data_17457 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; The Solution Structure of Bovine Ferricytochrome b5 Determined Using Heteronuclear NMR Methods ; _BMRB_accession_number 17457 _BMRB_flat_file_name bmr17457.str _Entry_type original _Submission_date 2011-02-11 _Accession_date 2011-02-11 _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 Muskett Frederick W. . 2 Kelly Geoffrey P. . 3 Whitford David . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count chemical_rates 1 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2012-06-06 original author . stop_ _Original_release_date 2012-06-06 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'The Solution Structure of Bovine Ferricytochrome b5 Determined Using Heteronuclear NMR Methods' _Citation_status 'in preparation' _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 Muskett Frederick W. . 2 Kelly Geoffrey P. . 3 Whitford David . . stop_ _Journal_abbreviation 'J. Mol. Biol.' _Journal_volume 258 _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 172 _Page_last 189 _Year 1996 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'b5 exchange' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label b5 $b5 HEM $HEM 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_b5 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common b5 _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 104 _Mol_residue_sequence ; AEESSKAVKYYTLEEIQKHN NSKSTWLILHYKVYDLTKFL EEHPGGEEVLREQAGGDATE NFEDVGHSTDARELSKTFII GELHPDDRSKITKPSESIIT TIDS ; loop_ _Residue_seq_code _Residue_label 1 ALA 2 GLU 3 GLU 4 SER 5 SER 6 LYS 7 ALA 8 VAL 9 LYS 10 TYR 11 TYR 12 THR 13 LEU 14 GLU 15 GLU 16 ILE 17 GLN 18 LYS 19 HIS 20 ASN 21 ASN 22 SER 23 LYS 24 SER 25 THR 26 TRP 27 LEU 28 ILE 29 LEU 30 HIS 31 TYR 32 LYS 33 VAL 34 TYR 35 ASP 36 LEU 37 THR 38 LYS 39 PHE 40 LEU 41 GLU 42 GLU 43 HIS 44 PRO 45 GLY 46 GLY 47 GLU 48 GLU 49 VAL 50 LEU 51 ARG 52 GLU 53 GLN 54 ALA 55 GLY 56 GLY 57 ASP 58 ALA 59 THR 60 GLU 61 ASN 62 PHE 63 GLU 64 ASP 65 VAL 66 GLY 67 HIS 68 SER 69 THR 70 ASP 71 ALA 72 ARG 73 GLU 74 LEU 75 SER 76 LYS 77 THR 78 PHE 79 ILE 80 ILE 81 GLY 82 GLU 83 LEU 84 HIS 85 PRO 86 ASP 87 ASP 88 ARG 89 SER 90 LYS 91 ILE 92 THR 93 LYS 94 PRO 95 SER 96 GLU 97 SER 98 ILE 99 ILE 100 THR 101 THR 102 ILE 103 ASP 104 SER 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 1323 "cytochrome b5" 78.85 82 100.00 100.00 1.24e-52 BMRB 1324 "cytochrome b5" 78.85 82 100.00 100.00 1.24e-52 PDB 1CYO "Bovine Cytochrome B(5)" 89.42 93 100.00 100.00 1.76e-60 PDB 1EHB "Crystal Structure Of Recombinant Trypsin-Solubilized Fragment Of Cytochrome B5" 78.85 82 100.00 100.00 1.24e-52 PDB 1ES1 "Crystal Structure Of Val61his Mutant Of Trypsin-Solubilized Fragment Of Cytochrome B5" 78.85 82 98.78 98.78 2.16e-51 PDB 1HKO "Nmr Structure Of Bovine Cytochrome B5" 99.04 104 100.00 100.00 3.29e-67 PDB 1J0Q "Solution Structure Of Oxidized Bovine Microsomal Cytochrome B5 Mutant V61h" 77.88 82 98.77 98.77 1.45e-50 PDB 1LQX "Crystal Structure Of V45e Mutant Of Cytochrome B5" 78.85 82 98.78 98.78 1.67e-51 PDB 1LR6 "Crystal Structure Of V45y Mutant Of Cytochrome B5" 78.85 82 98.78 98.78 9.16e-52 PDB 1M20 "Crystal Structure Of F35y Mutant Of Trypsin-Solubilized Fragment Of Cytochrome B5" 78.85 82 98.78 100.00 3.88e-52 PDB 1M2I "Crystal Structure Of E44aE56A MUTANT OF CYTOCHROME B5" 78.85 82 97.56 97.56 3.00e-51 PDB 1M59 "Crystal Structure Of P40v Mutant Of Trypsin-Solubilized Fragment Of Cytochrome B5" 78.85 82 98.78 98.78 2.14e-51 PDB 1NX7 "Solution Structure Of Oxidized Bovine Microsomal Cytochrome B5" 78.85 82 100.00 100.00 1.24e-52 PDB 1SH4 "Solution Structure Of Oxidized Bovine Microsomal Cytochrome B5 Mutant V45h" 78.85 82 98.78 98.78 2.16e-51 PDB 1U9M "Crystal Structure Of F58w Mutant Of Cytochrome B5" 78.85 82 98.78 100.00 8.40e-52 PDB 1U9U "Crystal Structure Of F58y Mutant Of Cytochrome B5" 78.85 82 98.78 100.00 3.88e-52 PDB 4HIN "2.4a Resolution Structure Of Bovine Cytochrome B5 (s71l)" 78.85 82 98.78 98.78 1.13e-51 EMBL CAA31949 "unnamed protein product [Bos taurus]" 100.00 134 100.00 100.00 1.23e-67 GB AAA72186 "microsomal cytochrome b-5 [synthetic construct]" 89.42 94 97.85 98.92 5.48e-59 GB AAB32285 "peditoxin, pedin=cytochrome b-like heme protein [Toxopneustes pileolus=sea urchins, Lamarck, Peptide, 82 aa]" 78.85 82 97.56 100.00 7.82e-51 GB AAC14455 "cytochrome b-5 [Bos taurus]" 93.27 98 100.00 100.00 3.70e-63 GB AAC48780 "cytochrome b5 [Sus scrofa]" 66.35 69 97.10 98.55 4.20e-40 GB AAI08114 "CYB5 protein [Bos taurus]" 100.00 134 100.00 100.00 1.23e-67 PRF 1106188A "cytochrome b5" 93.27 97 98.97 100.00 5.43e-63 PRF 1803548B "cytochrome b5" 100.00 134 100.00 100.00 1.23e-67 REF NP_001159663 "cytochrome b5 [Ovis aries]" 100.00 134 98.08 99.04 3.84e-66 REF NP_001274163 "cytochrome b5 [Capra hircus]" 100.00 134 98.08 99.04 3.84e-66 REF NP_776458 "cytochrome b5 [Bos taurus]" 100.00 134 100.00 100.00 1.23e-67 REF XP_005904370 "PREDICTED: cytochrome b5 isoform X1 [Bos mutus]" 100.00 134 100.00 100.00 1.23e-67 REF XP_005972547 "PREDICTED: cytochrome b5-like isoform X1 [Pantholops hodgsonii]" 100.00 134 97.12 99.04 6.40e-66 SP P00171 "RecName: Full=Cytochrome b5" 100.00 134 100.00 100.00 1.23e-67 TPG DAA15965 "TPA: cytochrome b5 [Bos taurus]" 100.00 134 100.00 100.00 1.23e-67 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 no _Mol_aromatic yes _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Wed Feb 16 11:34:07 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 '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 $b5 cattle 9913 Eukaryota Metazoa Bos taurus 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 $b5 'recombinant technology' . Escherichia coli BL21 pKK223-3 stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details 'ferricytochrome - HEM bound to protein' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $b5 2.4 mM [U-15N] phosphate 20 mM 'natural abundance' $HEM 2.4 mM 'natural abundance' D2O 100 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_Felix _Saveframe_category software _Name FELIX _Version 2.3 loop_ _Vendor _Address _Electronic_address 'Accelrys Software Inc.' . . stop_ loop_ _Task processing stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AMX _Field_strength 600 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model UnityPlus _Field_strength 500 _Details . save_ ############################# # NMR applied experiments # ############################# save_3D_1H-15N_NOESY_HSQC_1 _Saveframe_category NMR_applied_experiment _Experiment_name '3D 1H-15N NOESY HSQC' _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 pH 7.0 . pH pressure 1 . atm temperature 301 . K stop_ save_