data_4667 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR SOLUTION STRUCTURE OF CO(II)-Bleomycin A2 ; loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Lehmann T. E. . 2 Serrano M. L. . 3 Que L. . Jr. stop_ _BMRB_accession_number 4667 _BMRB_flat_file_name bmr4667.str _Entry_type new _Submission_date 2000-02-10 _Accession_date 2000-02-10 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count '1H chemical shifts' 37 '13C chemical shifts' 19 stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full ; Lehmann, T.E., Serrano, M.L., and Que, L. Jr., "Coordination Chemistry of Co(II)-bleomycin: Its Investigation through NMR and Molecular Dynamics," Biochemistry 39, 3886-3898 (2000). ; _Citation_title ; Coordination Chemistry of Co(II)-bleomycin: Its Investigation Through NMR and Molecular Dynamics ; _Citation_status published _Citation_type journal _MEDLINE_UI_code 20213236 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Lehmann T. E. . 2 Serrano M. L. . 3 Que L. . Jr. stop_ _Journal_abbreviation Biochemistry _Journal_name_full Biochemistry _Journal_volume 39 _Page_first 3886 _Page_last 3898 _Year 2000 loop_ _Keyword ANTIBIOTIC stop_ save_ ################################## # Molecular system description # ################################## save_system_bleomycin _Saveframe_category molecular_system _Mol_system_name Co(II)-Bleomycin _Abbreviation_common bleomycin _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label "BLEOMYCIN A2" $BLEOMYCIN_A2 "Co 2+" $CO_2+ stop_ _System_physical_state native _System_oligomer_state monomer _System_paramagnetic yes _System_thiol_state 'not present' save_ ######################## # Monomeric polymers # ######################## save_BLEOMYCIN_A2 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common "BLEOMYCIN A2" _Name_variant . _Abbreviation_common "bleomycin A2" _Mol_thiol_state 'not present' ############################## # Polymer residue sequence # ############################## _Residue_count 7 _Mol_residue_sequence ; XXXXTXX ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 BNA 2 2 PYR 3 3 B-HIS 4 4 M-VAL 5 5 THR 6 6 GUL 7 7 MAN stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-11-10 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 4666 "TRANSCARBOXYLASE 1.3S SUBUNIT" 100.00 77 100.00 100.00 1.51e-42 PDB 1DCZ "Biotin Carboxyl Carrier Domain Of Transcarboxylase (Tc 1.3s)" 100.00 77 100.00 100.00 1.51e-42 PDB 1DD2 "Biotin Carboxyl Carrier Domain Of Transcarboxylase (Tc 1.3s)" 100.00 77 100.00 100.00 1.51e-42 PDB 1O78 "Biotin Carboxyl Carrier Domain Of Transcarboxylase (1.3s) [10-48] Deletion Mutant" 98.70 84 100.00 100.00 5.32e-42 EMBL CAD59402 "putative methylmalonyl-CoA carboxyltransferase [Propionibacterium freudenreichii subsp. shermanii]" 100.00 123 100.00 100.00 6.47e-42 EMBL CBL57376 "Methylmalonyl-CoA carboxytransferase, 1.3S subunit (Transcarboxylase, 1.3S subunit). 123bp [Propionibacterium freudenreichii su" 100.00 123 100.00 100.00 6.47e-42 EMBL CDP49157 "Methylmalonyl-CoA carboxytransferase, 1.3S subunit (Transcarboxylase, 1.3S subunit). 123bp [Propionibacterium freudenreichii su" 100.00 123 100.00 100.00 6.47e-42 EMBL CEG86413 "Methylmalonyl-CoA carboxytransferase, 1.3S subunit (Transcarboxylase, 1.3S subunit). 123bp [Propionibacterium freudenreichii]" 100.00 123 100.00 100.00 6.47e-42 EMBL CEG88429 "Methylmalonyl-CoA carboxytransferase, 1.3S subunit (Transcarboxylase, 1.3S subunit). 123bp [Propionibacterium freudenreichii]" 100.00 123 100.00 100.00 6.47e-42 GB AAA25674 "transcarboxylase, 1.3S subunit [Propionibacterium freudenreichii subsp. shermanii]" 100.00 123 100.00 100.00 6.47e-42 GB AAA89090 "Biotin purification tag [Cloning vector PinPoint Xa-1]" 100.00 129 100.00 100.00 9.26e-42 GB AAA89092 "Biotin purification tag, partial [Cloning vector PinPoint Xa-2]" 100.00 129 100.00 100.00 9.26e-42 GB AAA89094 "Biotin purification tag [Cloning vector PinPoint Xa-3]" 100.00 129 100.00 100.00 9.26e-42 GB AJQ91496 "Biotin-requiring enzyme [Propionibacterium freudenreichii subsp. freudenreichii]" 100.00 123 100.00 100.00 6.47e-42 REF WP_013161729 "acetyl-CoA carboxylase biotin carboxyl carrier protein subunit [Propionibacterium freudenreichii]" 100.00 123 100.00 100.00 6.47e-42 REF WP_048769525 "acetyl-CoA carboxylase biotin carboxyl carrier protein subunit [Propionibacterium freudenreichii]" 100.00 127 100.00 100.00 8.28e-42 SP P02904 "RecName: Full=Methylmalonyl-CoA carboxyltransferase 1.3S subunit; AltName: Full=Biotin carboxyl carrier protein of transcarboxy" 100.00 123 100.00 100.00 6.47e-42 stop_ save_ ###################### # Polymer residues # ###################### save_M-VAL _Saveframe_category polymer_residue _Mol_type non-polymer _Name_common METHYL-VALERATE _Abbreviation_common . _PDB_code . _Standard_residue_derivative . loop_ _Mol_label _Residue_seq_code $BLEOMYCIN_A2 4 stop_ _Mol_paramagnetic no save_ save_B-HIS _Saveframe_category polymer_residue _Mol_type non-polymer _Name_common beta-hidroxy-histidine _Abbreviation_common . _PDB_code . _Standard_residue_derivative HIS loop_ _Mol_label _Residue_seq_code $BLEOMYCIN_A2 3 stop_ _Mol_paramagnetic no save_ save_PYR _Saveframe_category polymer_residue _Mol_type non-polymer _Name_common PIRIMIDINYL-PROPIONAMIDE _Abbreviation_common PYR _PDB_code PYR _Standard_residue_derivative . loop_ _Mol_label _Residue_seq_code $BLEOMYCIN_A2 2 stop_ _Mol_paramagnetic no save_ save_GUL _Saveframe_category polymer_residue _Mol_type non-polymer _Name_common A-L-GULOSE _Abbreviation_common . _PDB_code GUL _Standard_residue_derivative . loop_ _Mol_label _Residue_seq_code $BLEOMYCIN_A2 6 stop_ _Mol_paramagnetic no save_ save_MAN _Saveframe_category polymer_residue _Mol_type non-polymer _Name_common A-D-MANNOSE _Abbreviation_common MAN _PDB_code MAN _Standard_residue_derivative . loop_ _Mol_label _Residue_seq_code $BLEOMYCIN_A2 7 stop_ _Mol_paramagnetic no save_ save_BNA _Saveframe_category polymer_residue _Mol_type non-polymer _Name_common 'beta-amino-alanine' _Abbreviation_common BNA _Standard_residue_derivative alanine loop_ _Mol_label _Residue_seq_code $BLEOMYCIN_A2 1 stop_ _Mol_paramagnetic no save_ ############# # Ligands # ############# save_CO_2+ _Saveframe_category ligand _Mol_type non-polymer _Name_common 'COBALT (II) ION' _Abbreviation_common Co _Name_IUPAC . _BMRB_code CO_2+ _PDB_code CO _Mol_empirical_formula CO1 _Mol_charge 2+ _Mol_paramagnetic yes _Mol_aromatic no _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons CO CO CO ? 2+ ? ? stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $BLEOMYCIN_A2 ? . . . . . 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 $BLEOMYCIN_A2 ? . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $BLEOMYCIN_A2 10 mM . D2O 100 % . stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $BLEOMYCIN_A2 10 mM . D2O 10 % . H2O 90 % . stop_ save_ ############################ # Computer software used # ############################ save_DISCOVER_3 _Saveframe_category software _Name DISCOVER_3 _Version 97.0 loop_ _Task "structure solution" stop_ _Details Biosym/MSI save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AMX _Field_strength 360 save_ ############################# # NMR applied experiments # ############################# save_NMR_applied_experiment _Saveframe_category NMR_applied_experiment _Experiment_name ; 2D-COSY 2D-TOCSY 2D-HMQC T1 measurment ; save_ ####################### # Sample conditions # ####################### save_sample_cond_1 _Saveframe_category sample_conditions loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 6.5 . n/a temperature 298 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference_one _Saveframe_category chemical_shift_reference 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 HDO H 1 protons ppm . internal direct . . . . 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_set_1 _Saveframe_category assigned_chemical_shifts loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_cond_1 _Chem_shift_reference_set_label $chemical_shift_reference_one _Mol_system_component_name "BLEOMYCIN A2" loop_ _Atom_shift_assign_ID _Residue_seq_code _Residue_label _Atom_name _Atom_type _Chem_shift_value _Chem_shift_value_error _Chem_shift_ambiguity_code 1 1 BNA HA H 77.1 . 1 2 1 BNA HB11 H 152 . 2 3 1 BNA HB12 H -20.5 . 2 4 2 PYR HA11 H 15.1 . 2 5 2 PYR HA12 H 16.2 . 2 6 2 PYR HA22 H 24.7 . 2 7 2 PYR HA23 H 48.8 . 2 8 2 PYR HB H 114 . 1 9 2 PYR HH H 2.6 . 2 10 2 PYR CH C 20.4 . 1 11 3 B-HIS HA H 211 . 1 12 3 B-HIS HB2 H 31.5 . 2 13 3 B-HIS HD2 H 42.1 . 1 14 3 B-HIS HE1 H -30.5 . 1 15 3 B-HIS HE2 H 51.8 . 1 16 4 M-VAL HA H -23.1 . 1 17 4 M-VAL HB2 H -11.8 . 2 18 4 M-VAL HB3 H -4.9 . 2 19 4 M-VAL HG2 H -1.8 . 1 20 4 M-VAL HD2 H -3.4 . 2 21 4 M-VAL CB1 C 65.5 . 1 22 4 M-VAL CB2 C 3.0 . 1 23 4 M-VAL CG2 C 35.8 . 1 24 4 M-VAL CD2 C 12.0 . 1 25 5 THR H H 0.2 . 1 26 5 THR HA H -1.5 . 1 27 5 THR HB H 0.8 . 1 28 5 THR HG2 H -1.9 . 1 29 5 THR CA C 53.0 . 1 30 5 THR CB C 62.5 . 1 31 5 THR CG2 C 15.0 . 1 32 6 GUL "H1'" H 26.1 . 1 33 6 GUL "H2'" H 12.8 . 1 34 6 GUL "H3'" H 10.9 . 1 35 6 GUL "H4'" H 13.7 . 1 36 6 GUL "H5'" H 32.0 . 1 37 6 GUL "H6'" H 12.4 . 2 38 6 GUL "H6''" H 13.2 . 2 39 6 GUL "C1'" C 128 . 1 40 6 GUL "C2'" C 86.2 . 1 41 6 GUL "C3'" C 82.1 . 1 42 6 GUL "C4'" C 83.8 . 1 43 6 GUL "C5'" C 86.0 . 1 44 6 GUL "C6'" C 72.0 . 1 45 7 MAN "H1'" H 4.8 . 1 46 7 MAN "H2'" H -9.3 . 1 47 7 MAN "H3'" H -29.9 . 1 48 7 MAN "H4'" H -3.0 . 1 49 7 MAN "H5'" H 2.5 . 1 50 7 MAN "H6'" H 2.2 . 2 51 7 MAN "H6''" H 3.2 . 2 52 7 MAN "C1'" C 96.2 . 1 53 7 MAN "C2'" C 60.0 . 1 54 7 MAN "C4'" C 53.8 . 1 55 7 MAN "C5'" C 74.1 . 1 56 7 MAN "C6'" C 59.1 . 1 stop_ save_