data_17215 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; 13C NMR Spectroscopic and X-ray Crystallographic Study of the Role Played by Mitochondrial Cytochrome b5 Heme Propionates in the Electrostatic Binding to Cytochrome c ; _BMRB_accession_number 17215 _BMRB_flat_file_name bmr17215.str _Entry_type new _Submission_date 2010-09-29 _Accession_date 2010-09-29 _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 Rodriguez-Maranon Maria J. . 2 Qiu Feng . . 3 Stark Ruth E. . 4 White Steven P. . 5 Zhang Xuejun . . 6 Foundling Stephen I. . 7 Rodriguez Veronica . . 8 Schilling Curtis L. III 9 Bunce Richard A. . 10 Rivera Mario . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count binding_constants 1 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-11-10 original author . stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title '13C NMR Spectroscopic and X-ray Crystallographic Study of the Role Played by Mitochondrial Cytochrome b5 Heme Propionates in the Electrostatic Binding to Cytochrome c' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 8973214 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Rodriguez-Maranon Maria J. . 2 Qiu Feng . . 3 Stark Ruth E. . 4 White Steven P. . 5 Zhang Xuejun . . 6 Foundling Stephen I. . 7 Rodriguez Veronica . . 8 Schilling Curtis L. III 9 Bunce Richard A. . 10 Rivera Mario . . stop_ _Journal_abbreviation Biochemistry _Journal_name_full Biochemistry _Journal_volume 35 _Journal_issue 50 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 16378 _Page_last 16390 _Year 1996 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'OMcb5/Cc complex' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label OMcb5 $OMcb5 Cc $Cc 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_OMcb5 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common OMcb5 _Molecular_mass . _Mol_thiol_state 'not reported' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 146 _Mol_residue_sequence ; MAAVDASGSNGKGQGVETSV TYYRLEEVAKRNSSKEIWLV IHGRVYDVTRFLNEHPGGEE VLLEQAGADASESFEDVGHS SDAREMLKQYYIGDVHPNDL KPEGGGKDPSKNNTCKSCWI YWLLPVVGAVLLGFLCRYYT SESTSS ; loop_ _Residue_seq_code _Residue_label 1 MET 2 ALA 3 ALA 4 VAL 5 ASP 6 ALA 7 SER 8 GLY 9 SER 10 ASN 11 GLY 12 LYS 13 GLY 14 GLN 15 GLY 16 VAL 17 GLU 18 THR 19 SER 20 VAL 21 THR 22 TYR 23 TYR 24 ARG 25 LEU 26 GLU 27 GLU 28 VAL 29 ALA 30 LYS 31 ARG 32 ASN 33 SER 34 SER 35 LYS 36 GLU 37 ILE 38 TRP 39 LEU 40 VAL 41 ILE 42 HIS 43 GLY 44 ARG 45 VAL 46 TYR 47 ASP 48 VAL 49 THR 50 ARG 51 PHE 52 LEU 53 ASN 54 GLU 55 HIS 56 PRO 57 GLY 58 GLY 59 GLU 60 GLU 61 VAL 62 LEU 63 LEU 64 GLU 65 GLN 66 ALA 67 GLY 68 ALA 69 ASP 70 ALA 71 SER 72 GLU 73 SER 74 PHE 75 GLU 76 ASP 77 VAL 78 GLY 79 HIS 80 SER 81 SER 82 ASP 83 ALA 84 ARG 85 GLU 86 MET 87 LEU 88 LYS 89 GLN 90 TYR 91 TYR 92 ILE 93 GLY 94 ASP 95 VAL 96 HIS 97 PRO 98 ASN 99 ASP 100 LEU 101 LYS 102 PRO 103 GLU 104 GLY 105 GLY 106 GLY 107 LYS 108 ASP 109 PRO 110 SER 111 LYS 112 ASN 113 ASN 114 THR 115 CYS 116 LYS 117 SER 118 CYS 119 TRP 120 ILE 121 TYR 122 TRP 123 LEU 124 LEU 125 PRO 126 VAL 127 VAL 128 GLY 129 ALA 130 VAL 131 LEU 132 LEU 133 GLY 134 PHE 135 LEU 136 CYS 137 ARG 138 TYR 139 TYR 140 THR 141 SER 142 GLU 143 SER 144 THR 145 SER 146 SER stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-01-30 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 REF XP_001497331 "PREDICTED: cytochrome b5 type B-like isoform X1 [Equus caballus]" 100.00 146 100.00 100.00 6.34e-103 REF XP_005608424 "PREDICTED: cytochrome b5 type B-like isoform X2 [Equus caballus]" 73.29 140 100.00 100.00 4.31e-70 REF XP_008537435 "PREDICTED: cytochrome b5 type B isoform X1 [Equus przewalskii]" 100.00 146 100.00 100.00 6.34e-103 REF XP_008537436 "PREDICTED: cytochrome b5 type B isoform X2 [Equus przewalskii]" 73.29 130 100.00 100.00 1.65e-70 stop_ save_ save_Cc _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common Cc _Molecular_mass . _Mol_thiol_state 'not reported' _Details . _Residue_count 105 _Mol_residue_sequence ; MGDVEKGKKIFVQKCAQCHT VEKGGKHKTGPNLHGLFGRK TGQAPGFSYTDANKNKGITW KEETLMEYLENPKKYIPGTK MIFAGIKKKTEREDLIAYLK KATNE ; loop_ _Residue_seq_code _Residue_label 1 MET 2 GLY 3 ASP 4 VAL 5 GLU 6 LYS 7 GLY 8 LYS 9 LYS 10 ILE 11 PHE 12 VAL 13 GLN 14 LYS 15 CYS 16 ALA 17 GLN 18 CYS 19 HIS 20 THR 21 VAL 22 GLU 23 LYS 24 GLY 25 GLY 26 LYS 27 HIS 28 LYS 29 THR 30 GLY 31 PRO 32 ASN 33 LEU 34 HIS 35 GLY 36 LEU 37 PHE 38 GLY 39 ARG 40 LYS 41 THR 42 GLY 43 GLN 44 ALA 45 PRO 46 GLY 47 PHE 48 SER 49 TYR 50 THR 51 ASP 52 ALA 53 ASN 54 LYS 55 ASN 56 LYS 57 GLY 58 ILE 59 THR 60 TRP 61 LYS 62 GLU 63 GLU 64 THR 65 LEU 66 MET 67 GLU 68 TYR 69 LEU 70 GLU 71 ASN 72 PRO 73 LYS 74 LYS 75 TYR 76 ILE 77 PRO 78 GLY 79 THR 80 LYS 81 MET 82 ILE 83 PHE 84 ALA 85 GLY 86 ILE 87 LYS 88 LYS 89 LYS 90 THR 91 GLU 92 ARG 93 GLU 94 ASP 95 LEU 96 ILE 97 ALA 98 TYR 99 LEU 100 LYS 101 LYS 102 ALA 103 THR 104 ASN 105 GLU stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-01-30 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 1058 cytochrome_c 98.10 104 97.09 98.06 1.20e-64 BMRB 1107 cytochrome_c 98.10 104 97.09 98.06 1.20e-64 BMRB 1108 cytochrome_c 98.10 104 97.09 98.06 1.20e-64 BMRB 1109 cytochrome_c 98.10 104 97.09 98.06 1.20e-64 BMRB 1110 cytochrome_c 98.10 104 97.09 98.06 1.20e-64 BMRB 1111 cytochrome_c 98.10 104 97.09 98.06 1.20e-64 BMRB 1112 cytochrome_c 98.10 104 97.09 98.06 1.20e-64 BMRB 1113 cytochrome_c 98.10 104 97.09 98.06 1.20e-64 BMRB 1114 cytochrome_c 98.10 104 97.09 98.06 1.20e-64 BMRB 1116 cytochrome_c 98.10 104 97.09 98.06 1.20e-64 BMRB 1170 cytochrome_c 98.10 104 97.09 98.06 1.20e-64 BMRB 1171 cytochrome_c 98.10 104 97.09 98.06 1.20e-64 BMRB 1404 cytochrome_c 98.10 104 97.09 98.06 1.20e-64 BMRB 16759 cytochrome_c 99.05 104 99.04 100.00 4.72e-68 BMRB 17120 cytc 100.00 105 100.00 100.00 1.83e-69 BMRB 17340 cytc 99.05 104 99.04 100.00 4.72e-68 BMRB 1736 cytochrome_c 98.10 104 97.09 98.06 1.20e-64 BMRB 1783 cytochrome_c 98.10 104 97.09 98.06 1.20e-64 BMRB 17847 hCc 99.05 104 99.04 100.00 4.72e-68 BMRB 17848 hCc 99.05 104 99.04 100.00 4.72e-68 BMRB 1785 cytochrome_c 98.10 104 97.09 98.06 1.20e-64 BMRB 1787 cytochrome_c 98.10 104 97.09 98.06 1.20e-64 BMRB 1789 cytochrome_c 98.10 104 97.09 98.06 1.20e-64 BMRB 216 cytochrome_c 98.10 104 97.09 98.06 1.20e-64 BMRB 220 cytochrome_c 98.10 104 97.09 98.06 1.20e-64 BMRB 224 cytochrome_c 98.10 104 97.09 98.06 1.20e-64 BMRB 2366 cytochrome_c 98.10 104 97.09 98.06 1.20e-64 BMRB 2367 cytochrome_c 98.10 104 97.09 98.06 1.20e-64 BMRB 2368 cytochrome_c 98.10 104 97.09 98.06 1.20e-64 BMRB 243 "cytochrome c" 99.05 104 99.04 100.00 4.72e-68 BMRB 244 "cytochrome c" 99.05 104 99.04 100.00 4.72e-68 BMRB 274 "cytochrome c" 99.05 104 99.04 100.00 4.72e-68 BMRB 285 cytochrome_c 98.10 104 97.09 98.06 1.20e-64 BMRB 286 cytochrome_c 98.10 104 97.09 98.06 1.20e-64 BMRB 316 cytochrome_c 98.10 104 97.09 98.06 1.20e-64 BMRB 317 cytochrome_c 98.10 104 97.09 98.06 1.20e-64 BMRB 336 cytochrome_c 98.10 104 97.09 98.06 1.20e-64 BMRB 4189 hh_cytc 99.05 104 99.04 100.00 4.72e-68 BMRB 436 cytochrome_c 98.10 104 97.09 98.06 1.20e-64 BMRB 437 cytochrome_c 98.10 104 97.09 98.06 1.20e-64 BMRB 438 cytochrome_c 98.10 104 97.09 98.06 1.20e-64 BMRB 439 cytochrome_c 98.10 104 97.09 98.06 1.20e-64 BMRB 4805 cytc 99.05 104 99.04 100.00 4.72e-68 BMRB 4808 cytc 99.05 104 99.04 100.00 4.72e-68 BMRB 4809 cytc 99.05 104 99.04 100.00 4.72e-68 BMRB 4810 cytc 99.05 104 99.04 100.00 4.72e-68 BMRB 499 cytochrome_c 98.10 104 97.09 98.06 1.20e-64 BMRB 5026 cytochrome 99.05 104 99.04 100.00 4.72e-68 BMRB 5372 cyt_c 99.05 104 99.04 100.00 4.72e-68 BMRB 543 cytochrome_c 98.10 104 97.09 98.06 1.20e-64 BMRB 544 cytochrome_c 98.10 104 97.09 98.06 1.20e-64 BMRB 545 cytochrome_c 98.10 104 97.09 98.06 1.20e-64 BMRB 546 cytochrome_c 98.10 104 97.09 98.06 1.20e-64 BMRB 5660 cyt_c 99.05 104 99.04 100.00 4.72e-68 BMRB 5827 cyt_c 99.05 104 97.12 100.00 3.79e-66 BMRB 5828 cyt_c 99.05 104 97.12 100.00 3.79e-66 BMRB 5829 cyt_c 99.05 104 99.04 100.00 4.72e-68 BMRB 5830 cyt_c 99.05 104 99.04 100.00 4.72e-68 BMRB 630 cytochrome_c 98.10 104 97.09 98.06 1.20e-64 BMRB 645 cytochrome_c 98.10 104 97.09 98.06 1.20e-64 BMRB 665 cytochrome_c 98.10 104 97.09 98.06 1.20e-64 BMRB 672 cytochrome_c 98.10 104 97.09 98.06 1.20e-64 BMRB 673 cytochrome_c 98.10 104 97.09 98.06 1.20e-64 BMRB 944 cytochrome_c 98.10 104 97.09 98.06 1.20e-64 BMRB 946 cytochrome_c 98.10 104 97.09 98.06 1.20e-64 BMRB 947 cytochrome_c 98.10 104 97.09 98.06 1.20e-64 BMRB 948 cytochrome_c 98.10 104 97.09 98.06 1.20e-64 PDB 1AKK "Solution Structure Of Oxidized Horse Heart Cytochrome C, Nmr, Minimized Average Structure" 99.05 104 99.04 100.00 4.72e-68 PDB 1CRC "Cytochrome C At Low Ionic Strength" 99.05 105 99.04 100.00 4.87e-68 PDB 1FI7 "Solution Structure Of The Imidazole Complex Of Cytochrome C" 99.05 104 99.04 100.00 4.72e-68 PDB 1FI9 "Solution Structure Of The Imidazole Complex Of Cytochrome C" 99.05 104 99.04 100.00 4.72e-68 PDB 1GIW "Solution Structure Of Reduced Horse Heart Cytochrome C, Nmr, Minimized Average Structure" 98.10 104 99.03 100.00 2.32e-67 PDB 1HRC "High-Resolution Three-Dimensional Structure Of Horse Heart Cytochrome C" 99.05 105 99.04 100.00 4.87e-68 PDB 1I5T "Solution Structure Of Cyanoferricytochrome C" 99.05 104 99.04 100.00 4.72e-68 PDB 1LC1 "Solution Structure Of Reduced Horse Heart Cytochrome C In 30% Acetonitrile Solution, Nmr Minimized Average Structure" 99.05 104 99.04 100.00 4.72e-68 PDB 1LC2 "Solution Structure Of Reduced Horse Heart Cytochrome C In 30% Acetonitrile Solution, Nmr 30 Structures" 99.05 104 99.04 100.00 4.72e-68 PDB 1M60 "Solution Structure Of Zinc-Substituted Cytochrome C" 99.05 104 99.04 100.00 4.72e-68 PDB 1OCD "Cytochrome C (Oxidized) From Equus Caballus, Nmr, Minimized Average Structure" 99.05 104 99.04 100.00 4.72e-68 PDB 1U75 "Electron Transfer Complex Between Horse Heart Cytochrome C And Zinc- Porphyrin Substituted Cytochrome C Peroxidase" 99.05 104 99.04 100.00 4.72e-68 PDB 1WEJ "Igg1 Fab Fragment (Of E8 Antibody) Complexed With Horse Cytochrome C At 1.8 A Resolution" 99.05 105 99.04 100.00 4.87e-68 PDB 2B4Z "Crystal Structure Of Cytochrome C From Bovine Heart At 1.5 A Resolution." 99.05 104 98.08 98.08 1.51e-66 PDB 2FRC "Cytochrome C (Reduced) From Equus Caballus, Nmr, Minimized Average Structure" 99.05 104 99.04 100.00 4.72e-68 PDB 2GIW "Solution Structure Of Reduced Horse Heart Cytochrome C, Nmr, 40 Structures" 99.05 104 99.04 100.00 4.72e-68 PDB 2PCB "Crystal Structure Of A Complex Between Electron Transfer Partners, Cytochrome C Peroxidase And Cytochrome C" 99.05 104 99.04 100.00 4.72e-68 PDB 2YBB "Fitted Model For Bovine Mitochondrial Supercomplex I1iii2iv1 By Single Particle Cryo-Em (Emd-1876)" 99.05 104 98.08 98.08 1.51e-66 PDB 3J2T "An Improved Model Of The Human Apoptosome" 99.05 104 98.08 98.08 1.51e-66 PDB 3NBS "Crystal Structure Of Dimeric Cytochrome C From Horse Heart" 99.05 104 99.04 100.00 4.72e-68 PDB 3NBT "Crystal Structure Of Trimeric Cytochrome C From Horse Heart" 99.05 104 99.04 100.00 4.72e-68 PDB 3O1Y "Electron Transfer Complexes: Experimental Mapping Of The Redox- Dependent Cytochrome C Electrostatic Surface" 99.05 105 99.04 100.00 4.87e-68 PDB 3O20 "Electron Transfer Complexes:experimental Mapping Of The Redox- Dependent Cytochrome C Electrostatic Surface" 99.05 105 99.04 100.00 4.87e-68 PDB 3WC8 "Dimeric Horse Cytochrome C Obtained By Refolding With Desalting Method" 99.05 104 99.04 100.00 4.72e-68 PDB 3WUI "Dimeric Horse Cytochrome C Formed By Refolding From Molten Globule State" 99.05 104 99.04 100.00 4.72e-68 PDB 4RSZ "The X-ray Structure Of The Primary Adduct Formed In The Reaction Between Cisplatin And Cytochrome C" 99.05 104 99.04 100.00 4.72e-68 GB AAB33495 "apocytochrome c [horses, heart, Peptide, 104 aa]" 99.05 104 97.12 98.08 4.66e-66 GB AAI05398 "Cytochrome c, somatic [Bos taurus]" 100.00 105 98.10 98.10 1.73e-67 GB AAX77008 "cytochrome c-like protein [Sus scrofa]" 100.00 105 98.10 98.10 1.73e-67 GB ABA06540 "mitochondrial cytochrome c [Capra hircus]" 99.05 104 97.12 97.12 1.82e-65 GB ABA06541 "mitochondrial cytochrome c [Bubalus bubalis]" 99.05 104 98.08 98.08 1.51e-66 PRF 610169A "cytochrome c" 99.05 104 99.04 100.00 4.72e-68 PRF 711086A "cytochrome c" 99.05 104 98.08 100.00 4.19e-68 REF NP_001039526 "cytochrome c [Bos taurus]" 100.00 105 98.10 98.10 1.73e-67 REF NP_001123442 "cytochrome c [Sus scrofa]" 100.00 105 98.10 98.10 1.73e-67 REF NP_001157486 "cytochrome c [Equus caballus]" 100.00 105 100.00 100.00 1.83e-69 REF XP_004007999 "PREDICTED: cytochrome c-like [Ovis aries]" 100.00 105 98.10 98.10 1.73e-67 REF XP_004010578 "PREDICTED: cytochrome c-like [Ovis aries]" 100.00 105 97.14 97.14 1.45e-66 SP P00004 "RecName: Full=Cytochrome c [Equus caballus]" 100.00 105 99.05 100.00 5.74e-69 SP P62894 "RecName: Full=Cytochrome c [Bos taurus]" 100.00 105 98.10 98.10 1.73e-67 SP P62895 "RecName: Full=Cytochrome c [Sus scrofa]" 100.00 105 98.10 98.10 1.73e-67 SP P62896 "RecName: Full=Cytochrome c [Ovis aries]" 100.00 105 98.10 98.10 1.73e-67 SP P68096 "RecName: Full=Cytochrome c [Equus burchellii]" 100.00 105 100.00 100.00 1.83e-69 TPG DAA30512 "TPA: cytochrome c [Bos taurus]" 100.00 105 98.10 98.10 1.73e-67 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $OMcb5 Horse 9796 Eukaryota Metaoza Equus caballus $Cc Horse 9796 Eukaryota Metaoza Equus caballus stop_ save_ ######################### # Experimental source # ######################### save_experimental_source _Saveframe_category experimental_source loop_ _Mol_label _Production_method _Host_organism_name_common _Genus _Species _Strain _Variant _Vector_name $OMcb5 'recombinant technology' . . . BL21 DE3 MRL2 $Cc 'obtained from a vendor' . . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details 'Cc was titrated into solution' loop_ _Mol_label _Concentration_value _Concentration_value_units _Concentration_min_value _Concentration_max_value _Isotopic_labeling $OMcb5 . mM 1 2 [U-13C] 'perdeuterated phosphate buffer' 5 mM . . 'natural abundance' $Cc . mM 0 2.5 'natural abundance' D2O 100 % . . 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_software _Saveframe_category software _Name software _Version . loop_ _Vendor _Address _Electronic_address na . . stop_ loop_ _Task na stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model XL _Field_strength 400 _Details '13C frequency of 100.6 MHx' save_ ############################# # NMR applied experiments # ############################# save_13C_NMR_1 _Saveframe_category NMR_applied_experiment _Experiment_name '13C NMR' _Sample_label $sample_1 save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units temperature 303 . K pH 7.0 . pH pressure ambient . atm stop_ save_