data_4556

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

save_entry_information
   _Saveframe_category      entry_information

   _Entry_title            
;
31P NMR analysis of the DNA conformation induced by protein binding:SRY-DNA 
complexes
;
   _BMRB_accession_number   4556
   _BMRB_flat_file_name     bmr4556.str
   _Entry_type              original
   _Submission_date         1999-12-11
   _Accession_date          1999-12-13
   _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 Castagne   Claire    .  . 
      2 Murphy     Elizabeth C. . 
      3 Gronenborn Angela    M. . 
      4 Delepierre Muriel    .  . 

   stop_

   loop_
      _Saveframe_category_type
      _Saveframe_category_type_count

      assigned_chemical_shifts 2 

   stop_

   loop_
      _Data_type
      _Data_type_count

      "1H chemical shifts"  137 
      "31P chemical shifts"  14 

   stop_

   loop_
      _Revision_date
      _Revision_keyword
      _Revision_author
      _Revision_detail

      2010-07-16 update   BMRB   'update DNA residue label to two-letter code' 
      2000-01-11 original author 'original release'                            

   stop_

save_


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

save_entry_citation
   _Saveframe_category           entry_citation

   _Citation_full                .
   _Citation_title              
;
31P NMR analysis of the DNA conformation induced by protein binding:SRY-DNA 
complexes
;
   _Citation_status              submitted
   _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 Castagne   Claire    .  . 
      2 Murphy     Elizabeth C. . 
      3 Gronenborn Angela    M. . 
      4 Delepierre Muriel    .  . 

   stop_

   _Journal_abbreviation        'Eur. J. Biochem.'
   _Journal_name_full           'European Journal of Biochemistry'
   _Journal_volume               .
   _Journal_issue                .
   _Journal_CSD                  .
   _Book_chapter_title           .
   _Book_volume                  .
   _Book_series                  .
   _Book_ISBN                    .
   _Conference_state_province    .
   _Conference_abstract_number   .
   _Page_first                   .
   _Page_last                    .
   _Year                         .
   _Details                      .

   loop_
      _Keyword

      '31P NMR on protein:DNA complexes' 

   stop_

save_


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

save_SRY-8mer_duplex
   _Saveframe_category         molecular_system

   _Mol_system_name           'SRY-8mer duplex'
   _Abbreviation_common       '8mer duplex'
   _Enzyme_commission_number   .

   loop_
      _Mol_system_component_name
      _Mol_label

      '8mer strand 1' $SRY_8-mer_strand_1 
      '8mer strand 2' $SRY_8-mer_strand_2 

   stop_

   _System_molecular_weight    .
   _System_physical_state      native
   _System_oligomer_state      duplex
   _System_paramagnetic        no
   _System_thiol_state        'not present'
   _Database_query_date        .
   _Details                    .

save_


    ########################
    #  Monomeric polymers  #
    ########################

save_SRY_8-mer_strand_1
   _Saveframe_category                          monomeric_polymer

   _Mol_type                                    polymer
   _Mol_polymer_class                           DNA
   _Name_common                                'SRY 8mer strand 1'
   _Abbreviation_common                        'SRY 8-mer strand 1'
   _Molecular_mass                              .
   _Mol_thiol_state                            'not present'
   _Details                                     .

   	##############################
   	#  Polymer residue sequence  #
   	##############################
   
      _Residue_count                               8
   _Mol_residue_sequence                        GCACAAAC

   loop_
      _Residue_seq_code
      _Residue_author_seq_code
      _Residue_label

      1 1 DG  2 2 DC  3 3 DA  4 4 DC  5 5 DA 
      6 6 DA  7 7 DA  8 8 DC 

   stop_

   _Sequence_homology_query_date                .
   _Sequence_homology_query_revised_last_date   .

save_


save_SRY_8-mer_strand_2
   _Saveframe_category                          monomeric_polymer

   _Mol_type                                    polymer
   _Mol_polymer_class                           DNA
   _Name_common                                'SRY 8mer strand 2'
   _Abbreviation_common                        'SRY 8-mer strand 2'
   _Molecular_mass                              .
   _Mol_thiol_state                            'not present'
   _Details                                     .
   _Residue_count                               8
   _Mol_residue_sequence                        GTTTGTGC

   loop_
      _Residue_seq_code
      _Residue_author_seq_code
      _Residue_label

      1  9 DG  2 10 DT  3 11 DT  4 12 DT  5 13 DG 
      6 14 DT  7 15 DG  8 16 DC 

   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

      $SRY_8-mer_strand_1 . . Eukaryota . na na 
      $SRY_8-mer_strand_2 . . Eukaryota . na na 

   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

      $SRY_8-mer_strand_1 'chemical synthesis' . . . . . 
      $SRY_8-mer_strand_2 'chemical synthesis' . . . . . 

   stop_

save_


#####################################
#  Sample contents and methodology  #
#####################################
	 
    ########################
    #  Sample description  #
    ########################

save_SRY-8mer
   _Saveframe_category   sample

   _Sample_type          solution
   _Details              .

   loop_
      _Mol_label
      _Concentration_value
      _Concentration_value_units
      _Isotopic_labeling

      $SRY_8-mer_strand_1 2.5 mM . 
      $SRY_8-mer_strand_2 2.5 mM . 

   stop_

save_


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

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

save_NMR_spectrometer
   _Saveframe_category   NMR_spectrometer

   _Manufacturer         Varian
   _Model                Unity
   _Field_strength       500
   _Details              .

save_


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

save_1H-1H_COSY_1
   _Saveframe_category   NMR_applied_experiment

   _Experiment_name     '1H-1H COSY'
   _Sample_label        $SRY-8mer

save_


save_1H-1H_TOCSY_2
   _Saveframe_category   NMR_applied_experiment

   _Experiment_name     '1H-1H TOCSY'
   _Sample_label        $SRY-8mer

save_


save_1H-1H_NOESY_3
   _Saveframe_category   NMR_applied_experiment

   _Experiment_name     '1H-1H NOESY'
   _Sample_label        $SRY-8mer

save_


save_1H-31P_HSQC-TOCSY_4
   _Saveframe_category   NMR_applied_experiment

   _Experiment_name     '1H-31P HSQC-TOCSY'
   _Sample_label        $SRY-8mer

save_


save_1H-31P_HCOSYINV_5
   _Saveframe_category   NMR_applied_experiment

   _Experiment_name     '1H-31P HCOSYINV'
   _Sample_label        $SRY-8mer

save_


save_31P-31P_NOESY_Exchange_6
   _Saveframe_category   NMR_applied_experiment

   _Experiment_name     '31P-31P NOESY Exchange'
   _Sample_label        $SRY-8mer

save_


save_NMR_spec_expt__0_1
   _Saveframe_category                     NMR_applied_experiment

   _Experiment_name                       '1H-1H COSY'
   _BMRB_pulse_sequence_accession_number   .
   _Details                                .

save_


save_NMR_spec_expt__0_2
   _Saveframe_category                     NMR_applied_experiment

   _Experiment_name                       '1H-1H TOCSY'
   _BMRB_pulse_sequence_accession_number   .
   _Details                                .

save_


save_NMR_spec_expt__0_3
   _Saveframe_category                     NMR_applied_experiment

   _Experiment_name                       '1H-1H NOESY'
   _BMRB_pulse_sequence_accession_number   .
   _Details                                .

save_


save_NMR_spec_expt__0_4
   _Saveframe_category                     NMR_applied_experiment

   _Experiment_name                       '1H-31P HSQC-TOCSY'
   _BMRB_pulse_sequence_accession_number   .
   _Details                                .

save_


save_NMR_spec_expt__0_5
   _Saveframe_category                     NMR_applied_experiment

   _Experiment_name                       '1H-31P HCOSYINV'
   _BMRB_pulse_sequence_accession_number   .
   _Details                                .

save_


save_NMR_spec_expt__0_6
   _Saveframe_category                     NMR_applied_experiment

   _Experiment_name                       '31P-31P NOESY Exchange'
   _BMRB_pulse_sequence_accession_number   .
   _Details                                .

save_


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

save_cond1
   _Saveframe_category   sample_conditions

   _Details              .

   loop_
      _Variable_type
      _Variable_value
      _Variable_value_error
      _Variable_value_units

      pH            7 0.2 n/a 
      temperature 298  .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
      _Indirect_shift_ratio

      DSS H  1 'methyl protons' ppm 0.0 internal direct   . . . 1.0         
      DSS P 31 'methyl protons' ppm 0.0 .        indirect . . . 0.404808636 

   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_SRY-8mer-c1
   _Saveframe_category               assigned_chemical_shifts

   _Details                          .

   loop_
      _Sample_label

      $SRY-8mer 

   stop_

   _Sample_conditions_label         $cond1
   _Chem_shift_reference_set_label  $chemical_shift_reference
   _Mol_system_component_name       '8mer strand 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 DG H8   H  7.92 .03 1 
       2 . 1 DG H1'  H  5.93 .03 1 
       3 . 1 DG H2'  H  2.60 .03 1 
       4 . 1 DG H2'' H  2.76 .03 1 
       5 . 1 DG H3'  H  4.84 .03 1 
       6 . 1 DG H4'  H  4.26 .03 1 
       7 . 1 DG H5'  H  3.72 .03 2 
       8 . 1 DG H5'' H  3.72 .03 2 
       9 . 1 DG P    P -4.18 .03 1 
      10 . 2 DC H41  H  6.50 .03 2 
      11 . 2 DC H42  H  8.43 .03 2 
      12 . 2 DC H5   H  5.44 .03 1 
      13 . 2 DC H6   H  7.47 .03 1 
      14 . 2 DC H1'  H  5.63 .03 1 
      15 . 2 DC H2'  H  2.09 .03 1 
      16 . 2 DC H2'' H  2.42 .03 1 
      17 . 2 DC H3'  H  4.87 .03 1 
      18 . 2 DC H4'  H  4.21 .03 1 
      19 . 2 DC H5'  H  4.06 .03 2 
      20 . 2 DC H5'' H  4.13 .03 2 
      21 . 2 DC P    P -4.00 .03 1 
      22 . 3 DA H2   H  7.72 .03 1 
      23 . 3 DA H8   H  8.28 .03 1 
      24 . 3 DA H1'  H  6.19 .03 1 
      25 . 3 DA H2'  H  2.70 .03 1 
      26 . 3 DA H2'' H  2.87 .03 1 
      27 . 3 DA H3'  H  5.03 .03 1 
      28 . 3 DA H4'  H  4.42 .03 1 
      29 . 3 DA P    P -4.28 .03 1 
      30 . 4 DC H5   H  5.36 .03 1 
      31 . 4 DC H6   H  7.25 .03 1 
      32 . 4 DC H1'  H  5.30 .03 1 
      33 . 4 DC H2'  H  1.81 .03 1 
      34 . 4 DC H2'' H  2.17 .03 1 
      35 . 4 DC H3'  H  5.04 .03 1 
      36 . 4 DC H4'  H  4.10 .03 1 
      37 . 4 DC P    P -4.01 .03 1 
      38 . 5 DA H2   H  7.12 .03 1 
      39 . 5 DA H61  H  6.47 .03 2 
      40 . 5 DA H62  H  8.23 .03 2 
      41 . 5 DA H8   H  8.16 .03 1 
      42 . 5 DA H1'  H  5.73 .03 1 
      43 . 5 DA H2'  H  2.68 .03 1 
      44 . 5 DA H2'' H  2.81 .03 1 
      45 . 5 DA H3'  H  5.02 .03 1 
      46 . 5 DA H4'  H  4.35 .03 1 
      47 . 5 DA H5'  H  4.19 .03 2 
      48 . 5 DA H5'' H  4.19 .03 2 
      49 . 5 DA P    P -4.22 .03 1 
      50 . 6 DA H2   H  7.20 .03 1 
      51 . 6 DA H8   H  8.10 .03 1 
      52 . 6 DA H1'  H  5.85 .03 1 
      53 . 6 DA H2'  H  2.61 .03 1 
      54 . 6 DA H2'' H  2.81 .03 1 
      55 . 6 DA H3'  H  5.04 .03 1 
      56 . 6 DA H4'  H  4.42 .03 1 
      57 . 6 DA P    P -4.15 .03 1 
      58 . 7 DA H2   H  7.75 .03 1 
      59 . 7 DA H8   H  8.02 .03 1 
      60 . 7 DA H1'  H  6.10 .03 1 
      61 . 7 DA H2'  H  2.48 .03 1 
      62 . 7 DA H2'' H  2.81 .03 1 
      63 . 7 DA H3'  H  4.97 .03 1 
      64 . 7 DA H4'  H  4.43 .03 1 
      65 . 7 DA H5'  H  4.26 .03 2 
      66 . 7 DA H5'' H  4.26 .03 2 
      67 . 7 DA P    P -4.07 .03 1 
      68 . 8 DC H5   H  5.05 .03 1 
      69 . 8 DC H6   H  7.18 .03 1 
      70 . 8 DC H1'  H  5.95 .03 1 
      71 . 8 DC H2'  H  2.05 .03 1 
      72 . 8 DC H2'' H  2.13 .03 1 
      73 . 8 DC H3'  H  4.44 .03 1 
      74 . 8 DC H4'  H  4.00 .03 1 

   stop_

save_


save_SRY-8mer-c2
   _Saveframe_category               assigned_chemical_shifts

   _Details                          .

   loop_
      _Sample_label

      $SRY-8mer 

   stop_

   _Sample_conditions_label         $cond1
   _Chem_shift_reference_set_label  $chemical_shift_reference
   _Mol_system_component_name       '8mer strand 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 DG H1   H 12.46 .03 1 
       2 . 1 DG H8   H  7.91 .03 1 
       3 . 1 DG H1'  H  5.99 .03 1 
       4 . 1 DG H2'  H  2.71 .03 2 
       5 . 1 DG H2'' H  2.82 .03 2 
       6 . 1 DG H3'  H  4.82 .03 1 
       7 . 1 DG H4'  H  4.27 .03 1 
       8 . 1 DG H5'  H  4.17 .03 2 
       9 . 1 DG H5'' H  4.17 .03 2 
      10 . 1 DG P    P -4.23 .03 1 
      11 . 2 DT H3   H 14.06 .03 1 
      12 . 2 DT H6   H  7.48 .03 1 
      13 . 2 DT H71  H  1.33 .03 1 
      14 . 2 DT H72  H  1.33 .03 1 
      15 . 2 DT H73  H  1.33 .03 1 
      16 . 2 DT H1'  H  6.20 .03 1 
      17 . 2 DT H2'  H  2.24 .03 1 
      18 . 2 DT H2'' H  2.64 .03 1 
      19 . 2 DT H3'  H  4.92 .03 1 
      20 . 2 DT H4'  H  4.33 .03 1 
      21 . 2 DT P    P -4.34 .03 1 
      22 . 3 DT H3   H 13.96 .03 1 
      23 . 3 DT H6   H  7.53 .03 1 
      24 . 3 DT H71  H  1.65 .03 1 
      25 . 3 DT H72  H  1.65 .03 1 
      26 . 3 DT H73  H  1.65 .03 1 
      27 . 3 DT H1'  H  6.19 .03 1 
      28 . 3 DT H2'  H  2.24 .03 1 
      29 . 3 DT H2'' H  2.64 .03 1 
      30 . 3 DT H3'  H  4.93 .03 1 
      31 . 3 DT H4'  H  4.23 .03 1 
      32 . 3 DT P    P -4.34 .03 1 
      33 . 4 DT H3   H 13.64 .03 1 
      34 . 4 DT H6   H  7.40 .03 1 
      35 . 4 DT H71  H  1.73 .03 1 
      36 . 4 DT H72  H  1.73 .03 1 
      37 . 4 DT H73  H  1.73 .03 1 
      38 . 4 DT H1'  H  5.85 .03 1 
      39 . 4 DT H2'  H  2.21 .03 1 
      40 . 4 DT H2'' H  2.53 .03 1 
      41 . 4 DT H3'  H  4.93 .03 1 
      42 . 4 DT H4'  H  4.21 .03 1 
      43 . 4 DT P    P -4.09 .03 1 
      44 . 5 DG H1   H 12.46 .03 1 
      45 . 5 DG H8   H  7.92 .03 1 
      46 . 5 DG H1'  H  5.94 .03 1 
      47 . 5 DG H2'  H  2.64 .03 1 
      48 . 5 DG H2'' H  2.77 .03 1 
      49 . 5 DG H3'  H  4.99 .03 1 
      50 . 5 DG H4'  H  4.42 .03 5 
      51 . 5 DG P    P -4.33 .03 1 
      52 . 6 DT H3   H 13.66 .03 1 
      53 . 6 DT H6   H  7.19 .03 1 
      54 . 6 DT H71  H  1.43 .03 1 
      55 . 6 DT H72  H  1.43 .03 1 
      56 . 6 DT H73  H  1.43 .03 1 
      57 . 6 DT H1'  H  5.80 .03 1 
      58 . 6 DT H2'  H  2.02 .03 1 
      59 . 6 DT H2'' H  2.40 .03 1 
      60 . 6 DT H3'  H  4.88 .03 1 
      61 . 6 DT H4'  H  4.21 .03 1 
      62 . 6 DT P    P -4.15 .03 1 
      63 . 7 DG H1   H 12.87 .03 1 
      64 . 7 DG H8   H  7.87 .03 1 
      65 . 7 DG H1'  H  5.93 .03 1 
      66 . 7 DG H2'  H  2.60 .03 1 
      67 . 7 DG H2'' H  2.70 .03 1 
      68 . 7 DG H3'  H  4.98 .03 1 
      69 . 7 DG H4'  H  4.35 .03 1 
      70 . 7 DG P    P -3.91 .03 1 
      71 . 8 DC H5   H  5.31 .03 1 
      72 . 8 DC H6   H  7.40 .03 1 
      73 . 8 DC H1'  H  6.15 .03 1 
      74 . 8 DC H2'  H  2.22 .03 1 
      75 . 8 DC H2'' H  2.70 .03 5 
      76 . 8 DC H3'  H  4.50 .03 1 
      77 . 8 DC H4'  H  4.05 .03 1 

   stop_

save_