized cytochrome c' _Abbreviation_common 'cyt c' _Molecular_mass 12384 _Mol_thiol_state 'all other bound' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 104 _Mol_residue_sequence ; GDVEKGKKIFVQKCAQCHTV EKGGKHKTGPNLHGLFGRKT GQAPGFTYTDANKNKGITWK EETLMEYLENPKKYIPGTKM IFAGIKKKTEREDLIAYLKK ATNE ; loop_ _Residue_seq_code _Residue_label 1 GLY 2 ASP 3 VAL 4 GLU 5 LYS 6 GLY 7 LYS 8 LYS 9 ILE 10 PHE 11 VAL 12 GLN 13 LYS 14 CYS 15 ALA 16 GLN 17 CYS 18 HIS 19 THR 20 VAL 21 GLU 22 LYS 23 GLY 24 GLY 25 LYS 26 HIS 27 LYS 28 THR 29 GLY 30 PRO 31 ASN 32 LEU 33 HIS 34 GLY 35 LEU 36 PHE 37 GLY 38 ARG 39 LYS 40 THR 41 GLY 42 GLN 43 ALA 44 PRO 45 GLY 46 PHE 47 THR 48 TYR 49 THR 50 ASP 51 ALA 52 ASN 53 LYS 54 ASN 55 LYS 56 GLY 57 ILE 58 THR 59 TRP 60 LYS 61 GLU 62 GLU 63 THR 64 LEU 65 MET 66 GLU 67 TYR 68 LEU 69 GLU 70 ASN 71 PRO 72 LYS 73 LYS 74 TYR 75 ILE 76 PRO 77 GLY 78 THR 79 LYS 80 MET 81 ILE 82 PHE 83 ALA 84 GLY 85 ILE 86 LYS 87 LYS 88 LYS 89 THR 90 GLU 91 ARG 92 GLU 93 ASP 94 LEU 95 ILE 96 ALA 97 TYR 98 LEU 99 LYS 100 LYS 101 ALA 102 THR 103 ASN 104 GLU 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 P68097 'Cytochrome c' 100.00 105 99.04 100.00 1.64e-53 SWISS-PROT P68096 'Cytochrome c' 100.00 105 99.04 100.00 1.64e-53 SWISS-PROT P00004 'Cytochrome c' 100.00 105 100.00 100.00 9.71e-54 REF XP_001498872 'PREDICTED: similar to Cytochrome c, somatic [Equus caballus]' 100.00 105 99.04 100.00 1.64e-53 PRF 610169A 'cytochrome c' 100.00 104 100.00 100.00 1.19e-53 GenBank AAB33495 'apocytochrome c [horses, heart, Peptide, 104 aa]' 100.00 104 98.08 98.08 4.15e-52 PDB 2PCB 'Crystal Structure Of A Complex Between Electron Transfer Partners, Cytochrome C Peroxidase And Cytochrome C' 100.00 104 100.00 100.00 1.19e-53 PDB 2GIW 'Solution Structure Of Reduced Horse Heart Cytochrome C, Nmr, 40 Structures' 100.00 104 100.00 100.00 1.19e-53 PDB 2FRC 'Cytochrome C (Reduced) From Equus Caballus, Nmr, Minimized Average Structure' 100.00 104 100.00 100.00 1.19e-53 PDB 1WEJ 'Igg1 Fab Fragment (Of E8 Antibody) Complexed With Horse Cytochrome C At 1.8 A Resolution' 100.00 104 100.00 100.00 1.19e-53 PDB 1U75 'Electron Transfer Complex Between Horse Heart Cytochrome C And Zinc-Porphyrin Substituted Cytochrome C Peroxidase' 100.00 104 100.00 100.00 1.19e-53 PDB 1OCD 'Cytochrome C (Oxidized) From Equus Caballus, Nmr, Minimized Average Structure' 100.00 104 100.00 100.00 1.19e-53 PDB 1M60 'Solution Structure Of Zinc-Substituted Cytochrome C' 100.00 104 100.00 100.00 1.19e-53 PDB 1LC2 'Solution Structure Of Reduced Horse Heart Cytochrome C In 30% Acetonitrile Solution, Nmr 30 Structures' 100.00 104 100.00 100.00 1.19e-53 PDB 1LC1 'Solution Structure Of Reduced Horse Heart Cytochrome C In 30% Acetonitrile Solution, Nmr Minimized Average Structure' 100.00 104 100.00 100.00 1.19e-53 PDB 1I5T 'Solution Structure Of Cyanoferricytochrome C' 100.00 104 100.00 100.00 1.19e-53 PDB 1HRC 'High-Resolution Three-Dimensional Structure Of Horse Heart Cytochrome C' 100.00 104 100.00 100.00 1.19e-53 PDB 1GIW 'Solution Structure Of Reduced Horse Heart Cytochrome C, Nmr, Minimized Average Structure' 99.04 104 100.00 100.00 4.08e-53 PDB 1FI9 'Solution Structure Of The Imidazole Complex Of Cytochrome C' 100.00 104 100.00 100.00 1.19e-53 PDB 1FI7 'Solution Structure Of The Imidazole Complex Of Cytochrome C' 100.00 104 100.00 100.00 1.19e-53 PDB 1CRC 'Cytochrome C At Low Ionic Strength' 100.00 104 100.00 100.00 1.19e-53 PDB 1AKK 'Solution Structure Of Oxidized Horse Heart Cytochrome C, Nmr, Minimized Average Structure' 100.00 104 100.00 100.00 1.19e-53 BMRB 948 'cytochrome c' 99.04 104 98.06 98.06 4.26e-51 BMRB 947 'cytochrome c' 99.04 104 98.06 98.06 4.26e-51 BMRB 946 'cytochrome c' 99.04 104 98.06 98.06 4.26e-51 BMRB 944 'cytochrome c' 99.04 104 98.06 98.06 4.26e-51 BMRB 673 'cytochrome c' 99.04 104 98.06 98.06 4.26e-51 BMRB 672 'cytochrome c' 99.04 104 98.06 98.06 4.26e-51 BMRB 665 'cytochrome c' 99.04 104 98.06 98.06 4.26e-51 BMRB 645 'cytochrome c' 99.04 104 98.06 98.06 4.26e-51 BMRB 630 'cytochrome c' 99.04 104 98.06 98.06 4.26e-51 BMRB 5830 'Horse cytochrome c' 100.00 104 100.00 100.00 1.19e-53 BMRB 5829 'Horse cytochrome c' 100.00 104 100.00 100.00 1.19e-53 BMRB 5828 'Horse cytochrome c' 100.00 104 98.08 100.00 2.67e-52 BMRB 5827 'Horse cytochrome c' 100.00 104 98.08 100.00 2.67e-52 BMRB 546 'cytochrome c' 99.04 104 98.06 98.06 4.26e-51 BMRB 545 'cytochrome c' 99.04 104 98.06 98.06 4.26e-51 BMRB 544 'cytochrome c' 99.04 104 98.06 98.06 4.26e-51 BMRB 543 'cytochrome c' 99.04 104 98.06 98.06 4.26e-51 BMRB 5372 'cytochrome c' 100.00 104 100.00 100.00 1.19e-53 BMRB 5026 'cytochrome C' 100.00 104 100.00 100.00 1.19e-53 BMRB 499 'cytochrome c' 99.04 104 98.06 98.06 4.26e-51 BMRB 4810 'ferric cytochrome c' 100.00 104 100.00 100.00 1.19e-53 BMRB 4809 'cytochrome c' 100.00 104 100.00 100.00 1.19e-53 BMRB 4808 'cytochrome c' 100.00 104 100.00 100.00 1.19e-53 BMRB 4805 'cytochrome c' 100.00 104 100.00 100.00 1.19e-53 BMRB 439 'cytochrome c' 99.04 104 98.06 98.06 4.26e-51 BMRB 438 'cytochrome c' 99.04 104 98.06 98.06 4.26e-51 BMRB 437 'cytochrome c' 99.04 104 98.06 98.06 4.26e-51 BMRB 436 'cytochrome c' 99.04 104 98.06 98.06 4.26e-51 BMRB 4189 'cytochrome c' 100.00 104 100.00 100.00 1.19e-53 BMRB 336 'cytochrome c' 99.04 104 98.06 98.06 4.26e-51 BMRB 317 'cytochrome c' 99.04 104 98.06 98.06 4.26e-51 BMRB 316 'cytochrome c' 99.04 104 98.06 98.06 4.26e-51 BMRB 286 'cytochrome c' 99.04 104 98.06 98.06 4.26e-51 BMRB 285 'cytochrome c' 99.04 104 98.06 98.06 4.26e-51 BMRB 274 'cytochrome c' 100.00 104 100.00 100.00 1.19e-53 BMRB 244 'cytochrome c' 100.00 104 100.00 100.00 1.19e-53 BMRB 243 'cytochrome c' 100.00 104 100.00 100.00 1.19e-53 BMRB 2368 'cytochrome c' 99.04 104 98.06 98.06 4.26e-51 BMRB 2367 'cytochrome c' 99.04 104 98.06 98.06 4.26e-51 BMRB 2366 'cytochrome c' 99.04 104 98.06 98.06 4.26e-51 BMRB 224 'cytochrome c' 99.04 104 98.06 98.06 4.26e-51 BMRB 220 'cytochrome c' 99.04 104 98.06 98.06 4.26e-51 BMRB 216 'cytochrome c' 99.04 104 98.06 98.06 4.26e-51 BMRB 1789 'cytochrome c' 99.04 104 98.06 98.06 4.26e-51 BMRB 1787 'cytochrome c' 99.04 104 98.06 98.06 4.26e-51 BMRB 1785 'cytochrome c' 99.04 104 98.06 98.06 4.26e-51 BMRB 1783 'cytochrome c' 99.04 104 98.06 98.06 4.26e-51 BMRB 1736 'cytochrome c' 99.04 104 98.06 98.06 4.26e-51 BMRB 1404 'cytochrome c' 99.04 104 98.06 98.06 4.26e-51 BMRB 1171 'cytochrome c' 99.04 104 98.06 98.06 4.26e-51 BMRB 1170 'cytochrome c' 99.04 104 98.06 98.06 4.26e-51 BMRB 1116 'cytochrome c' 99.04 104 98.06 98.06 4.26e-51 BMRB 1114 'cytochrome c' 99.04 104 98.06 98.06 4.26e-51 BMRB 1113 'cytochrome c' 99.04 104 98.06 98.06 4.26e-51 BMRB 1112 'cytochrome c' 99.04 104 98.06 98.06 4.26e-51 BMRB 1111 'cytochrome c' 99.04 104 98.06 98.06 4.26e-51 BMRB 1110 'cytochrome c' 99.04 104 98.06 98.06 4.26e-51 BMRB 1109 'cytochrome c' 99.04 104 98.06 98.06 4.26e-51 BMRB 1108 'cytochrome c' 99.04 104 98.06 98.06 4.26e-51 BMRB 1107 'cytochrome c' 99.04 104 98.06 98.06 4.26e-51 BMRB 1058 'cytochrome c' 99.04 104 98.06 98.06 4.26e-51 stop_ save_ ############# # Ligands # ############# save_HEM _Saveframe_category ligand _Mol_type non-polymer _Name_common "HEM (PROTOPORPHYRIN IX CONTAINING FE)" _BMRB_code . _PDB_code HEM _Molecular_mass 616.487 _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 Tue Jul 26 11:01:26 2011 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons CHA CHA C . 0 . ? CHB CHB C . 0 . ? CHC CHC C . 0 . ? CHD CHD C . 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 . ? 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 . ? 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 . ? 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 . ? NA NA N . 0 . ? NB NB N . 0 . ? NC NC N . 0 . ? ND ND N . 0 . ? FE FE FE . 0 . ? HHB HHB H . 0 . ? HHC HHC H . 0 . ? HHD HHD H . 0 . ? HMA HMA H . 0 . ? HMAA HMAA H . 0 . ? HMAB HMAB H . 0 . ? HAA HAA H . 0 . ? HAAA HAAA H . 0 . ? HBA HBA H . 0 . ? HBAA HBAA H . 0 . ? HMB HMB H . 0 . ? HMBA HMBA H . 0 . ? HMBB HMBB H . 0 . ? HAB HAB H . 0 . ? HBB HBB H . 0 . ? HBBA HBBA H . 0 . ? HMC HMC H . 0 . ? HMCA HMCA H . 0 . ? HMCB HMCB H . 0 . ? HAC HAC H . 0 . ? HBC HBC H . 0 . ? HBCA HBCA H . 0 . ? HMD HMD H . 0 . ? HMDA HMDA H . 0 . ? HMDB HMDB H . 0 . ? HAD HAD H . 0 . ? HADA HADA H . 0 . ? HBD HBD H . 0 . ? HBDA HBDA H . 0 . ? H2A H2A H . 0 . ? H2D H2D H . 0 . ? HHA HHA 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 CHA C1A ? ? DOUB CHA C4D ? ? SING CHA HHA ? ? SING CHB C4A ? ? DOUB CHB C1B ? ? SING CHB HHB ? ? SING CHC C4B ? ? DOUB CHC C1C ? ? SING CHC HHC ? ? DOUB CHD C4C ? ? SING CHD C1D ? ? SING CHD HHD ? ? DOUB C1A C2A ? ? SING C1A NA ? ? SING C2A C3A ? ? SING C2A CAA ? ? DOUB C3A C4A ? ? SING C3A CMA ? ? SING C4A NA ? ? SING CMA HMA ? ? SING CMA HMAA ? ? SING CMA HMAB ? ? SING CAA CBA ? ? SING CAA HAA ? ? SING CAA HAAA ? ? SING CBA CGA ? ? SING CBA HBA ? ? SING CBA HBAA ? ? DOUB CGA O1A ? ? SING CGA O2A ? ? SING C1B C2B ? ? SING C1B NB ? ? DOUB C2B C3B ? ? SING C2B CMB ? ? SING C3B C4B ? ? SING C3B CAB ? ? DOUB C4B NB ? ? SING CMB HMB ? ? SING CMB HMBA ? ? SING CMB HMBB ? ? DOUB CAB CBB ? ? SING CAB HAB ? ? SING CBB HBB ? ? SING CBB HBBA ? ? SING C1C C2C ? ? SING C1C NC ? ? DOUB C2C C3C ? ? SING C2C CMC ? ? SING C3C C4C ? ? SING C3C CAC ? ? SING C4C NC ? ? SING CMC HMC ? ? SING CMC HMCA ? ? SING CMC HMCB ? ? DOUB CAC CBC ? ? SING CAC HAC ? ? SING CBC HBC ? ? SING CBC HBCA ? ? SING C1D C2D ? ? DOUB C1D ND ? ? DOUB C2D C3D ? ? SING C2D CMD ? ? SING C3D C4D ? ? SING C3D CAD ? ? SING C4D ND ? ? SING CMD HMD ? ? SING CMD HMDA ? ? SING CMD HMDB ? ? SING CAD CBD ? ? SING CAD HAD ? ? SING CAD HADA ? ? SING CBD CGD ? ? SING CBD HBD ? ? SING CBD HBDA ? ? DOUB CGD O1D ? ? SING CGD O2D ? ? SING O2A H2A ? ? SING O2D H2D ? ? SING FE NA ? ? SING FE NB ? ? SING FE NC ? ? SING FE ND ? ? 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 _Organ _Tissue _Fraction $cyt_c Horse 9796 Eukaryota Metazoa Equus caballus heart muscle mitochrondrion 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 _Vendor_name $cyt_c vendor . . . . . Sigma stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details ; Oxidized cytochrome c dissolved in 30% acetonitrile-70% aqueous solution resulted in formation of four NMR observable cyt c forms distingushed by the identity of the sixth axial ligand of the heme iron. One met80-ligated cyt c designated as III* form, two lysine-ligated cyt c designated as IVa* and IVb* forms, and one histidine ligated cyt c designated as V* form are produced. ; loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $cyt_c 2 mM . $HEM 2 mM . acetonitrile 30 % . H2O 70 % . stop_ save_ ############################ # Computer software used # ############################ save_FELIX _Saveframe_category software _Name FELIX _Version 2000 loop_ _Task 'spectral processing' 'spectral analysis' stop_ _Details http://www.accelyrs.com save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model Mercury _Field_strength 300 _Details . save_ save_NMR_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer 'home made' _Model . _Field_strength 500 _Details 'Home made, Center for Magnetic Resonance at MIT/Harvard.' save_ save_NMR_spectrometer_3 _Saveframe_category NMR_spectrometer _Manufacturer 'home made' _Model . _Field_strength 600 _Details 'Home made, Center for Magnetic Resonance at MIT/Harvard.' save_ ############################# # NMR applied experiments # ############################# save_1H_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '1H NOESY' _Sample_label $sample_1 save_ save_NMR_applied_experiment _Saveframe_category NMR_applied_experiment _Experiment_name '1H NOESY' _BMRB_pulse_sequence_accession_number . _Details . save_ ####################### # Sample conditions # ####################### save_Ex-cond_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH* 7.2 0.2 n/a temperature 293 1 K stop_ save_ save_Ex-cond_2 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH* 7.2 0.2 n/a temperature 313 1 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 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_shift_set_protein _Saveframe_category assigned_chemical_shifts _Details ; Ferricytochrome c in 30% acetonitrile and 70% water solution exists as mixture of atleast four NMR-observable conformers. For this deposition we described each conformer as a component for a single sample (i.e., sample 1). So there are four components representing four conformers of ferricyt c. Proton chemical shifts of component 1 of sample 1. M80-ligated ferricytochrome c (III*-form). ; loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $Ex-cond_1 _Chem_shift_reference_set_label $chemical_shift_reference _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 . 18 HIS HB2 H 9.00 0.02 2 2 . 18 HIS HB3 H 14.60 0.02 2 3 . 18 HIS HD2 H 24.50 0.02 2 4 . 30 PRO HG2 H -0.90 0.02 2 5 . 30 PRO HD2 H -4.43 0.02 2 6 . 30 PRO HD3 H -2.32 0.02 2 7 . 59 TRP HH2 H 7.51 0.02 2 stop_ save_ save_shift_set_1 _Saveframe_category assigned_chemical_shifts _Details ; Ferricytochrome c in 30% acetonitrile and 70% water solution exists as mixture of atleast four NMR-observable conformers. For this deposition we described each conformer as a component for a single sample (i.e., sample 1). So there are four components representing four conformers of ferricyt c. Proton chemical shifts of component 1 of sample 1. M80-ligated ferricytochrome c (III*-form). ; loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $Ex-cond_1 _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name 'HEME 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 . 1 HEM HBA1 H 1.51 0.02 1 2 . 1 HEM HBA2 H -0.59 0.02 1 3 . 1 HEM HAA1 H 11.61 0.02 1 4 . 1 HEM HAA2 H 19.14 0.02 1 5 . 1 HEM HMB1 H 7.20 0.02 2 6 . 1 HEM HBB1 H -2.63 0.02 2 7 . 1 HEM HBC1 H 3.10 0.02 2 8 . 1 HEM HAC H 2.17 0.02 1 9 . 1 HEM HMC1 H 32.44 0.02 2 10 . 1 HEM HMD1 H 9.77 0.02 2 11 . 1 HEM HAD1 H -1.33 0.02 1 12 . 1 HEM HAD2 H 1.95 0.02 1 13 . 1 HEM HMA1 H 35.74 0.02 2 14 . 1 HEM HHB H -2.75 0.02 1 stop_ save_ save_shift_set_2 _Saveframe_category assigned_chemical_shifts _Details ; Ferricytochrome c in 30% acetonitrile and 70% water solution exists as mixture of atleast four NMR-observable conformers. For this deposition we described each conformer as a component for a single sample (i.e., sample 1). So there are four components representing four conformers of ferricyt c. Proton chemical shifts of component 1 of sample 1. Lysine-ligated ferricytochrome c (IVa* form). ; loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $Ex-cond_1 _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name 'HEME 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 . 1 HEM HBA1 H 2.00 0.02 1 2 . 1 HEM HBA2 H 0.98 0.02 1 3 . 1 HEM HAA1 H 0.00 0.02 1 4 . 1 HEM HAA2 H -1.02 0.02 1 5 . 1 HEM HMB1 H 12.93 0.02 2 6 . 1 HEM HMC1 H 11.45 0.02 2 7 . 1 HEM HMD1 H 21.11 0.02 2 8 . 1 HEM HMA1 H 22.87 0.02 2 9 . 1 HEM HHB H -6.06 0.02 1 stop_ save_ save_shift_set_3 _Saveframe_category assigned_chemical_shifts _Details ; Ferricytochrome c in 30% acetonitrile and 70% water solution exists as mixture of at least four NMR-observable conformers. For this deposition we described each conformer as a component for a single sample (i.e., sample 1). So there are four components representing four conformers of ferricyt c. Proton chemical shifts of component 1 of sample 1. Lysine-ligated ferricytochrome c (IVb* form). ; loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $Ex-cond_1 _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name 'HEME 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 . 1 HEM HAA2 H -0.81 0.02 1 2 . 1 HEM HMB1 H 13.64 0.02 2 3 . 1 HEM HMC1 H 11.81 0.02 2 4 . 1 HEM HMD1 H 21.11 0.02 2 5 . 1 HEM HMA1 H 21.56 0.02 2 6 . 1 HEM HHB H -5.68 0.02 1 stop_ save_ save_shift_set_4 _Saveframe_category assigned_chemical_shifts _Details ; Ferricytochrome c in 30% acetonitrile and 70% water solution exists as mixture of atleast four NMR-observable conformers. For this deposition we described each conformer as a component for a single sample (i.e., sample 1). So there are four components representing four conformers of ferricyt c. Proton chemical shifts of component 1 of sample 1. Histidine -ligated ferricytochrome c (V* form). ; loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $Ex-cond_1 _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name 'HEME 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 . 1 HEM HMC1 H 12.10 0.02 2 2 . 1 HEM HMD1 H 19.34 0.02 2 3 . 1 HEM HMA1 H 24.50 0.02 2 stop_ save_