data_4361 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Structure determination by restrained molecular dynamics using NMR pseudocontact shifts as experimentally determined constraints ; _BMRB_accession_number 4361 _BMRB_flat_file_name bmr4361.str _Entry_type original _Submission_date 1999-06-22 _Accession_date 1999-06-22 _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 Tu K. . . 2 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" 152 "13C chemical shifts" 80 "31P chemical shifts" 7 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2013-08-09 update BMRB 'update non-standard residue saveframes' 2010-07-19 update BMRB 'update DNA residue label to two-letter code' 2000-12-04 original author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 4362 zinc-complex stop_ _Original_release_date 1999-06-22 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _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 ? 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 . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 9276 _Page_last 9285 _Year 1999 _Details . loop_ _Keyword 'DNA structure' 'DNA-drug interaction' 'hyperfine shifts' 'paramagnetic NMR' stop_ save_ ####################################### # Cited references within the entry # ####################################### save_ref_1 _Saveframe_category citation _Citation_full ; Gochin M. Nuclear magnetic resonance characterization of a paramagnetic DNA-drug complex with high spin cobalt; assignment of the 1H and 31P NMR spectra, and determination of electronic, spectroscopic and molecular properties. J Biomol NMR. 1998 Aug;12(2):243-57 ; _Citation_title ; Nuclear magnetic resonance characterization of a paramagnetic DNA-drug complex with high spin cobalt; assignment of the 1H and 31P NMR spectra, and determination of electronic, spectroscopic and molecular properties. ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 9751997 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Gochin M . . stop_ _Journal_abbreviation 'J. Biomol. NMR' _Journal_name_full 'Journal of biomolecular NMR' _Journal_volume 12 _Journal_issue 2 _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 243 _Page_last 257 _Year 1998 _Details ; The proton NMR spectrum of the ternary complex between the octamer duplex d(TTGGCCAA)2, two molecules of the drug chromomycin-A3, and a divalent cobalt ion has been assigned. Assignment procedures used standard two-dimensional techniques and relied upon the expected NOE contacts observed in the equivalent diamagnetic complex containing zinc. The magnetic susceptibility tensor for the cobalt was determined and used to calculate shifts for all nuclei, aiding in the assignment process and verification. Relaxation, susceptibility, temperature and field dependence studies of the paramagnetic spectrum enabled determination of electronic properties of the octahedral cobalt complex. The electronic relaxation tau(s) was determined to be 2.5 +/- 1.5 ps; the effective isotropic g value was found to be 2.6 +/- 0.2, indicating strong spin-orbit coupling. The magnetic susceptibility tensor was determined to be chi(xx) = 8.9 x 10(-3) cm3/mol, chi(yy) = 9.5 x 10(-3) cm3/mol, chi(zz) = 12.8 * 10(-3) cm3/mol. A tentative rotational correlation time of 8 ns was obtained for the complex. Both macroscopic and microscopic susceptibility measurements revealed deviations from Curie behavior over the temperature range accessible in the study. Non-selective relaxation rates were found to be inaccurate for defining distances from the metal center. However, pseudocontact shifts could be calculated with high accuracy using the dipolar shift equation. Isotropic hyperfine shifts were factored into contact and dipolar terms, revealing that the dipolar shift predominates and that contact shifts are relatively small. ; save_ save_ref_2 _Saveframe_category citation _Citation_full ; Gochin M. Structure with Folding & Design., 2000 Apr 15, 8(4):441-52 ; _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 . _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 _Journal_name_full 'Structure (London, England : 1993)' _Journal_volume 8 _Journal_issue 4 _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 441 _Page_last 452 _Year 2000 _Details ; BACKGROUND: The drug chromomycin-A(3) binds to the minor groove of DNA and requires a divalent metal ion for complex formation. (1)H, (31)P and (13)C pseudocontact shifts occurring in the presence of a tightly bound divalent cobalt ion in the complex between d(TTGGCCAA)(2) and chromomycin-A(3) have been used to determine the structure of the complex. The accuracy of the structure was verified by validation with nuclear Overhauser enhancements (NOEs) and J-coupling constants not used in the structure calculation. RESULTS: The final structure was determined to 0.7 A resolution. The structure was compared with a structure obtained in an earlier study using NOEs, in order to assess the accuracy of NOEs in giving global structural information for a DNA complex. Although some basic features of the structures agreed, they differed substantially in the fine structural details and in the DNA axis curvature generated by the drug. The distortion of base-pair planarity that was observed in the NOE structure was not seen in our structure. Differences in drug orientation and hydrogen bonding also occurred. The curvature and elongation of the DNA that was obtained previously was not found to occur in our study. CONCLUSIONS: The use of pseudocontact shifts has enabled us to obtain a high-precision global structure of the chromomycin-DNA complex, which provides an accurate template on which to consider targeting minor groove binding drugs. The effect of such binding is not propagated far along the helix but is restricted to a local kink in the axis that reverts to its original direction within four base pairs. ; save_ ################################## # Molecular system description # ################################## save_DNA-drug _Saveframe_category molecular_system _Mol_system_name 'chromomycin-DNA complex' _Abbreviation_common DNA-drug _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'chr-DNA 1' $chr-DNA 'chr-DNA 2' $chr-DNA 'chromomycin 1' $chromomycin 'chromomycin 2' $chromomycin 'Co 1' $CO 'Co 2' $CO stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state complex _System_paramagnetic yes _System_thiol_state 'not present' loop_ _Magnetic_equivalence_ID _Magnetically_equivalent_system_component 1 'chr-DNA 1' 1 'chr-DNA 2' 2 'chromomycin 1' 2 'chromomycin 2' stop_ _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_chr-DNA _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common 'chromomycin-DNA complex' _Abbreviation_common chr-DNA _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 8 _Mol_residue_sequence ; TTGGCCAA ; loop_ _Residue_seq_code _Residue_label 1 DT 2 DT 3 DG 4 DG 5 DC 6 DC 7 DA 8 DA stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ save_chromomycin _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class carbohydrate _Name_common chromomycin _Abbreviation_common chr _Molecular_mass . _Mol_thiol_state 'not present' _Details . _Residue_count 6 _Mol_residue_sequence ; XXXXXX ; loop_ _Residue_seq_code _Residue_label 1 1GL 2 2GL 3 DXB 4 1AR 5 DDA 6 DDA stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_1GL _Saveframe_category polymer_residue _Mol_type D-SACCHARIDE _Name_common 4-O-METHYL-2,6-DIDEOXY-ALPHA-D-GALACTO-HEXOPYRANOSE _BMRB_code 1GL _PDB_code 1GL _Standard_residue_derivative . _Molecular_mass 162.184 _Mol_paramagnetic . _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 . ? H21 H21 H . 0 . ? H22 H22 H . 0 . ? H3 H3 H . 0 . ? HO3 HO3 H . 0 . ? H4 H4 H . 0 . ? HM41 HM41 H . 0 . ? HM42 HM42 H . 0 . ? HM43 HM43 H . 0 . ? H5 H5 H . 0 . ? H61 H61 H . 0 . ? H62 H62 H . 0 . ? H63 H63 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 H21 ? ? SING C2 H22 ? ? 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 H61 ? ? SING C6 H62 ? ? SING C6 H63 ? ? stop_ save_ save_chem_comp_2GL _Saveframe_category polymer_residue _Mol_type D-SACCHARIDE _Name_common 4-O-ACETYL-2,6-DIDEOXY-ALPHA-D-GALACTO-HEXOPYRANOSE _BMRB_code 2GL _PDB_code 2GL _Standard_residue_derivative . _Molecular_mass 190.194 _Mol_paramagnetic . _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons O5 O5 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 . ? O1 O1 O . 0 . ? C6 C6 C . 0 . ? HO1 HO1 H . 0 . ? H1 H1 H . 0 . ? H21 H21 H . 0 . ? H22 H22 H . 0 . ? H3 H3 H . 0 . ? HO3 HO3 H . 0 . ? H4 H4 H . 0 . ? HM41 HM41 H . 0 . ? HM42 HM42 H . 0 . ? HM43 HM43 H . 0 . ? H5 H5 H . 0 . ? H61 H61 H . 0 . ? H62 H62 H . 0 . ? H63 H63 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 O5 C1 ? ? SING O1 HO1 ? ? SING C1 C2 ? ? SING C1 O1 ? ? SING C1 H1 ? ? SING C2 C3 ? ? SING C2 H21 ? ? SING C2 H22 ? ? SING C3 O3 ? ? SING C3 C4 ? ? 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 H61 ? ? SING C6 H62 ? ? SING C6 H63 ? ? stop_ save_ save_chem_comp_1AR _Saveframe_category polymer_residue _Mol_type L-SACCHARIDE _Name_common 4-O-ACETYL-2,6-DIDEOXY-3-C-METHYL-ALPHA-L-ARABINO-HEXOPYRANOSE _BMRB_code 1AR _PDB_code 1AR _Standard_residue_derivative . _Molecular_mass 204.220 _Mol_paramagnetic . _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 . ? HO1 HO1 H . 0 . ? H1 H1 H . 0 . ? H21 H21 H . 0 . ? H22 H22 H . 0 . ? HO3 HO3 H . 0 . ? HM31 HM31 H . 0 . ? HM32 HM32 H . 0 . ? HM33 HM33 H . 0 . ? H4 H4 H . 0 . ? HM41 HM41 H . 0 . ? HM42 HM42 H . 0 . ? HM43 HM43 H . 0 . ? H5 H5 H . 0 . ? H61 H61 H . 0 . ? H62 H62 H . 0 . ? H63 H63 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 H21 ? ? SING C2 H22 ? ? 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 H61 ? ? SING C6 H62 ? ? SING C6 H63 ? ? stop_ save_ save_chem_comp_DDA _Saveframe_category polymer_residue _Mol_type D-SACCHARIDE _Name_common 2,6-DIDEOXY-BETA-D-GLUCOSE _BMRB_code DDA _PDB_code DDA _Standard_residue_derivative . _Molecular_mass 148.157 _Mol_paramagnetic . _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 . ? O5 O5 O . 0 . ? O1 O1 O . 0 . ? O3 O3 O . 0 . ? O4 O4 O . 0 . ? H1 H1 H . 0 . ? H21 H21 H . 0 . ? H22 H22 H . 0 . ? H3 H3 H . 0 . ? H4 H4 H . 0 . ? H5 H5 H . 0 . ? H61 H61 H . 0 . ? H62 H62 H . 0 . ? H63 H63 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 H21 ? ? SING C2 H22 ? ? 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 H61 ? ? SING C6 H62 ? ? SING C6 H63 ? ? SING O1 HO1 ? ? SING O3 HO3 ? ? SING O4 HO4 ? ? stop_ save_ save_chem_comp_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 _BMRB_code DXB _PDB_code DXB _Standard_residue_derivative . _Molecular_mass 388.411 _Mol_paramagnetic . _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 . ? H21 H21 H . 0 . ? H22 H22 H . 0 . ? H3 H3 H . 0 . ? H4A H4A H . 0 . ? H4E H4E H . 0 . ? H10 H10 H . 0 . ? H5 H5 H . 0 . ? H6 H6 H . 0 . ? HM71 HM71 H . 0 . ? HM72 HM72 H . 0 . ? HM73 HM73 H . 0 . ? HO8 HO8 H . 0 . ? HO9 HO9 H . 0 . ? HM11 HM11 H . 0 . ? HM12 HM12 H . 0 . ? HM13 HM13 H . 0 . ? HS1 HS1 H . 0 . ? HS3 HS3 H . 0 . ? HO3 HO3 H . 0 . ? HS4 HS4 H . 0 . ? HO4 HO4 H . 0 . ? HM51 HM51 H . 0 . ? HM52 HM52 H . 0 . ? HM53 HM53 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 H21 ? ? SING C2 H22 ? ? SING C3 C4 ? ? SING C3 C1S ? ? SING C3 H3 ? ? 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 O1S ? ? SING C1S C2S ? ? SING C1S HS1 ? ? DOUB C2S O2S ? ? SING C2S C3S ? ? SING C3S O3S ? ? SING C3S C4S ? ? SING C3S HS3 ? ? SING O3S HO3 ? ? SING C4S O4S ? ? SING C4S C5S ? ? SING C4S HS4 ? ? SING O4S HO4 ? ? SING C5S HM51 ? ? SING C5S HM52 ? ? SING C5S HM53 ? ? stop_ save_ ############# # Ligands # ############# save_CO _Saveframe_category ligand _Mol_type "non-polymer (NON-POLYMER)" _Name_common "CO (COBALT (II) ION)" _BMRB_code CO _PDB_code CO _Molecular_mass 58.933 _Mol_charge 2 _Mol_paramagnetic . _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_ _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 $chr-DNA . . Eukaryota . . . $chromomycin . . . . . . 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 $chr-DNA 'chemical synthesis' . . . . . $chromomycin '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 $chr-DNA 2.0 mM . $chromomycin 2.0 mM . stop_ save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer GE _Model Omega _Field_strength 500 _Details . save_ ############################# # NMR applied experiments # ############################# save_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name NOESY _Sample_label $sample_1 save_ save_COSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name COSY _Sample_label $sample_1 save_ save_TOCSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name TOCSY _Sample_label $sample_1 save_ ####################### # Sample conditions # ####################### save_sample_cond_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 100 . mM pH 6.5 0.2 n/a pressure 1 . atm temperature 298 0.5 K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference _Saveframe_category chemical_shift_reference _Details . 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 TSP C 13 methyl ppm 0 external direct cylindrical external parallel_to_Bo TSP H 1 'methyl protons' ppm 0 external direct cylindrical external parallel_to_Bo TMP P 31 phosphate ppm 0 external direct cylindrical external parallel_to_Bo 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_shift_set_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label NOESY COSY TOCSY stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_cond_1 _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name 'chr-DNA 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 H22 H -26.86 0.325 1 58 . 4 DG H21 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 H42 H -0.26 0.035 1 90 . 6 DC H41 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_shift_set_2 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label NOESY COSY TOCSY stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_cond_1 _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name 'chromomycin 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 H21 H 4.07 0.027 1 5 . 1 1GL H22 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 HM41 H 4.76 0.013 1 12 . 1 1GL HM42 H 4.76 0.013 1 13 . 1 1GL HM43 H 4.76 0.013 1 14 . 1 1GL C5 C 72.84 0.144 1 15 . 1 1GL H5 H 7.31 0.028 1 16 . 1 1GL C6 C 21.50 0.107 1 17 . 1 1GL H61 H 3.21 0.022 1 18 . 1 1GL H62 H 3.21 0.022 1 19 . 1 1GL H63 H 3.21 0.022 1 20 . 2 2GL C1 C 112.40 0.181 1 21 . 2 2GL H1 H 18.13 0.041 1 22 . 2 2GL C2 C 44.61 0.134 1 23 . 2 2GL H21 H 10.49 0.030 1 24 . 2 2GL H22 H 10.64 0.042 1 25 . 2 2GL C3 C 76.68 0.185 1 26 . 2 2GL H3 H 9.77 0.033 1 27 . 2 2GL C4 C 76.79 0.073 1 28 . 2 2GL H4 H 9.90 0.018 1 29 . 2 2GL CME C 27.54 0.082 1 30 . 2 2GL HM41 H 6.46 0.017 1 31 . 2 2GL HM42 H 6.46 0.017 1 32 . 2 2GL HM43 H 6.46 0.017 1 33 . 2 2GL C5 C 80.49 0.129 1 34 . 2 2GL H5 H 11.20 0.031 1 35 . 2 2GL C6 C 25.97 0.106 1 36 . 2 2GL H61 H 7.48 0.024 1 37 . 2 2GL H62 H 7.48 0.024 1 38 . 2 2GL H63 H 7.48 0.024 1 39 . 3 DXB H21 H -59.28 0.375 1 40 . 3 DXB H22 H -59.28 0.375 1 41 . 3 DXB H3 H -19.06 0.135 1 42 . 3 DXB H4A H -8.82 0.111 1 43 . 3 DXB H4E H -1.41 0.066 1 44 . 3 DXB H5 H 32.16 0.057 1 45 . 3 DXB CC7 C 36.67 0.331 1 46 . 3 DXB HM71 H 26.93 0.084 1 47 . 3 DXB HM72 H 26.93 0.084 1 48 . 3 DXB HM73 H 26.93 0.084 1 49 . 3 DXB H10 H 15.25 0.074 1 50 . 3 DXB C1S C 118.15 0.227 1 51 . 3 DXB HS1 H -11.45 0.056 1 52 . 3 DXB CME C 51.55 0.111 1 53 . 3 DXB HM11 H -5.60 0.028 1 54 . 3 DXB HM12 H -5.60 0.028 1 55 . 3 DXB HM13 H -5.60 0.028 1 56 . 3 DXB C3S C 74.50 0.098 1 57 . 3 DXB HS3 H -3.21 0.024 1 58 . 3 DXB C4S C 65.69 0.139 1 59 . 3 DXB HS4 H -1.69 0.033 1 60 . 3 DXB C5S C 16.72 0.107 1 61 . 3 DXB HM51 H -3.16 0.021 1 62 . 3 DXB HM52 H -3.16 0.021 1 63 . 3 DXB HM53 H -3.16 0.021 1 64 . 4 1AR C1 C 102.98 0.125 1 65 . 4 1AR H1 H 14.84 0.027 1 66 . 4 1AR C2 C 51.90 0.097 1 67 . 4 1AR H21 H 6.98 0.031 1 68 . 4 1AR H22 H 6.90 0.024 1 69 . 4 1AR CC3 C 28.47 0.086 1 70 . 4 1AR HM31 H 6.03 0.020 1 71 . 4 1AR HM32 H 6.03 0.020 1 72 . 4 1AR HM33 H 6.03 0.020 1 73 . 4 1AR C4 C 87.58 0.124 1 74 . 4 1AR H4 H 9.29 0.025 1 75 . 4 1AR CME C 25.89 0.102 1 76 . 4 1AR HM41 H 4.78 0.009 1 77 . 4 1AR HM42 H 4.78 0.009 1 78 . 4 1AR HM43 H 4.78 0.009 1 79 . 4 1AR C5 C 76.14 0.172 1 80 . 4 1AR H5 H 12.05 0.032 1 81 . 4 1AR C6 C 27.73 0.150 1 82 . 4 1AR H61 H 8.31 0.025 1 83 . 4 1AR H62 H 8.31 0.025 1 84 . 4 1AR H63 H 8.31 0.025 1 85 . 5 DDA H1 H 45.07 0.160 1 86 . 5 DDA C2 C 56.80 0.195 1 87 . 5 DDA H21 H 13.46 0.051 1 88 . 5 DDA H22 H 23.17 0.516 1 89 . 5 DDA C3 C 89.42 0.100 1 90 . 5 DDA H3 H 21.82 0.055 1 91 . 5 DDA C4 C 90.11 0.137 1 92 . 5 DDA H4 H 12.13 0.036 1 93 . 5 DDA HO4 H 14.63 0.045 1 94 . 5 DDA C5 C 88.35 0.100 1 95 . 5 DDA H5 H 22.68 0.058 1 96 . 5 DDA C6 C 29.64 0.114 1 97 . 5 DDA H61 H 9.64 0.024 1 98 . 5 DDA H62 H 9.64 0.024 1 99 . 5 DDA H63 H 9.64 0.024 1 100 . 6 DDA C4 C 84.40 0.150 1 101 . 6 DDA H4 H 5.96 0.048 1 102 . 6 DDA C6 C 14.66 0.189 1 103 . 6 DDA H61 H -3.84 0.034 1 104 . 6 DDA H62 H -3.84 0.034 1 105 . 6 DDA H63 H -3.84 0.034 1 stop_ save_