data_17120 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Binding of 1-methylimidazole to cytochrome c: kinetic analysis and resonance assignments by two-dimensional NMR ; _BMRB_accession_number 17120 _BMRB_flat_file_name bmr17120.str _Entry_type new _Submission_date 2010-08-11 _Accession_date 2010-08-11 _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 Shao Weiping . . 2 Liu Gaohua . . 3 Tang Wenxia . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count kinetic_rates 1 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 'Binding of 1-methylimidazole to cytochrome c: kinetic analysis and resonance assignments by two-dimensional NMR' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 7748900 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Shao Weiping . . 2 Liu Gaohua . . 3 Tang Wenxia . . stop_ _Journal_abbreviation 'Biochim. Biophys. Acta' _Journal_volume 1248 _Journal_issue 2 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 177 _Page_last 185 _Year 1995 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'cytc/1MZ complex' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label cytc $cytc 1MZ $1MZ 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_cytc _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common cytc _Molecular_mass . _Mol_thiol_state 'not reported' _Details . ############################## # Polymer residue sequence # ############################## _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 2015-11-04 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 1.72e-64 BMRB 1107 "cytochrome c" 98.10 104 97.09 98.06 1.72e-64 BMRB 1108 "cytochrome c" 98.10 104 99.03 100.00 3.32e-67 BMRB 1109 "cytochrome c" 98.10 104 99.03 100.00 3.32e-67 BMRB 1110 "cytochrome c" 98.10 104 99.03 100.00 3.32e-67 BMRB 1111 "cytochrome c" 98.10 104 99.03 100.00 3.32e-67 BMRB 1112 "cytochrome c" 98.10 104 99.03 100.00 3.32e-67 BMRB 1113 "cytochrome c" 98.10 104 97.09 98.06 1.72e-64 BMRB 1114 "cytochrome c" 98.10 104 99.03 100.00 3.32e-67 BMRB 1116 "cytochrome c" 98.10 104 99.03 100.00 3.32e-67 BMRB 1170 "cytochrome c" 98.10 104 99.03 100.00 3.32e-67 BMRB 1171 "cytochrome c" 98.10 104 97.09 98.06 1.72e-64 BMRB 1404 "cytochrome c" 98.10 104 99.03 100.00 3.32e-67 BMRB 16759 cytochrome_c 99.05 104 99.04 100.00 6.75e-68 BMRB 17340 cytc 99.05 104 99.04 100.00 6.75e-68 BMRB 1736 "cytochrome c" 98.10 104 97.09 98.06 1.72e-64 BMRB 1783 "cytochrome c" 98.10 104 97.09 98.06 1.72e-64 BMRB 17847 hCc 99.05 104 99.04 100.00 6.75e-68 BMRB 17848 hCc 99.05 104 99.04 100.00 6.75e-68 BMRB 1785 "cytochrome c" 98.10 104 97.09 98.06 1.72e-64 BMRB 1787 "cytochrome c" 98.10 104 97.09 98.06 1.72e-64 BMRB 1789 "cytochrome c" 98.10 104 97.09 98.06 1.72e-64 BMRB 216 "cytochrome c" 98.10 104 97.09 98.06 1.72e-64 BMRB 220 "cytochrome c" 98.10 104 97.09 98.06 1.72e-64 BMRB 224 "cytochrome c" 98.10 104 97.09 98.06 1.72e-64 BMRB 2366 "cytochrome c" 98.10 104 99.03 100.00 3.32e-67 BMRB 2367 "cytochrome c" 98.10 104 99.03 100.00 3.32e-67 BMRB 2368 "cytochrome c" 98.10 104 99.03 100.00 3.32e-67 BMRB 243 "cytochrome c" 99.05 104 99.04 100.00 6.75e-68 BMRB 244 "cytochrome c" 99.05 104 99.04 100.00 6.75e-68 BMRB 25640 entity_1 99.05 105 98.08 99.04 1.15e-66 BMRB 274 "cytochrome c" 99.05 104 99.04 100.00 6.75e-68 BMRB 285 "cytochrome c" 98.10 104 99.03 100.00 3.32e-67 BMRB 286 "cytochrome c" 98.10 104 99.03 100.00 3.32e-67 BMRB 316 "cytochrome c" 98.10 104 99.03 100.00 3.32e-67 BMRB 317 "cytochrome c" 98.10 104 99.03 100.00 3.32e-67 BMRB 336 "cytochrome c" 98.10 104 97.09 98.06 1.72e-64 BMRB 4189 "cytochrome c" 99.05 104 99.04 100.00 6.75e-68 BMRB 436 "cytochrome c" 98.10 104 97.09 98.06 1.72e-64 BMRB 437 "cytochrome c" 98.10 104 97.09 98.06 1.72e-64 BMRB 438 "cytochrome c" 98.10 104 97.09 98.06 1.72e-64 BMRB 439 "cytochrome c" 98.10 104 97.09 98.06 1.72e-64 PDB 1AKK "Solution Structure Of Oxidized Horse Heart Cytochrome C, Nmr, Minimized Average Structure" 99.05 104 99.04 100.00 6.75e-68 PDB 1CRC "Cytochrome C At Low Ionic Strength" 99.05 105 99.04 100.00 6.97e-68 PDB 1FI7 "Solution Structure Of The Imidazole Complex Of Cytochrome C" 99.05 104 99.04 100.00 6.75e-68 PDB 1FI9 "Solution Structure Of The Imidazole Complex Of Cytochrome C" 99.05 104 99.04 100.00 6.75e-68 PDB 1GIW "Solution Structure Of Reduced Horse Heart Cytochrome C, Nmr, Minimized Average Structure" 98.10 104 99.03 100.00 3.32e-67 PDB 1HRC "High-Resolution Three-Dimensional Structure Of Horse Heart Cytochrome C" 99.05 105 99.04 100.00 6.97e-68 PDB 1I5T "Solution Structure Of Cyanoferricytochrome C" 99.05 104 99.04 100.00 6.75e-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 6.75e-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 6.75e-68 PDB 1M60 "Solution Structure Of Zinc-Substituted Cytochrome C" 99.05 104 99.04 100.00 6.75e-68 PDB 1OCD "Cytochrome C (Oxidized) From Equus Caballus, Nmr, Minimized Average Structure" 99.05 104 99.04 100.00 6.75e-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 6.75e-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 6.97e-68 PDB 2B4Z "Crystal Structure Of Cytochrome C From Bovine Heart At 1.5 A Resolution." 99.05 104 98.08 98.08 2.17e-66 PDB 2FRC "Cytochrome C (Reduced) From Equus Caballus, Nmr, Minimized Average Structure" 99.05 104 99.04 100.00 6.75e-68 PDB 2GIW "Solution Structure Of Reduced Horse Heart Cytochrome C, Nmr, 40 Structures" 99.05 104 99.04 100.00 6.75e-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 6.75e-68 PDB 2YBB "Fitted Model For Bovine Mitochondrial Supercomplex I1iii2iv1 By Single Particle Cryo-Em (Emd-1876)" 99.05 104 98.08 98.08 2.17e-66 PDB 3J2T "An Improved Model Of The Human Apoptosome" 99.05 104 98.08 98.08 2.17e-66 PDB 3NBS "Crystal Structure Of Dimeric Cytochrome C From Horse Heart" 99.05 104 99.04 100.00 6.75e-68 PDB 3NBT "Crystal Structure Of Trimeric Cytochrome C From Horse Heart" 99.05 104 99.04 100.00 6.75e-68 PDB 3O1Y "Electron Transfer Complexes: Experimental Mapping Of The Redox- Dependent Cytochrome C Electrostatic Surface" 99.05 105 99.04 100.00 6.97e-68 PDB 3O20 "Electron Transfer Complexes:experimental Mapping Of The Redox- Dependent Cytochrome C Electrostatic Surface" 99.05 105 99.04 100.00 6.97e-68 PDB 3WC8 "Dimeric Horse Cytochrome C Obtained By Refolding With Desalting Method" 99.05 104 99.04 100.00 6.75e-68 PDB 3WUI "Dimeric Horse Cytochrome C Formed By Refolding From Molten Globule State" 99.05 104 99.04 100.00 6.75e-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 6.75e-68 GB AAB33495 "apocytochrome c [horses, heart, Peptide, 104 aa]" 99.05 104 97.12 98.08 6.67e-66 GB AAI05398 "Cytochrome c, somatic [Bos taurus]" 100.00 105 98.10 98.10 2.47e-67 GB AAX77008 "cytochrome c-like protein [Sus scrofa]" 100.00 105 98.10 98.10 2.47e-67 GB ABA06540 "mitochondrial cytochrome c [Capra hircus]" 99.05 104 97.12 97.12 2.61e-65 GB ABA06541 "mitochondrial cytochrome c [Bubalus bubalis]" 99.05 104 98.08 98.08 2.17e-66 PRF 610169A "cytochrome c" 99.05 104 99.04 100.00 6.75e-68 PRF 711086A "cytochrome c" 99.05 104 98.08 100.00 5.99e-68 REF NP_001039526 "cytochrome c [Bos taurus]" 100.00 105 98.10 98.10 2.47e-67 REF NP_001123442 "cytochrome c [Sus scrofa]" 100.00 105 98.10 98.10 2.47e-67 REF NP_001157486 "cytochrome c [Equus caballus]" 100.00 105 100.00 100.00 2.61e-69 REF XP_004007999 "PREDICTED: cytochrome c [Ovis aries]" 100.00 105 98.10 98.10 2.47e-67 REF XP_004418964 "PREDICTED: cytochrome c-like [Ceratotherium simum simum]" 100.00 105 99.05 99.05 1.15e-68 SP P00004 "RecName: Full=Cytochrome c" 100.00 105 99.05 100.00 8.21e-69 SP P62894 "RecName: Full=Cytochrome c" 100.00 105 98.10 98.10 2.47e-67 SP P62895 "RecName: Full=Cytochrome c" 100.00 105 98.10 98.10 2.47e-67 SP P62896 "RecName: Full=Cytochrome c" 100.00 105 98.10 98.10 2.47e-67 SP P68096 "RecName: Full=Cytochrome c" 100.00 105 100.00 100.00 2.61e-69 TPG DAA30512 "TPA: cytochrome c [Bos taurus]" 100.00 105 98.10 98.10 2.47e-67 stop_ save_ ############# # Ligands # ############# save_1MZ _Saveframe_category ligand _Mol_type non-polymer _Name_common "1MZ (1-METHYLIMIDAZOLE)" _BMRB_code . _PDB_code 1MZ _Molecular_mass 83.112 _Mol_charge 1 _Mol_paramagnetic no _Mol_aromatic yes _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Tue Jun 9 12:01:15 2009 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons N1 N1 N . 0 . ? C2 C2 C . 0 . ? N3 N3 N . 1 . ? C4 C4 C . 0 . ? C5 C5 C . 0 . ? CM1 CM1 C . 0 . ? H2 H2 H . 0 . ? HN3 HN3 H . 0 . ? H4 H4 H . 0 . ? H5 H5 H . 0 . ? HM11 HM11 H . 0 . ? HM12 HM12 H . 0 . ? HM13 HM13 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 N1 C2 ? ? SING N1 C5 ? ? SING N1 CM1 ? ? DOUB C2 N3 ? ? SING C2 H2 ? ? SING N3 C4 ? ? SING N3 HN3 ? ? DOUB C4 C5 ? ? SING C4 H4 ? ? SING C5 H5 ? ? SING CM1 HM11 ? ? SING CM1 HM12 ? ? SING CM1 HM13 ? ? 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 $cytc Horse 9795 Eukaryota Metazoa 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 _Vector_name _Details $cytc 'obtained from a vendor' . . . . . Sigma $1MZ 'chemical synthesis' . . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $cytc 8 mM 'natural abundance' $1MZ 40 mM '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 Bruker _Model AM _Field_strength 500 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_EXSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D EXSY' _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 319 . K pH 7.0 . pH pressure ambient . atm stop_ save_