data_16951

#######################
#  Entry information  #
#######################

save_entry_information
   _Saveframe_category      entry_information

   _Entry_title            
;
The Structure of RNA Internal Loops with Tandem AG Pairs: 5'GAGC/3'CGAG
;
   _BMRB_accession_number   16951
   _BMRB_flat_file_name     bmr16951.str
   _Entry_type              new
   _Submission_date         2010-05-25
   _Accession_date          2010-05-25
   _Entry_origination       author
   _NMR_STAR_version        2.1.1
   _Experimental_method     NMR
   _Details                'Tandem AG pairs with GC closing pairs: r(GACGAGCGUCA)2'

   loop_
      _Author_ordinal
      _Author_family_name
      _Author_given_name
      _Author_middle_initials
      _Author_family_title

      1 Hammond Nicholas B. . 
      2 Kennedy Scott    D. . 
      3 Turner  Douglas  H. . 

   stop_

   loop_
      _Saveframe_category_type
      _Saveframe_category_type_count

      assigned_chemical_shifts 1 

   stop_

   loop_
      _Data_type
      _Data_type_count

      "1H chemical shifts"  107 
      "13C chemical shifts"  50 
      "31P chemical shifts"  10 

   stop_

   loop_
      _Revision_date
      _Revision_keyword
      _Revision_author
      _Revision_detail

      2010-07-09 update   BMRB   'complete entry citation' 
      2010-07-02 original author 'original release'        

   stop_

   loop_
      _Related_BMRB_accession_number
      _Relationship

      16950 GACAAGUGUCA 
      16952 GACUAGAGUCA 
      16953 GGUAGGCCA   

   stop_

save_


#############################
#  Citation for this entry  #
#############################

save_entry_citation
   _Saveframe_category           entry_citation

   _Citation_full                .
   _Citation_title              'RNA internal loops with tandem AG pairs: the structure of the 5'GAGU/3'UGAG loop can be dramatically different from others, including 5'AAGU/3'UGAA.'
   _Citation_status              published
   _Citation_type                journal
   _CAS_abstract_code            .
   _MEDLINE_UI_code              .
   _PubMed_ID                    20481618

   loop_
      _Author_ordinal
      _Author_family_name
      _Author_given_name
      _Author_middle_initials
      _Author_family_title

      1 Hammond Nicholas B. . 
      2 Tolbert Blanton  S. . 
      3 Kierzek Ryszard  .  . 
      4 Turner  Douglas  H. . 
      5 Kennedy Scott    D. . 

   stop_

   _Journal_abbreviation         Biochemistry
   _Journal_name_full            Biochemistry
   _Journal_volume               49
   _Journal_issue                27
   _Journal_CSD                  .
   _Book_chapter_title           .
   _Book_volume                  .
   _Book_series                  .
   _Book_ISBN                    .
   _Conference_state_province    .
   _Conference_abstract_number   .
   _Page_first                   5817
   _Page_last                    5827
   _Year                         2010
   _Details                      .

save_


##################################
#  Molecular system description  #
##################################

save_assembly
   _Saveframe_category         molecular_system

   _Mol_system_name            5'-R(*GP*AP*CP*AP*AP*GP*UP*GP*UP*CP*A)-3'
   _Enzyme_commission_number   .

   loop_
      _Mol_system_component_name
      _Mol_label

      'RNA (5'-R(*GP*AP*CP*GP*AP*GP*CP*GP*UP*CP*A)-3')_1' $RNA_(5'-R(*GP*AP*CP*GP*AP*GP*CP*GP*UP*CP*A)-3') 
      'RNA (5'-R(*GP*AP*CP*GP*AP*GP*CP*GP*UP*CP*A)-3')_2' $RNA_(5'-R(*GP*AP*CP*GP*AP*GP*CP*GP*UP*CP*A)-3') 

   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_RNA_(5'-R(*GP*AP*CP*GP*AP*GP*CP*GP*UP*CP*A)-3')
   _Saveframe_category                          monomeric_polymer

   _Mol_type                                    polymer
   _Mol_polymer_class                           RNA
   _Name_common                                 RNA_(5'-R(*GP*AP*CP*GP*AP*GP*CP*GP*UP*CP*A)-3')
   _Molecular_mass                              3530.203
   _Mol_thiol_state                            'not present'
   _Details                                     .

   	##############################
   	#  Polymer residue sequence  #
   	##############################
   
      _Residue_count                               11
   _Mol_residue_sequence                        GACGAGCGUCA

   loop_
      _Residue_seq_code
      _Residue_label

       1 G   2 A   3 C   4 G   5 A 
       6 G   7 C   8 G   9 U  10 C 
      11 A 

   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

      $RNA_(5'-R(*GP*AP*CP*GP*AP*GP*CP*GP*UP*CP*A)-3') . . . . . . 

   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

      $RNA_(5'-R(*GP*AP*CP*GP*AP*GP*CP*GP*UP*CP*A)-3') 'obtained from a vendor' . . . . . Dharmacon 

   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

      $RNA_(5'-R(*GP*AP*CP*GP*AP*GP*CP*GP*UP*CP*A)-3')  1   mM 'natural abundance' 
      'sodium chloride'                                80   mM 'natural abundance' 
      'sodium phosphate'                               10   mM 'natural abundance' 
       EDTA                                             0.5 mM 'natural abundance' 
       H2O                                             90   %  'natural abundance' 
       D2O                                             10   %  'natural abundance' 

   stop_

save_


save_sample_2
   _Saveframe_category   sample

   _Sample_type          solution
   _Details              .

   loop_
      _Mol_label
      _Concentration_value
      _Concentration_value_units
      _Isotopic_labeling

      $RNA_(5'-R(*GP*AP*CP*GP*AP*GP*CP*GP*UP*CP*A)-3')   1   mM 'natural abundance' 
      'sodium chloride'                                 80   mM 'natural abundance' 
      'sodium phosphate'                                10   mM 'natural abundance' 
       EDTA                                              0.5 mM 'natural abundance' 
       D2O                                             100   %  'natural abundance' 

   stop_

save_


############################
#  Computer software used  #
############################

save_SPARKY
   _Saveframe_category   software

   _Name                 SPARKY
   _Version              3.12

   loop_
      _Vendor
      _Address
      _Electronic_address

      Goddard . . 

   stop_

   loop_
      _Task

      'chemical shift assignment' 
      'data analysis'             

   stop_

   _Details              .

save_


save_VNMR
   _Saveframe_category   software

   _Name                 VNMR
   _Version              6.1C

   loop_
      _Vendor
      _Address
      _Electronic_address

      Varian . . 

   stop_

   loop_
      _Task

      collection 

   stop_

   _Details              .

save_


save_CNS
   _Saveframe_category   software

   _Name                 CNS
   _Version              1.2

   loop_
      _Vendor
      _Address
      _Electronic_address

      'Brunger, Adams, Clore, Gros, Nilges and Read' . . 

   stop_

   loop_
      _Task

      'structure solution' 

   stop_

   _Details              .

save_


save_AMBER
   _Saveframe_category   software

   _Name                 AMBER
   _Version              9

   loop_
      _Vendor
      _Address
      _Electronic_address

      'Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm' . . 

   stop_

   loop_
      _Task

      refinement 

   stop_

   _Details              .

save_


#########################
#  Experimental detail  #
#########################

    ##################################
    #  NMR Spectrometer definitions  #
    ##################################

save_spectrometer_1
   _Saveframe_category   NMR_spectrometer

   _Manufacturer         Varian
   _Model                INOVA
   _Field_strength       600
   _Details              .

save_


save_spectrometer_2
   _Saveframe_category   NMR_spectrometer

   _Manufacturer         Varian
   _Model                INOVA
   _Field_strength       500
   _Details              .

save_


    #############################
    #  NMR applied experiments  #
    #############################

save_2D_1H-1H_NOESY_1
   _Saveframe_category   NMR_applied_experiment

   _Experiment_name     '2D 1H-1H NOESY'
   _Sample_label        $sample_1

save_


save_2D_1H-13C_HSQC_2
   _Saveframe_category   NMR_applied_experiment

   _Experiment_name     '2D 1H-13C HSQC'
   _Sample_label        $sample_1

save_


save_2D_1H-1H_TOCSY_3
   _Saveframe_category   NMR_applied_experiment

   _Experiment_name     '2D 1H-1H TOCSY'
   _Sample_label        $sample_2

save_


save_2D_DQF-COSY_4
   _Saveframe_category   NMR_applied_experiment

   _Experiment_name     '2D DQF-COSY'
   _Sample_label        $sample_2

save_


save_2D_1H-31P_HETCOR_5
   _Saveframe_category   NMR_applied_experiment

   _Experiment_name     '2D 1H-31P HETCOR'
   _Sample_label        $sample_2

save_


save_2D_1H-1H_NOESY_6
   _Saveframe_category   NMR_applied_experiment

   _Experiment_name     '2D 1H-1H NOESY'
   _Sample_label        $sample_2

save_


#######################
#  Sample conditions  #
#######################

save_sample_conditions_1
   _Saveframe_category   sample_conditions

   _Details              .

   loop_
      _Variable_type
      _Variable_value
      _Variable_value_error
      _Variable_value_units

       temperature     273   . K   
       pH                6.1 . pH  
       pressure          1   . atm 
      'ionic strength'   0.1 . M   

   stop_

save_


save_sample_conditions_2
   _Saveframe_category   sample_conditions

   _Details              .

   loop_
      _Variable_type
      _Variable_value
      _Variable_value_error
      _Variable_value_units

       temperature     288   . K   
       pH                6.1 . pH  
       pressure          1   . atm 
      'ionic strength'   0.1 . M   

   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 
      DSS P 31 'methyl protons' ppm 0.00 na       indirect . . . 0.404808636 
      DSS C 13 'methyl protons' ppm 0.00 na       indirect . . . 0.251449530 

   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
   _Saveframe_category               assigned_chemical_shifts

   _Details                          .

   loop_
      _Software_label

      $SPARKY 

   stop_

   loop_
      _Experiment_label

      '2D 1H-1H NOESY'   
      '2D 1H-13C HSQC'   
      '2D 1H-1H TOCSY'   
      '2D DQF-COSY'      
      '2D 1H-31P HETCOR' 

   stop_

   loop_
      _Sample_label

      $sample_1 
      $sample_2 

   stop_

   _Sample_conditions_label         $sample_conditions_2
   _Chem_shift_reference_set_label  $chemical_shift_reference_1
   _Mol_system_component_name       'RNA (5'-R(*GP*AP*CP*GP*AP*GP*CP*GP*UP*CP*A)-3')_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 G H1   H  12.006 0.002 1 
        2  1  1 G H1'  H   5.845 0.001  . 
        3  1  1 G H2'  H   4.818 0.000  . 
        4  1  1 G H3'  H   4.647 0.001  . 
        5  1  1 G H4'  H   4.445 0.001  . 
        6  1  1 G H5'  H   4.112 0.002  . 
        7  1  1 G H5'' H   3.974 0.001 2 
        8  1  1 G H8   H   8.115 0.001 1 
        9  1  1 G H21  H   7.745 0.000 2 
       10  1  1 G H22  H   6.160 0.002 2 
       11  1  1 G C1'  C  93.112 0.000  . 
       12  1  1 G C2'  C  75.152 0.000  . 
       13  1  1 G C3'  C  74.017 0.000  . 
       14  1  1 G C4'  C  84.751 0.000  . 
       15  1  1 G C8   C 138.786 0.000 1 
       16  2  2 A H1'  H   6.004 0.001  . 
       17  2  2 A H2   H   7.699 0.001 1 
       18  2  2 A H2'  H   4.628 0.001  . 
       19  2  2 A H3'  H   4.725 0.001  . 
       20  2  2 A H4'  H   4.538 0.002  . 
       21  2  2 A H5'  H   4.651 0.001  . 
       22  2  2 A H5'' H   4.212 0.001 2 
       23  2  2 A H8   H   8.066 0.000 1 
       24  2  2 A H61  H   7.898 0.000 2 
       25  2  2 A H62  H   6.494 0.000 2 
       26  2  2 A HO2' H   6.918 0.000  . 
       27  2  2 A C1'  C  92.814 0.000  . 
       28  2  2 A C2   C 154.042 0.000 1 
       29  2  2 A C2'  C  75.554 0.000  . 
       30  2  2 A C3'  C  72.527 0.000  . 
       31  2  2 A C4'  C  82.244 0.000  . 
       32  2  2 A C8   C 139.685 0.000 1 
       33  2  2 A P    P  -4.012 0.000 1 
       34  3  3 C H1'  H   5.306 0.001  . 
       35  3  3 C H2'  H   4.215 0.000  . 
       36  3  3 C H3'  H   4.395 0.004  . 
       37  3  3 C H4'  H   4.371 0.002  . 
       38  3  3 C H5   H   5.243 0.001 1 
       39  3  3 C H5'  H   4.492 0.002  . 
       40  3  3 C H5'' H   4.075 0.004 2 
       41  3  3 C H6   H   7.388 0.001 1 
       42  3  3 C H41  H   8.150 0.000 2 
       43  3  3 C H42  H   6.892 0.001 2 
       44  3  3 C C2'  C  75.511 0.000  . 
       45  3  3 C C3'  C  72.292 0.000  . 
       46  3  3 C C4'  C  81.821 0.000  . 
       47  3  3 C C5   C  97.700 0.000 1 
       48  3  3 C C6   C 139.843 0.000 1 
       49  3  3 C P    P  -3.925 0.000 1 
       50  4  4 G H1   H  12.444 0.003 1 
       51  4  4 G H1'  H   5.584 0.001  . 
       52  4  4 G H2'  H   3.973 0.001  . 
       53  4  4 G H3'  H   4.808 0.002  . 
       54  4  4 G H4'  H   4.354 0.000  . 
       55  4  4 G H5'  H   4.573 0.000  . 
       56  4  4 G H5'' H   4.099 0.000 2 
       57  4  4 G H8   H   7.570 0.001 1 
       58  4  4 G H21  H   7.301 0.004 2 
       59  4  4 G H22  H   5.444 0.001 2 
       60  4  4 G C1'  C  92.658 0.000  . 
       61  4  4 G C2'  C  75.726 0.000  . 
       62  4  4 G C3'  C  72.617 0.000  . 
       63  4  4 G C4'  C  81.893 0.000  . 
       64  4  4 G C8   C 136.651 0.000 1 
       65  4  4 G P    P  -4.021 0.000 1 
       66  5  5 A H1'  H   6.119 0.001  . 
       67  5  5 A H2   H   7.763 0.001 1 
       68  5  5 A H2'  H   4.812 0.000  . 
       69  5  5 A H3'  H   4.813 0.001  . 
       70  5  5 A H4'  H   4.489 0.002  . 
       71  5  5 A H5'  H   4.572 0.000  . 
       72  5  5 A H5'' H   4.172 0.000 2 
       73  5  5 A H8   H   8.226 0.001 1 
       74  5  5 A H61  H   7.668 0.000 2 
       75  5  5 A H62  H   7.668 0.000 2 
       76  5  5 A C1'  C  91.071 0.000  . 
       77  5  5 A C2   C 153.981 0.000 1 
       78  5  5 A C2'  C  76.229 0.000  . 
       79  5  5 A C8   C 140.094 0.000 1 
       80  5  5 A P    P  -4.301 0.000 1 
       81  6  6 G H1   H  12.831 0.002 1 
       82  6  6 G H1'  H   5.559 0.001  . 
       83  6  6 G H2'  H   4.573 0.000  . 
       84  6  6 G H3'  H   4.102 0.006  . 
       85  6  6 G H4'  H   4.529 0.000  . 
       86  6  6 G H5'  H   4.276 0.001  . 
       87  6  6 G H5'' H   4.116 0.000 2 
       88  6  6 G H8   H   7.104 0.001 1 
       89  6  6 G H21  H   5.753 0.003 2 
       90  6  6 G H22  H   5.753 0.003 2 
       91  6  6 G C2'  C  75.367 0.000  . 
       92  6  6 G P    P  -3.530 0.001 1 
       93  7  7 C H1'  H   5.563 0.001  . 
       94  7  7 C H2'  H   4.463 0.000  . 
       95  7  7 C H3'  H   4.507 0.002  . 
       96  7  7 C H4'  H   4.425 0.000  . 
       97  7  7 C H5   H   5.170 0.001 1 
       98  7  7 C H6   H   7.451 0.001 1 
       99  7  7 C H41  H   8.397 0.000 2 
      100  7  7 C H42  H   6.828 0.002 2 
      101  7  7 C C2'  C  75.090 0.000  . 
      102  7  7 C C3'  C  71.892 0.000  . 
      103  7  7 C C4'  C  81.903 0.000  . 
      104  7  7 C C5   C  98.039 0.000 1 
      105  7  7 C C6   C 140.142 0.000 1 
      106  7  7 C P    P  -4.403 0.000 1 
      107  8  8 G H1   H  13.173 0.001 1 
      108  8  8 G H1'  H   5.604 0.001  . 
      109  8  8 G H2'  H   4.363 0.001  . 
      110  8  8 G H3'  H   4.589 0.001  . 
      111  8  8 G H4'  H   4.421 0.003  . 
      112  8  8 G H5'  H   4.516 0.002  . 
      113  8  8 G H5'' H   4.067 0.004 2 
      114  8  8 G H8   H   7.549 0.000 1 
      115  8  8 G H21  H   8.147 0.006 2 
      116  8  8 G H22  H   5.854 0.001 2 
      117  8  8 G C2'  C  75.464 0.000  . 
      118  8  8 G C3'  C  72.364 0.000  . 
      119  8  8 G C4'  C  82.163 0.000  . 
      120  8  8 G C8   C 135.933 0.000 1 
      121  8  8 G P    P  -3.965 0.000 1 
      122  9  9 U H1'  H   5.452 0.001  . 
      123  9  9 U H2'  H   4.395 0.000  . 
      124  9  9 U H3   H  14.348 0.002 1 
      125  9  9 U H3'  H   4.440 0.002  . 
      126  9  9 U H4'  H   4.380 0.000  . 
      127  9  9 U H5   H   5.046 0.001 1 
      128  9  9 U H5'  H   4.536 0.001  . 
      129  9  9 U H5'' H   4.049 0.000 2 
      130  9  9 U H6   H   7.726 0.001 1 
      131  9  9 U C1'  C  93.542 0.000  . 
      132  9  9 U C2'  C  75.383 0.000  . 
      133  9  9 U C3'  C  72.227 0.000  . 
      134  9  9 U C4'  C  81.602 0.000  . 
      135  9  9 U C5   C 102.613 0.000 1 
      136  9  9 U C6   C 141.404 0.000 1 
      137  9  9 U P    P  -4.510 0.000 1 
      138 10 10 C H1'  H   5.543 0.001  . 
      139 10 10 C H2'  H   4.381 0.000  . 
      140 10 10 C H3'  H   4.442 0.002  . 
      141 10 10 C H4'  H   4.381 0.000  . 
      142 10 10 C H5   H   5.521 0.001 1 
      143 10 10 C H5'  H   4.498 0.000  . 
      144 10 10 C H5'' H   4.075 0.000 2 
      145 10 10 C H6   H   7.737 0.002 1 
      146 10 10 C H41  H   8.201 0.001 2 
      147 10 10 C H42  H   7.000 0.002 2 
      148 10 10 C C2'  C  75.240 0.000  . 
      149 10 10 C C5   C  97.729 0.000 1 
      150 10 10 C C6   C 140.942 0.000 1 
      151 10 10 C P    P  -4.074 0.000 1 
      152 11 11 A H1'  H   5.924 0.001  . 
      153 11 11 A H2   H   7.324 0.001 1 
      154 11 11 A H2'  H   4.022 0.001  . 
      155 11 11 A H3'  H   4.284 0.002  . 
      156 11 11 A H4'  H   4.223 0.002  . 
      157 11 11 A H5'  H   4.445 0.000  . 
      158 11 11 A H5'' H   4.046 0.001 2 
      159 11 11 A H8   H   8.037 0.000 1 
      160 11 11 A H61  H   6.526 0.003 2 
      161 11 11 A C1'  C  91.720 0.000  . 
      162 11 11 A C2   C 154.336 0.000 1 
      163 11 11 A C2'  C  77.965 0.000  . 
      164 11 11 A C3'  C  70.301 0.000  . 
      165 11 11 A C4'  C  83.921 0.000  . 
      166 11 11 A C8   C 140.130 0.000 1 
      167 11 11 A P    P  -3.801 0.000 1 

   stop_

save_