data_4612
#######################
# Entry information #
#######################
save_entry_information
_Saveframe_category entry_information
_Entry_title
;
NMR observation of a novel C-tetrad in a DNA quadruplex
;
_BMRB_accession_number 4612
_BMRB_flat_file_name bmr4612.str
_Entry_type new
_Submission_date 2000-06-01
_Accession_date 2000-09-07
_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 Patel P. K. .
2 Bhavesh N. S. .
3 Hosur R. V. .
stop_
loop_
_Saveframe_category_type
_Saveframe_category_type_count
assigned_chemical_shifts 1
stop_
loop_
_Data_type
_Data_type_count
"1H chemical shifts" 62
stop_
loop_
_Revision_date
_Revision_keyword
_Revision_author
_Revision_detail
2010-07-16 update BMRB 'update DNA residue label to two-letter code'
2000-12-19 original author 'original release'
stop_
save_
#############################
# Citation for this entry #
#############################
save_entry_citation
_Saveframe_category entry_citation
_Citation_full .
_Citation_title
;
NMR Observation of a Novel C-Tetrad in the Structure of the SV40 Repeat Sequence
GGGCGG
;
_Citation_status published
_Citation_type journal
_CAS_abstract_code .
_MEDLINE_UI_code 20237111
_PubMed_ID ?
loop_
_Author_ordinal
_Author_family_name
_Author_given_name
_Author_middle_initials
_Author_family_title
1 Patel P. K. .
2 Bhavesh N. S. .
3 Hosur R. V. .
stop_
_Journal_abbreviation 'Biochem. Biophys. Res. Commun.'
_Journal_name_full 'Biochemical and Biophysical Research Communications'
_Journal_volume 270
_Journal_issue .
_Journal_CSD .
_Book_chapter_title .
_Book_volume .
_Book_series .
_Book_ISBN .
_Conference_state_province .
_Conference_abstract_number .
_Page_first 967
_Page_last 971
_Year 2000
_Details .
loop_
_Keyword
'NMR structure'
G-quadruplex
C-tetrad
'GGGCGG repeat'
SV40
stop_
save_
##################################
# Molecular system description #
##################################
save_system_TGGGCGGT
_Saveframe_category molecular_system
_Mol_system_name 5'-D(*TP*GP*GP*GP*CP*GP*GP*T)-3'
_Enzyme_commission_number .
loop_
_Mol_system_component_name
_Mol_label
'5'-D(*TP*GP*GP*GP*CP*GP*GP*T)-3', strand 1a' $TGGGCGGT
'5'-D(*TP*GP*GP*GP*CP*GP*GP*T)-3', strand 1b' $TGGGCGGT
'5'-D(*TP*GP*GP*GP*CP*GP*GP*T)-3', strand 2a' $TGGGCGGT
'5'-D(*TP*GP*GP*GP*CP*GP*GP*T)-3', strand 2b' $TGGGCGGT
stop_
_System_molecular_weight .
_System_physical_state native
_System_oligomer_state tetramer
_System_paramagnetic no
_System_thiol_state 'not present'
loop_
_Magnetic_equivalence_ID
_Magnetically_equivalent_system_component
1 '5'-D(*TP*GP*GP*GP*CP*GP*GP*T)-3', strand 1a'
1 '5'-D(*TP*GP*GP*GP*CP*GP*GP*T)-3', strand 1b'
1 '5'-D(*TP*GP*GP*GP*CP*GP*GP*T)-3', strand 2a'
1 '5'-D(*TP*GP*GP*GP*CP*GP*GP*T)-3', strand 2b'
stop_
_Database_query_date .
_Details .
save_
########################
# Monomeric polymers #
########################
save_TGGGCGGT
_Saveframe_category monomeric_polymer
_Mol_type polymer
_Mol_polymer_class DNA
_Name_common TGGGCGGT
_Molecular_mass .
_Mol_thiol_state 'not present'
_Details .
##############################
# Polymer residue sequence #
##############################
_Residue_count 8
_Mol_residue_sequence TGGGCGGT
loop_
_Residue_seq_code
_Residue_author_seq_code
_Residue_label
1 101 DT 2 102 DG 3 103 DG 4 104 DG 5 105 DC
6 106 DG 7 107 DG 8 108 DT
stop_
_Sequence_homology_query_date .
_Sequence_homology_query_revised_last_date .
save_
####################
# Natural source #
####################
save_natural_source
_Saveframe_category natural_source
loop_
_Mol_label
_Organism_name_common
_NCBI_taxonomy_ID
_Superkingdom
_Kingdom
_Genus
_Species
$TGGGCGGT 'SV 40 virus' 10633 virus . . .
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
_Details
$TGGGCGGT 'chemical synthesis' . . . . .
;
"The oligonucleotide was synthesized on an applied
Bio-systems 392 automated DNA-synthesizer on 10 uM
scale using solid phase (-cyanoethyl phosphoramidite
chemistry, cleaved from support and purified by
standard procedures
;
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
$TGGGCGGT . mM .
'sodium phosphate' 10 mM .
EDTA 0.2 mM .
NaCl 200 mM .
H2O 90 % .
D2O 10 % .
stop_
save_
save_sample_2
_Saveframe_category sample
_Sample_type solution
_Details .
loop_
_Mol_label
_Concentration_value
_Concentration_value_units
_Concentration_min_value
_Concentration_max_value
_Isotopic_labeling
$TGGGCGGT . mM 1 2 .
'sodium phosphate' 10 mM . . .
EDTA 0.2 mM . . .
NaCl 200 mM . . .
D2O 100 % . . .
stop_
save_
############################
# Computer software used #
############################
save_VNMR
_Saveframe_category software
_Name VNMR
_Version 6.1
loop_
_Task
'data collection'
'data processing'
stop_
_Details Varian
save_
save_FELIX
_Saveframe_category software
_Name FELIX
_Version '230 and 97'
loop_
_Task
'data processing'
stop_
_Details BIOSYM
save_
save_DISCOVER
_Saveframe_category software
_Name DISCOVER
_Version 3.1
loop_
_Task
'structure solution'
stop_
_Details BIOSYM
save_
save_IRMA
_Saveframe_category software
_Name IRMA
_Version 2.3
loop_
_Task
refinement
stop_
_Details BIOSYM
save_
#########################
# Experimental detail #
#########################
##################################
# NMR Spectrometer definitions #
##################################
save_NMR_spectrometer
_Saveframe_category NMR_spectrometer
_Manufacturer Varian
_Model UNITYplus
_Field_strength 600
_Details .
save_
#############################
# NMR applied experiments #
#############################
save_2D_NOESY_1
_Saveframe_category NMR_applied_experiment
_Experiment_name '2D NOESY'
_Sample_label .
save_
save_2D_TOCSY_2
_Saveframe_category NMR_applied_experiment
_Experiment_name '2D TOCSY'
_Sample_label .
save_
save_DQF-COSY_3
_Saveframe_category NMR_applied_experiment
_Experiment_name DQF-COSY
_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 '2D TOCSY'
_BMRB_pulse_sequence_accession_number .
_Details .
save_
save_NMR_spec_expt__0_3
_Saveframe_category NMR_applied_experiment
_Experiment_name DQF-COSY
_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 7.0 . n/a
temperature . . n/a
pressure 1 . atm
stop_
save_
####################
# NMR parameters #
####################
##############################
# Assigned chemical shifts #
##############################
################################
# Chemical shift referencing #
################################
save_chemical_shift_ref_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
. H 1 . ppm . . . . . .
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 '5'-D(*TP*GP*GP*GP*CP*GP*GP*T)-3', strand 1a'
_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 7.380 . 1
2 . 1 DT H1' H 5.950 . 1
3 . 1 DT H2' H 2.340 . 1
4 . 1 DT H2'' H 2.090 . 1
5 . 1 DT H3' H 4.730 . 1
6 . 1 DT H4' H 4.108 . 1
7 . 1 DT H5' H 3.730 . 2
8 . 1 DT H71 H 1.420 . 1
9 . 1 DT H72 H 1.420 . 1
10 . 1 DT H73 H 1.420 . 1
11 . 2 DG H8 H 8.060 . 1
12 . 2 DG H1' H 6.176 . 1
13 . 2 DG H2'' H 2.752 . 1
14 . 2 DG H2' H 3.020 . 1
15 . 2 DG H3' H 5.050 . 1
16 . 2 DG H4' H 4.492 . 1
17 . 2 DG H5' H 4.150 . 2
18 . 3 DG H8 H 7.620 . 1
19 . 3 DG H1' H 6.160 . 1
20 . 3 DG H2' H 2.850 . 1
21 . 3 DG H2'' H 2.440 . 1
22 . 3 DG H3' H 5.000 . 1
23 . 3 DG H4' H 4.590 . 1
24 . 3 DG H5'' H 4.382 . 1
25 . 3 DG H5' H 4.242 . 1
26 . 4 DG H8 H 7.410 . 1
27 . 4 DG H1' H 6.173 . 1
28 . 4 DG H2' H 2.930 . 1
29 . 4 DG H2'' H 2.490 . 1
30 . 4 DG H3' H 5.045 . 1
31 . 4 DG H4' H 4.586 . 1
32 . 4 DG H5' H 4.370 . 2
33 . 5 DC H6 H 7.240 . 1
34 . 5 DC H5 H 5.320 . 1
35 . 5 DC H1' H 5.748 . 1
36 . 5 DC H2' H 2.270 . 2
37 . 5 DC H3' H 4.963 . 1
38 . 5 DC H4' H 4.165 . 1
39 . 5 DC H5' H 4.655 . 2
40 . 6 DG H8 H 8.020 . 1
41 . 6 DG H1' H 6.010 . 1
42 . 6 DG H2'' H 2.700 . 1
43 . 6 DG H2' H 2.830 . 1
44 . 6 DG H3' H 5.123 . 1
45 . 6 DG H4' H 4.565 . 1
46 . 6 DG H5' H 4.234 . 2
47 . 7 DG H8 H 7.680 . 1
48 . 7 DG H1' H 6.230 . 1
49 . 7 DG H2' H 2.660 . 1
50 . 7 DG H2'' H 2.530 . 1
51 . 7 DG H3' H 5.020 . 1
52 . 7 DG H4' H 4.522 . 1
53 . 7 DG H5' H 4.280 . 2
54 . 8 DT H6 H 7.296 . 1
55 . 8 DT H1' H 6.100 . 1
56 . 8 DT H2' H 2.120 . 2
57 . 8 DT H3' H 4.520 . 1
58 . 8 DT H4' H 4.070 . 1
59 . 8 DT H5' H 4.300 . 2
60 . 8 DT H71 H 1.630 . 1
61 . 8 DT H72 H 1.630 . 1
62 . 8 DT H73 H 1.630 . 1
stop_
save_