data_4746 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Average solution structure of d(TTGGCCAA)2 bound to Chromomycin-A3 and cobalt ; _BMRB_accession_number 4746 _BMRB_flat_file_name bmr4746.str _Entry_type new _Submission_date 2000-05-23 _Accession_date 2000-05-23 _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 Gochin M. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 2 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 127 "13C chemical shifts" 80 "31P chemical shifts" 7 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-07-19 update BMRB 'update DNA residue label to two-letter code' 2000-06-29 original author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 4753 'zinc complex' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; A high-resolution structure of a DNA-chromomycin-Co(II) complex determined from pseudocontact shifts in nuclear magnetic resonance ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code 20264310 _PubMed_ID 10801486 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Gochin M. . . stop_ _Journal_abbreviation 'Structure Fold. Des.' _Journal_volume 8 _Journal_issue 4 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 441 _Page_last 452 _Year 2000 _Details . loop_ _Keyword 'drug bound in the minor groove of DNA' stop_ save_ ####################################### # Cited references within the entry # ####################################### save_ref_1 _Saveframe_category citation _Citation_full 'Tu, K. and Gochin, M., J. AM. CHEM. SOC. 1999, v121, 9276-85' _Citation_title 'Structure determination by restrained molecular dynamics using NMR pseudocontact shifts as experimentally determined constraints.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 17917690 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Tu K . . 2 Gochin M . . stop_ _Journal_abbreviation 'J. Am. Chem. Soc.' _Journal_name_full 'Journal of the American Chemical Society' _Journal_volume 121 _Journal_issue 40 _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 9276 _Page_last 9285 _Year 1999 _Details ; The structure of a DNA octamer d(TTGGCCAA)(2) complexed to chromomycin-A(3) and a single divalent cobalt ion has been solved by using the pseudocontact shifts due to the unpaired electrons on the cobalt. A protocol was developed and critically evaluated for using the pseudocontact shifts in structure determination. The pseudocontact shifts were input as experimental restraints in molecular dynamics simulations with or without NOE constraints. Both the magnitude and orientation of the susceptibility anisotropy tensor required for the shift calculations were determined during the simulations by iterative refinement. The pseudocontact shifts could be used to define the structure to a very high precision and accuracy compared with a corresponding NOE-determined structure. Convergence was obtained from different starting structures and tensors. A structure determination using both NOE's and pseudocontact shifts revealed a general agreement between the two data sets. However, some evidence for a discrepancy between NOE's and pseudocontact shifts was observed in the backbone and terminal base pairs of the DNA. Violations in shift or NOE restraints remaining in the final structures were examined and may be a reflection of motional averaging of the constraints and evidence for flexibility. This work demonstrates that pseudocontact shifts are a powerful tool for NMR structure determination. ; save_ ################################## # Molecular system description # ################################## save_DNA-drug _Saveframe_category molecular_system _Mol_system_name 'D(TTGGCCAA)2 BOUND TO CHROMOMYCIN-A3 AND COBALT' _Abbreviation_common DNA-drug _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'd(TTGGCCAA) DNA octamer 1' $DNA_octamer 'd(TTGGCCAA) DNA octamer 2' $DNA_octamer 'chromomycin-A3 1' $chromomycin 'chromomycin-A3 2' $chromomycin 'cobalt(II) 1' $CO2+ 'cobalt(II) 2' $CO2+ stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state monomer _System_paramagnetic yes _System_thiol_state 'not present' loop_ _Magnetic_equivalence_ID _Magnetically_equivalent_system_component 1 'd(TTGGCCAA) DNA octamer 1' 1 'd(TTGGCCAA) DNA octamer 2' 2 'chromomycin-A3 1' 2 'chromomycin-A3 2' 3 'cobalt(II) 1' 3 'cobalt(II) 2' stop_ _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_DNA_octamer _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common 'DNA octamer' _Abbreviation_common DNA _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 8 _Mol_residue_sequence TTGGCCAA loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 11 DT 2 12 DT 3 13 DG 4 14 DG 5 15 DC 6 16 DC 7 17 DA 8 18 DA stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ save_chromomycin _Saveframe_category monomeric_polymer _Mol_type polymer _Name_common chromomycin _Abbreviation_common chromomycin _Molecular_mass . _Mol_thiol_state 'not present' _Details . _Residue_count 6 _Mol_residue_sequence XXXXXX loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 21 1GL 2 22 2GL 3 23 DXB 4 24 1AR 5 25 DDA 6 26 DDA stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_1AR _Saveframe_category polymer_residue _Mol_type non-polymer _Name_common 4-O-ACETYL-2,6-DIDEOXY-3-C-METHYL-ALPHA-L-ARABINO-HEXOPYRANOSE _Abbreviation_common 1AR _BMRB_code . _PDB_code 1AR _Standard_residue_derivative . loop_ _Mol_label _Residue_seq_code $chromomycin 4 stop_ _Molecular_mass . _Mol_paramagnetic no _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons O1 O1 O . 0 . ? C1 C1 C . 0 . ? C2 C2 C . 0 . ? C3 C3 C . 0 . ? O3 O3 O . 0 . ? CC3 CC3 C . 0 . ? C4 C4 C . 0 . ? O4 O4 O . 0 . ? CME CME C . 0 . ? CO4 CO4 C . 0 . ? OC4 OC4 O . 0 . ? C5 C5 C . 0 . ? O5 O5 O . 0 . ? C6 C6 C . 0 . ? H1 H1 H . 0 . ? HO1 HO1 H . 0 . ? HO3 HO3 H . 0 . ? H4 H4 H . 0 . ? H5 H5 H . 0 . ? 1H2 1H2 H . 0 . ? 2H2 2H2 H . 0 . ? HM31 HM31 H . 0 . ? HM32 HM32 H . 0 . ? HM33 HM33 H . 0 . ? HM41 HM41 H . 0 . ? HM42 HM42 H . 0 . ? HM43 HM43 H . 0 . ? 1H6 1H6 H . 0 . ? 2H6 2H6 H . 0 . ? 3H6 3H6 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 O1 C1 ? ? SING O1 HO1 ? ? SING C1 C2 ? ? SING C1 O5 ? ? SING C1 H1 ? ? SING C2 C3 ? ? SING C2 1H2 ? ? SING C2 2H2 ? ? SING C3 O3 ? ? SING C3 CC3 ? ? SING C3 C4 ? ? SING O3 HO3 ? ? SING CC3 HM31 ? ? SING CC3 HM32 ? ? SING CC3 HM33 ? ? SING C4 O4 ? ? SING C4 C5 ? ? SING C4 H4 ? ? SING O4 CO4 ? ? SING CME CO4 ? ? SING CME HM41 ? ? SING CME HM42 ? ? SING CME HM43 ? ? DOUB CO4 OC4 ? ? SING C5 O5 ? ? SING C5 C6 ? ? SING C5 H5 ? ? SING C6 1H6 ? ? SING C6 2H6 ? ? SING C6 3H6 ? ? stop_ save_ save_1GL _Saveframe_category polymer_residue _Mol_type non-polymer _Name_common 4-O-METHYL-2,6-DIDEOXY-ALPHA-D-GALACTO-HEXOPYRANOSE _Abbreviation_common 1GL _BMRB_code . _PDB_code 1GL _Standard_residue_derivative . loop_ _Mol_label _Residue_seq_code $chromomycin 1 stop_ _Molecular_mass . _Mol_paramagnetic no _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons O1 O1 O . 0 . ? C1 C1 C . 0 . ? C2 C2 C . 0 . ? C3 C3 C . 0 . ? O3 O3 O . 0 . ? C4 C4 C . 0 . ? O4 O4 O . 0 . ? CME CME C . 0 . ? C5 C5 C . 0 . ? O5 O5 O . 0 . ? C6 C6 C . 0 . ? HO1 HO1 H . 0 . ? H1 H1 H . 0 . ? HO3 HO3 H . 0 . ? H3 H3 H . 0 . ? H4 H4 H . 0 . ? H5 H5 H . 0 . ? 1H2 1H2 H . 0 . ? 2H2 2H2 H . 0 . ? HM41 HM41 H . 0 . ? HM42 HM42 H . 0 . ? HM43 HM43 H . 0 . ? 1H6 1H6 H . 0 . ? 2H6 2H6 H . 0 . ? 3H6 3H6 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 O1 C1 ? ? SING O1 HO1 ? ? SING C1 C2 ? ? SING C1 O5 ? ? SING C1 H1 ? ? SING C2 C3 ? ? SING C2 1H2 ? ? SING C2 2H2 ? ? SING C3 O3 ? ? SING C3 C4 ? ? SING C3 H3 ? ? SING O3 HO3 ? ? SING C4 O4 ? ? SING C4 C5 ? ? SING C4 H4 ? ? SING O4 CME ? ? SING CME HM41 ? ? SING CME HM42 ? ? SING CME HM43 ? ? SING C5 O5 ? ? SING C5 C6 ? ? SING C5 H5 ? ? SING C6 1H6 ? ? SING C6 2H6 ? ? SING C6 3H6 ? ? stop_ save_ save_2GL _Saveframe_category polymer_residue _Mol_type non-polymer _Name_common 4-O-ACETYL-2,6-DIDEOXY-ALPHA-D-GALACTO-HEXOPYRANOSE _Abbreviation_common 2GL _BMRB_code . _PDB_code 2GL _Standard_residue_derivative . loop_ _Mol_label _Residue_seq_code $chromomycin 2 stop_ _Molecular_mass . _Mol_paramagnetic no _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons O1 O1 O . 0 . ? C1 C1 C . 0 . ? C2 C2 C . 0 . ? C3 C3 C . 0 . ? O3 O3 O . 0 . ? C4 C4 C . 0 . ? O4 O4 O . 0 . ? CME CME C . 0 . ? CO4 CO4 C . 0 . ? OC4 OC4 O . 0 . ? C5 C5 C . 0 . ? O5 O5 O . 0 . ? C6 C6 C . 0 . ? HO1 HO1 H . 0 . ? H1 H1 H . 0 . ? HO3 HO3 H . 0 . ? H4 H4 H . 0 . ? H5 H5 H . 0 . ? 1H2 1H2 H . 0 . ? 2H2 2H2 H . 0 . ? H3 H3 H . 0 . ? HM41 HM41 H . 0 . ? HM42 HM42 H . 0 . ? HM43 HM43 H . 0 . ? 1H6 1H6 H . 0 . ? 2H6 2H6 H . 0 . ? 3H6 3H6 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 O1 C1 ? ? SING O1 HO1 ? ? SING C1 C2 ? ? SING C1 O5 ? ? SING C1 H1 ? ? SING C2 C3 ? ? SING C2 1H2 ? ? SING C2 2H2 ? ? SING C3 C4 ? ? SING C3 O3 ? ? SING C3 H3 ? ? SING O3 HO3 ? ? SING C4 O4 ? ? SING C4 C5 ? ? SING C4 H4 ? ? SING O4 CO4 ? ? SING CME CO4 ? ? SING CME HM41 ? ? SING CME HM42 ? ? SING CME HM43 ? ? DOUB CO4 OC4 ? ? SING C5 O5 ? ? SING C5 C6 ? ? SING C5 H5 ? ? SING C6 1H6 ? ? SING C6 2H6 ? ? SING C6 3H6 ? ? stop_ save_ save_DDA _Saveframe_category polymer_residue _Mol_type non-polymer _Name_common 2,6-DIDEOXY-BETA-D-GLUCOSE _Abbreviation_common DDA _BMRB_code . _PDB_code DDA _Standard_residue_derivative . loop_ _Mol_label _Residue_seq_code $chromomycin 5 $chromomycin 6 stop_ _Molecular_mass . _Mol_paramagnetic no _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons C1 C1 C . 0 . ? C2 C2 C . 0 . ? C3 C3 C . 0 . ? C4 C4 C . 0 . ? C5 C5 C . 0 . ? C6 C6 C . 0 . ? O1 O1 O . 0 . ? O5 O5 O . 0 . ? O3 O3 O . 0 . ? O4 O4 O . 0 . ? H1 H1 H . 0 . ? 1H2 1H2 H . 0 . ? 2H2 2H2 H . 0 . ? H3 H3 H . 0 . ? H4 H4 H . 0 . ? H5 H5 H . 0 . ? 1H6 1H6 H . 0 . ? 2H6 2H6 H . 0 . ? 3H6 3H6 H . 0 . ? HO1 HO1 H . 0 . ? HO3 HO3 H . 0 . ? HO4 HO4 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 C1 C2 ? ? SING C1 O5 ? ? SING C1 O1 ? ? SING C1 H1 ? ? SING C2 C3 ? ? SING C2 1H2 ? ? SING C2 2H2 ? ? SING C3 C4 ? ? SING C3 O3 ? ? SING C3 H3 ? ? SING C4 C5 ? ? SING C4 O4 ? ? SING C4 H4 ? ? SING C5 C6 ? ? SING C5 O5 ? ? SING C5 H5 ? ? SING C6 1H6 ? ? SING C6 2H6 ? ? SING C6 3H6 ? ? SING O1 HO1 ? ? SING O3 HO3 ? ? SING O4 HO4 ? ? stop_ save_ save_DXB _Saveframe_category polymer_residue _Mol_type non-polymer _Name_common ; 1,2-HYDRO-1-OXY-3,4-HYDRO-3-(1-METHOXY-2-OXY-3,4-DIHYDROXYPENTYL)-8,9-DIHYDROXY-7-METHYL-ANTHRACENE ; _Abbreviation_common DXB _BMRB_code . _PDB_code DXB _Standard_residue_derivative . loop_ _Mol_label _Residue_seq_code $chromomycin 3 stop_ _Molecular_mass . _Mol_paramagnetic no _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons C1 C1 C . 0 . ? O1 O1 O . 0 . ? C9A C9A C . 0 . ? C2 C2 C . 0 . ? C3 C3 C . 0 . ? C4 C4 C . 0 . ? C4A C4A C . 0 . ? C10 C10 C . 0 . ? C5A C5A C . 0 . ? C5 C5 C . 0 . ? C6 C6 C . 0 . ? C7 C7 C . 0 . ? CC7 CC7 C . 0 . ? C8 C8 C . 0 . ? O8 O8 O . 0 . ? C8A C8A C . 0 . ? C9 C9 C . 0 . ? O9 O9 O . 0 . ? CME CME C . 0 . ? C1S C1S C . 0 . ? O1S O1S O . 0 . ? C2S C2S C . 0 . ? O2S O2S O . 0 . ? C3S C3S C . 0 . ? O3S O3S O . 0 . ? C4S C4S C . 0 . ? O4S O4S O . 0 . ? C5S C5S C . 0 . ? 1H2 1H2 H . 0 . ? 2H2 2H2 H . 0 . ? H3 H3 H . 0 . ? H5 H5 H . 0 . ? HO8 HO8 H . 0 . ? HO9 HO9 H . 0 . ? HO3 HO3 H . 0 . ? HO4 HO4 H . 0 . ? H4A H4A H . 0 . ? H4E H4E H . 0 . ? HM71 HM71 H . 0 . ? HM72 HM72 H . 0 . ? HM73 HM73 H . 0 . ? H10 H10 H . 0 . ? HS1 HS1 H . 0 . ? HM11 HM11 H . 0 . ? HM12 HM12 H . 0 . ? HM13 HM13 H . 0 . ? HS3 HS3 H . 0 . ? HS4 HS4 H . 0 . ? HM51 HM51 H . 0 . ? HM52 HM52 H . 0 . ? HM53 HM53 H . 0 . ? H6 H6 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 DOUB C1 O1 ? ? SING C1 C9A ? ? SING C1 C2 ? ? DOUB C9A C4A ? ? SING C9A C9 ? ? SING C2 C3 ? ? SING C2 1H2 ? ? SING C2 2H2 ? ? SING C3 C4 ? ? SING C3 H3 ? ? SING C3 C1S ? ? SING C4 C4A ? ? SING C4 H4A ? ? SING C4 H4E ? ? SING C4A C10 ? ? DOUB C10 C5A ? ? SING C10 H10 ? ? SING C5A C5 ? ? SING C5A C8A ? ? DOUB C5 C6 ? ? SING C5 H5 ? ? SING C6 C7 ? ? SING C6 H6 ? ? SING C7 CC7 ? ? DOUB C7 C8 ? ? SING CC7 HM71 ? ? SING CC7 HM72 ? ? SING CC7 HM73 ? ? SING C8 O8 ? ? SING C8 C8A ? ? SING O8 HO8 ? ? DOUB C8A C9 ? ? SING C9 O9 ? ? SING O9 HO9 ? ? SING CME O1S ? ? SING CME HM11 ? ? SING CME HM12 ? ? SING CME HM13 ? ? SING C1S HS1 ? ? SING C1S O1S ? ? SING C1S C2S ? ? DOUB C2S O2S ? ? SING C2S C3S ? ? SING C3S HS3 ? ? SING C3S O3S ? ? SING C3S C4S ? ? SING O3S HO3 ? ? SING C4S HS4 ? ? SING C4S O4S ? ? SING C4S C5S ? ? SING O4S HO4 ? ? SING C5S HM51 ? ? SING C5S HM52 ? ? SING C5S HM53 ? ? stop_ save_ ############# # Ligands # ############# save_CO2+ _Saveframe_category ligand _Mol_type non-polymer _Name_common 'COBALT (II) ION' _Abbreviation_common Co _BMRB_code CO2+ _PDB_code CO _Molecular_mass . _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+ 2+ ? 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 $DNA_octamer . . . . . . $chromomycin . . . . . . $CO2+ . . . . . . 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 $DNA_octamer 'chemical synthesis' . . . . . 'Oligo's etc.' $chromomycin vendor . . . . . . $CO2+ vendor . . . . . Sigma 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 $DNA_octamer 2 mM . $chromomycin 2 mM . $CO2+ 2 mM . NaCl 100 mM . 'Na borate' 10 mM . stop_ save_ ############################ # Computer software used # ############################ save_NMRPipe _Saveframe_category software _Name NMRPipe _Version 1.7 loop_ _Task processing stop_ _Details 'DeLaglio and Bax' save_ save_Sparky _Saveframe_category software _Name Sparky _Version 3.0 loop_ _Task 'data analysis' stop_ _Details 'Kneller and Goddard' save_ save_X-PLOR _Saveframe_category software _Name X-PLOR _Version '3.0, 3.851' loop_ _Task refinement stop_ _Details 'Brunger (modified Gochin and Tu)' save_ save_FELIX _Saveframe_category software _Name FELIX _Version 2.1 loop_ _Task 'data analysis' stop_ _Details Biosym save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer _Saveframe_category NMR_spectrometer _Manufacturer GE _Model Omega _Field_strength 500 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _Sample_label . save_ save_13C-1H_HMQC_2 _Saveframe_category NMR_applied_experiment _Experiment_name '13C-1H HMQC' _Sample_label . save_ save_NMR_spec_expt__0_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_2 _Saveframe_category NMR_applied_experiment _Experiment_name '13C-1H HMQC' _BMRB_pulse_sequence_accession_number . _Details . save_ ####################### # Sample conditions # ####################### save_sample_cond_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 6 0.2 n/a temperature 298 1 K 'ionic strength' 110 . mM pressure 1 . atm stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_ref_1 _Saveframe_category chemical_shift_reference _Details ; Internal TSP referenced to external TSP (in a co-axial capillary) because of susceptibility effects in the sample. All reported chemical shifts are relative to external TSP. ; 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 TSP H 1 'methyl protons' ppm 0.00 External_in_the_sample direct cylindrical External_in_the_sample parallel_to_Bo 1 TSP C 13 'methyl protons' ppm 0.00 External_in_the_sample direct cylindrical External_in_the_sample parallel_to_Bo 1 TMP P 31 phosphorous ppm 0.00 External_in_the_sample direct cylindrical External_in_the_sample parallel_to_Bo 1 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 _Details . loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_cond_1 _Chem_shift_reference_set_label $chemical_shift_ref_1 _Mol_system_component_name 'd(TTGGCCAA) DNA octamer 1' _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 DT H6 H 7.07 0.017 1 2 . 1 DT H71 H 0.78 0.021 1 3 . 1 DT H72 H 0.78 0.021 1 4 . 1 DT H73 H 0.78 0.021 1 5 . 1 DT C6 C 139.03 0.089 1 6 . 1 DT C7 C 13.52 0.066 1 7 . 1 DT H1' H 5.76 0.020 1 8 . 1 DT H2' H 1.87 0.035 1 9 . 1 DT H2'' H 2.31 0.032 1 10 . 1 DT H3' H 4.39 0.020 1 11 . 1 DT H4' H 3.91 0.014 1 12 . 1 DT H5' H 3.46 0.033 1 13 . 1 DT H5'' H 3.46 0.033 1 14 . 1 DT C1' C 87.38 0.094 1 15 . 1 DT C2' C 40.05 0.351 1 16 . 1 DT C3' C 77.31 0.104 1 17 . 1 DT C4' C 88.25 0.081 1 18 . 1 DT C5' C 63.16 0.124 1 19 . 2 DT H6 H 7.22 0.023 1 20 . 2 DT H71 H 0.72 0.025 1 21 . 2 DT H72 H 0.72 0.025 1 22 . 2 DT H73 H 0.72 0.025 1 23 . 2 DT C6 C 139.13 0.110 1 24 . 2 DT C7 C 13.52 0.066 1 25 . 2 DT H1' H 6.31 0.023 1 26 . 2 DT H2' H 2.53 0.026 1 27 . 2 DT H2'' H 2.80 0.032 1 28 . 2 DT H3' H 4.99 0.024 1 29 . 2 DT H4' H 4.50 0.017 1 30 . 2 DT H5' H 4.15 0.029 1 31 . 2 DT H5'' H 4.15 0.029 1 32 . 2 DT C1' C 86.62 0.108 1 33 . 2 DT C2' C 40.37 0.191 1 34 . 2 DT C3' C 77.29 0.104 1 35 . 2 DT C4' C 86.86 0.133 1 36 . 2 DT C5' C 68.13 0.183 1 37 . 2 DT P P -3.99 0.025 1 38 . 3 DG H1 H 12.11 0.027 1 39 . 3 DG H21 H 15.06 0.090 1 40 . 3 DG H22 H 13.09 0.096 1 41 . 3 DG H8 H 8.05 0.023 1 42 . 3 DG C8 C 137.39 0.199 1 43 . 3 DG H1' H 8.41 0.026 1 44 . 3 DG H2' H 4.48 0.037 1 45 . 3 DG H2'' H 4.97 0.041 1 46 . 3 DG H3' H 5.86 0.032 1 47 . 3 DG H4' H 5.76 0.020 1 48 . 3 DG H5' H 5.03 0.025 1 49 . 3 DG H5'' H 5.11 0.046 1 50 . 3 DG C1' C 87.73 0.133 1 51 . 3 DG C2' C 43.60 0.285 1 52 . 3 DG C3' C 76.09 0.130 1 53 . 3 DG C4' C 86.86 0.133 1 54 . 3 DG C5' C 68.13 0.183 1 55 . 3 DG P P -2.94 0.030 1 56 . 4 DG H1 H -2.91 0.045 1 57 . 4 DG H21 H -26.86 0.325 1 58 . 4 DG H22 H 18.44 0.073 1 59 . 4 DG H8 H 7.54 0.026 1 60 . 4 DG C8 C 136.27 0.192 1 61 . 4 DG H1' H 11.89 0.033 1 62 . 4 DG H2' H 8.23 0.063 1 63 . 4 DG H2'' H 11.50 0.052 1 64 . 4 DG H3' H 6.23 0.030 1 65 . 4 DG H4' H 8.53 0.030 1 66 . 4 DG H5' H 5.79 0.030 1 67 . 4 DG H5'' H 6.17 0.027 1 68 . 4 DG C1' C 91.82 0.155 1 69 . 4 DG C2' C 49.00 0.133 1 70 . 4 DG C3' C 77.45 0.170 1 71 . 4 DG C4' C 90.64 0.173 1 72 . 4 DG C5' C 71.42 0.143 1 73 . 4 DG P P -2.02 0.030 1 74 . 5 DC H41 H 1.07 0.030 1 75 . 5 DC H42 H 0.25 0.029 1 76 . 5 DC H5 H 0.34 0.033 1 77 . 5 DC H6 H 4.66 0.056 1 78 . 5 DC C5 C 89.65 0.193 1 79 . 5 DC C6 C 133.73 0.199 1 80 . 5 DC H2' H -29.45 0.234 1 81 . 5 DC H2'' H -20.82 0.500 1 82 . 5 DC H3' H -0.48 0.053 1 83 . 5 DC H4' H 28.54 0.224 1 84 . 5 DC H5' H 11.19 0.040 1 85 . 5 DC H5'' H 15.96 0.037 1 86 . 5 DC C3' C 69.52 0.226 1 87 . 5 DC C5' C 71.72 0.192 1 88 . 5 DC P P -1.71 0.045 1 89 . 6 DC H41 H -0.26 0.035 1 90 . 6 DC H42 H 3.47 0.046 1 91 . 6 DC H5 H -6.22 0.036 1 92 . 6 DC H6 H -14.72 0.088 1 93 . 6 DC C5 C 84.55 0.189 1 94 . 6 DC H2' H -3.58 0.215 1 95 . 6 DC H3' H -7.37 0.040 1 96 . 6 DC H4' H -38.59 0.658 1 97 . 6 DC H5' H -18.35 0.067 1 98 . 6 DC H5'' H -41.21 0.522 1 99 . 6 DC C3' C 66.41 0.144 1 100 . 6 DC P P -14.20 0.045 1 101 . 7 DA H2 H 8.04 0.031 1 102 . 7 DA H8 H 6.32 0.032 1 103 . 7 DA C2 C 155.14 0.089 1 104 . 7 DA C8 C 140.57 0.133 1 105 . 7 DA H1' H 8.50 0.031 1 106 . 7 DA H2' H 2.48 0.027 1 107 . 7 DA H2'' H 3.57 0.020 1 108 . 7 DA H3' H 5.79 0.024 1 109 . 7 DA H4' H 9.13 0.052 1 110 . 7 DA H5' H 5.95 0.058 1 111 . 7 DA H5'' H 8.41 0.060 1 112 . 7 DA C1' C 87.56 0.157 1 113 . 7 DA C2' C 42.29 0.133 1 114 . 7 DA C3' C 83.26 0.100 1 115 . 7 DA C4' C 91.33 0.273 1 116 . 7 DA C5' C 70.96 0.199 1 117 . 7 DA P P -8.80 0.045 1 118 . 8 DA H2 H 7.72 0.016 1 119 . 8 DA H8 H 8.20 0.024 1 120 . 8 DA C2 C 154.83 0.085 1 121 . 8 DA C8 C 141.86 0.127 1 122 . 8 DA H1' H 6.95 0.024 1 123 . 8 DA H2' H 2.79 0.029 1 124 . 8 DA H2'' H 3.04 0.034 1 125 . 8 DA H3' H 5.48 0.016 1 126 . 8 DA H4' H 5.60 0.018 1 127 . 8 DA H5' H 5.77 0.033 1 128 . 8 DA H5'' H 6.40 0.032 1 129 . 8 DA C1' C 85.30 0.188 1 130 . 8 DA C2' C 42.83 0.186 1 131 . 8 DA C3' C 73.49 0.080 1 132 . 8 DA C4' C 88.78 0.097 1 133 . 8 DA C5' C 68.93 0.199 1 134 . 8 DA P P -2.62 0.030 1 stop_ save_ save_chemical_shift_set_2 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_cond_1 _Chem_shift_reference_set_label $chemical_shift_ref_1 _Mol_system_component_name 'chromomycin-A3 1' _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 1GL C1 C 99.75 0.084 1 2 . 1 1GL H1 H 8.45 0.018 1 3 . 1 1GL C2 C 36.31 0.114 1 4 . 1 1GL H2A H 4.07 0.027 1 5 . 1 1GL H2E H 4.42 0.022 1 6 . 1 1GL C3 C 71.04 0.138 1 7 . 1 1GL H3 H 7.11 0.025 1 8 . 1 1GL C4 C 86.04 0.090 1 9 . 1 1GL H4 H 5.43 0.019 1 10 . 1 1GL CME C 65.69 0.080 1 11 . 1 1GL HM4 H 4.76 0.013 1 12 . 1 1GL C5 C 72.84 0.144 1 13 . 1 1GL H5 H 7.31 0.028 1 14 . 1 1GL C6 C 21.50 0.107 1 15 . 1 1GL HM6 H 3.21 0.022 1 16 . 2 2GL C1 C 112.40 0.181 1 17 . 2 2GL H1 H 18.13 0.041 1 18 . 2 2GL C2 C 44.61 0.134 1 19 . 2 2GL H2A H 10.49 0.030 1 20 . 2 2GL H2E H 10.64 0.042 1 21 . 2 2GL C3 C 76.68 0.185 1 22 . 2 2GL H3 H 9.77 0.033 1 23 . 2 2GL C4 C 76.79 0.073 1 24 . 2 2GL H4 H 9.90 0.018 1 25 . 2 2GL CME C 27.54 0.082 1 26 . 2 2GL HM4 H 6.46 0.017 1 27 . 2 2GL C5 C 80.49 0.129 1 28 . 2 2GL H5 H 11.20 0.031 1 29 . 2 2GL C6 C 25.97 0.106 1 30 . 2 2GL HM6 H 7.48 0.024 1 31 . 3 DXB H2 H -59.28 0.375 1 32 . 3 DXB H3 H -19.06 0.135 1 33 . 3 DXB H4A H -8.82 0.111 1 34 . 3 DXB H4E H -1.41 0.066 1 35 . 3 DXB H5 H 32.16 0.057 1 36 . 3 DXB CC7 C 36.67 0.331 1 37 . 3 DXB HM7 H 26.93 0.084 1 38 . 3 DXB H10 H 15.25 0.074 1 39 . 3 DXB C1S C 118.15 0.227 1 40 . 3 DXB HS1 H -11.45 0.056 1 41 . 3 DXB CME C 51.55 0.111 1 42 . 3 DXB HM1 H -5.60 0.028 1 43 . 3 DXB C3S C 74.50 0.098 1 44 . 3 DXB HS3 H -3.21 0.024 1 45 . 3 DXB C4S C 65.69 0.139 1 46 . 3 DXB HS4 H -1.69 0.033 1 47 . 3 DXB C5S C 16.72 0.107 1 48 . 3 DXB HM5 H -3.16 0.021 1 49 . 4 1AR C1 C 102.98 0.125 1 50 . 4 1AR H1 H 14.84 0.027 1 51 . 4 1AR C2 C 51.90 0.097 1 52 . 4 1AR H2A H 6.98 0.031 1 53 . 4 1AR H2E H 6.90 0.024 1 54 . 4 1AR CC3 C 28.47 0.086 1 55 . 4 1AR HM3 H 6.03 0.020 1 56 . 4 1AR C4 C 87.58 0.124 1 57 . 4 1AR H4 H 9.29 0.025 1 58 . 4 1AR CME C 25.89 0.102 1 59 . 4 1AR HM4 H 4.78 0.009 1 60 . 4 1AR C5 C 76.14 0.172 1 61 . 4 1AR H5 H 12.05 0.032 1 62 . 4 1AR C6 C 27.73 0.150 1 63 . 4 1AR HM6 H 8.31 0.025 1 64 . 5 DDA H1 H 45.07 0.160 1 65 . 5 DDA C2 C 56.80 0.195 1 66 . 5 DDA H2A H 13.46 0.051 1 67 . 5 DDA H2E H 23.17 0.516 1 68 . 5 DDA C3 C 89.42 0.100 1 69 . 5 DDA H3 H 21.82 0.055 1 70 . 5 DDA C4 C 90.11 0.137 1 71 . 5 DDA H4 H 12.13 0.036 1 72 . 5 DDA HO4 H 14.63 0.045 1 73 . 5 DDA C5 C 88.35 0.100 1 74 . 5 DDA H5 H 22.68 0.058 1 75 . 5 DDA C6 C 29.64 0.114 1 76 . 5 DDA HM6 H 9.64 0.024 1 77 . 6 DDA C4 C 84.40 0.150 1 78 . 6 DDA H4 H 5.96 0.048 1 79 . 6 DDA C6 C 14.66 0.189 1 80 . 6 DDA HM6 H -3.84 0.034 1 stop_ save_