data_16290
#######################
# Entry information #
#######################
save_entry_information
_Saveframe_category entry_information
_Entry_title
;
d(GCTATAGC)2 1:1 complex with dqdppn assignments
;
_BMRB_accession_number 16290
_BMRB_flat_file_name bmr16290.str
_Entry_type original
_Submission_date 2009-05-07
_Accession_date 2009-05-07
_Entry_origination author
_NMR_STAR_version 2.1.1
_Experimental_method NMR
_Details '1H assignments for 1:1 complex of d(GCTATAGC)2 with dqdppn'
loop_
_Author_ordinal
_Author_family_name
_Author_given_name
_Author_middle_initials
_Author_family_title
1 Waywell Phil . .
2 Thomas James A. .
stop_
loop_
_Saveframe_category_type
_Saveframe_category_type_count
assigned_chemical_shifts 2
stop_
loop_
_Data_type
_Data_type_count
"1H chemical shifts" 50
stop_
loop_
_Revision_date
_Revision_keyword
_Revision_author
_Revision_detail
2010-07-16 update BMRB 'update DNA residue label to two-letter code'
2010-01-28 original author 'original release'
stop_
loop_
_Related_BMRB_accession_number
_Relationship
16289 'free oligo'
stop_
save_
#############################
# Citation for this entry #
#############################
save_entry_citation
_Saveframe_category entry_citation
_Citation_full .
_Citation_title 'Structural analysis of the binding of the diquaternary pyridophenazine derivative dqdppn to B-DNA oligonucleotides.'
_Citation_status published
_Citation_type journal
_CAS_abstract_code .
_MEDLINE_UI_code .
_PubMed_ID 20090983
loop_
_Author_ordinal
_Author_family_name
_Author_given_name
_Author_middle_initials
_Author_family_title
1 Waywell Philip . .
2 Thomas James A. .
3 Williamson Mike P. .
stop_
_Journal_abbreviation 'Org. Biomol. Chem.'
_Journal_name_full 'Organic & biomolecular chemistry'
_Journal_volume 8
_Journal_issue 3
_Journal_CSD .
_Book_chapter_title .
_Book_volume .
_Book_series .
_Book_ISBN .
_Conference_state_province .
_Conference_abstract_number .
_Page_first 648
_Page_last 654
_Year 2010
_Details .
loop_
_Keyword
intercalation
'major groove'
'induced CD'
'chemical shift'
stop_
save_
##################################
# Molecular system description #
##################################
save_assembly
_Saveframe_category molecular_system
_Mol_system_name '1:1 complex'
_Enzyme_commission_number .
loop_
_Mol_system_component_name
_Mol_label
d(GCTATAGC),1 $d(GCTATAGC)2
d(GCTATAGC),2 $d(GCTATAGC)2
dqdppn $DQDPPN
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_d(GCTATAGC)2
_Saveframe_category monomeric_polymer
_Mol_type polymer
_Mol_polymer_class DNA
_Name_common d(GCTATAGC)2
_Molecular_mass .
_Mol_thiol_state 'not present'
_Details .
##############################
# Polymer residue sequence #
##############################
_Residue_count 8
_Mol_residue_sequence GCTATAGC
loop_
_Residue_seq_code
_Residue_author_seq_code
_Residue_label
1 1 DG 2 2 DC 3 3 DT 4 4 DA 5 5 DT
6 6 DA 7 7 DG 8 8 DC
stop_
_Sequence_homology_query_date .
_Sequence_homology_query_revised_last_date .
save_
#############
# Ligands #
#############
save_DQDPPN
_Saveframe_category ligand
_Mol_type non-polymer
_Name_common DQDPPN
_Molecular_mass .
_Details .
_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
$d(GCTATAGC)2 . . . . . .
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
$d(GCTATAGC)2 'chemical synthesis' . . . . .
stop_
save_
#####################################
# Sample contents and methodology #
#####################################
########################
# Sample description #
########################
save_sample_1
_Saveframe_category sample
_Sample_type solution
_Details '1:1 complex'
loop_
_Mol_label
_Concentration_value
_Concentration_value_units
_Isotopic_labeling
$d(GCTATAGC)2 2 mM 'natural abundance'
$dqdppn 2 mM 'natural abundance'
D2O 100 % 'natural abundance'
stop_
save_
############################
# Computer software used #
############################
save_Felix
_Saveframe_category software
_Name Felix
_Version .
loop_
_Vendor
_Address
_Electronic_address
'Accelrys Software Inc.' . .
stop_
loop_
_Task
'chemical shift assignment'
processing
stop_
_Details .
save_
#########################
# Experimental detail #
#########################
##################################
# NMR Spectrometer definitions #
##################################
save_spectrometer_1
_Saveframe_category NMR_spectrometer
_Manufacturer Bruker
_Model Avance
_Field_strength 500
_Details .
save_
save_spectrometer_2
_Saveframe_category NMR_spectrometer
_Manufacturer Bruker
_Model Avance
_Field_strength 800
_Details .
save_
#############################
# NMR applied experiments #
#############################
save_2D_DQF-COSY_1
_Saveframe_category NMR_applied_experiment
_Experiment_name '2D DQF-COSY'
_Sample_label $sample_1
save_
save_2D_1H-1H_TOCSY_2
_Saveframe_category NMR_applied_experiment
_Experiment_name '2D 1H-1H TOCSY'
_Sample_label $sample_1
save_
save_2D_1H-1H_NOESY_3
_Saveframe_category NMR_applied_experiment
_Experiment_name '2D 1H-1H NOESY'
_Sample_label $sample_1
save_
save_2D_31P-1H_COSY_4
_Saveframe_category NMR_applied_experiment
_Experiment_name '2D 31P-1H COSY'
_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 313 . K
pH 7 . pH
pressure 1 . atm
stop_
save_
####################
# NMR parameters #
####################
##############################
# Assigned chemical shifts #
##############################
################################
# Chemical shift referencing #
################################
save_chemical_shift_reference_1
_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
_Indirect_shift_ratio
DSS H 1 'methyl protons' ppm 0.00 internal direct . . . 1.000000000
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_assigned_chem_shift_list_1_1
_Saveframe_category assigned_chemical_shifts
_Details .
loop_
_Experiment_label
'2D DQF-COSY'
'2D 1H-1H TOCSY'
'2D 1H-1H NOESY'
'2D 31P-1H COSY'
stop_
loop_
_Sample_label
$sample_1
stop_
_Sample_conditions_label $sample_conditions_1
_Chem_shift_reference_set_label $chemical_shift_reference_1
_Mol_system_component_name d(GCTATAGC),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 1 DG H1' H 5.95 0.02 1
2 1 1 DG H2' H 2.64 0.02 2
3 1 1 DG H2'' H 2.75 0.02 2
4 1 1 DG H3' H 4.87 0.02 1
5 1 1 DG H8 H 7.92 0.02 1
6 2 2 DC H1' H 6.03 0.02 1
7 2 2 DC H2' H 2.15 0.02 2
8 2 2 DC H2'' H 2.54 0.02 2
9 2 2 DC H3' H 4.85 0.02 1
10 2 2 DC H6 H 7.47 0.02 1
11 3 3 DT H2' H 2.30 0.02 2
12 3 3 DT H2'' H 2.51 0.02 2
13 3 3 DT H3' H 4.85 0.02 1
14 3 3 DT H6 H 7.45 0.02 1
15 3 3 DT H71 H 1.57 0.02 1
16 3 3 DT H72 H 1.57 0.02 1
17 3 3 DT H73 H 1.57 0.02 1
18 4 4 DA H2' H 2.68 0.02 2
19 4 4 DA H2'' H 2.86 0.02 2
20 4 4 DA H3' H 5.03 0.02 1
21 4 4 DA H8 H 8.34 0.02 1
22 5 5 DT H1' H 5.36 0.02 1
23 5 5 DT H2'' H 2.07 0.02 2
24 5 5 DT H6 H 7.15 0.02 1
25 5 5 DT H71 H 1.34 0.02 1
26 5 5 DT H72 H 1.34 0.02 1
27 5 5 DT H73 H 1.34 0.02 1
28 6 6 DA H1' H 5.89 0.02 1
29 6 6 DA H2' H 2.73 0.02 2
30 6 6 DA H2'' H 2.81 0.02 2
31 6 6 DA H3' H 5.04 0.02 1
32 6 6 DA H8 H 8.19 0.02 1
33 7 7 DG H1' H 5.73 0.02 1
34 7 7 DG H2' H 2.48 0.02 1
35 7 7 DG H2'' H 2.63 0.02 1
36 7 7 DG H3' H 4.97 0.02 1
37 7 7 DG H8 H 7.64 0.02 1
38 8 8 DC H1' H 6.08 0.02 1
39 8 8 DC H2' H 2.15 0.02 2
40 8 8 DC H2'' H 2.23 0.02 2
41 8 8 DC H3' H 4.52 0.02 1
42 8 8 DC H6 H 7.35 0.02 1
stop_
save_
save_assigned_chem_shift_list_1_2
_Saveframe_category assigned_chemical_shifts
_Details .
loop_
_Experiment_label
'2D DQF-COSY'
'2D 1H-1H TOCSY'
'2D 1H-1H NOESY'
'2D 31P-1H COSY'
stop_
loop_
_Sample_label
$sample_1
stop_
_Sample_conditions_label $sample_conditions_1
_Chem_shift_reference_set_label $chemical_shift_reference_1
_Mol_system_component_name d(GCTATAGC),2
_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 DQDPPN H1 H 9.62 0.02 1
2 . 1 DQDPPN H2 H 8.60 0.02 1
3 . 1 DQDPPN H3 H 9.86 0.02 1
4 . 1 DQDPPN H4 H 7.99 0.02 1
5 . 1 DQDPPN H5 H 7.87 0.02 1
6 . 1 DQDPPN H6 H 7.61 0.02 1
7 . 1 DQDPPN CH21 H 5.73 0.02 2
8 . 1 DQDPPN CH22 H 5.79 0.02 2
stop_
save_