data_1YBN
# 
_entry.id   1YBN 
# 
_audit_conform.dict_name       mmcif_pdbx.dic 
_audit_conform.dict_version    5.391 
_audit_conform.dict_location   http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 
# 
loop_
_database_2.database_id 
_database_2.database_code 
_database_2.pdbx_database_accession 
_database_2.pdbx_DOI 
PDB   1YBN         pdb_00001ybn 10.2210/pdb1ybn/pdb 
RCSB  RCSB031349   ?            ?                   
WWPDB D_1000031349 ?            ?                   
# 
loop_
_pdbx_audit_revision_history.ordinal 
_pdbx_audit_revision_history.data_content_type 
_pdbx_audit_revision_history.major_revision 
_pdbx_audit_revision_history.minor_revision 
_pdbx_audit_revision_history.revision_date 
1 'Structure model' 1 0 2005-01-11 
2 'Structure model' 1 1 2008-04-30 
3 'Structure model' 1 2 2011-07-13 
4 'Structure model' 1 3 2018-06-06 
5 'Structure model' 1 4 2024-05-01 
# 
_pdbx_audit_revision_details.ordinal             1 
_pdbx_audit_revision_details.revision_ordinal    1 
_pdbx_audit_revision_details.data_content_type   'Structure model' 
_pdbx_audit_revision_details.provider            repository 
_pdbx_audit_revision_details.type                'Initial release' 
_pdbx_audit_revision_details.description         ? 
_pdbx_audit_revision_details.details             ? 
# 
loop_
_pdbx_audit_revision_group.ordinal 
_pdbx_audit_revision_group.revision_ordinal 
_pdbx_audit_revision_group.data_content_type 
_pdbx_audit_revision_group.group 
1 2 'Structure model' 'Version format compliance' 
2 3 'Structure model' 'Version format compliance' 
3 4 'Structure model' 'Data collection'           
4 4 'Structure model' 'Derived calculations'      
5 4 'Structure model' 'Experimental preparation'  
6 4 'Structure model' 'Source and taxonomy'       
7 5 'Structure model' 'Data collection'           
8 5 'Structure model' 'Database references'       
# 
loop_
_pdbx_audit_revision_category.ordinal 
_pdbx_audit_revision_category.revision_ordinal 
_pdbx_audit_revision_category.data_content_type 
_pdbx_audit_revision_category.category 
1  4 'Structure model' ndb_struct_conf_na               
2  4 'Structure model' ndb_struct_na_base_pair          
3  4 'Structure model' ndb_struct_na_base_pair_step     
4  4 'Structure model' pdbx_entity_src_syn              
5  4 'Structure model' pdbx_nmr_exptl_sample_conditions 
6  4 'Structure model' pdbx_struct_assembly             
7  4 'Structure model' pdbx_struct_assembly_prop        
8  4 'Structure model' pdbx_struct_oper_list            
9  4 'Structure model' struct_conn                      
10 5 'Structure model' chem_comp_atom                   
11 5 'Structure model' chem_comp_bond                   
12 5 'Structure model' database_2                       
# 
loop_
_pdbx_audit_revision_item.ordinal 
_pdbx_audit_revision_item.revision_ordinal 
_pdbx_audit_revision_item.data_content_type 
_pdbx_audit_revision_item.item 
1 4 'Structure model' '_ndb_struct_na_base_pair.hbond_type_28'        
2 4 'Structure model' '_ndb_struct_na_base_pair_step.helical_twist'   
3 4 'Structure model' '_ndb_struct_na_base_pair_step.twist'           
4 4 'Structure model' '_pdbx_nmr_exptl_sample_conditions.temperature' 
5 4 'Structure model' '_struct_conn.details'                          
6 4 'Structure model' '_struct_conn.ptnr1_label_atom_id'              
7 4 'Structure model' '_struct_conn.ptnr2_label_atom_id'              
8 5 'Structure model' '_database_2.pdbx_DOI'                          
9 5 'Structure model' '_database_2.pdbx_database_accession'           
# 
_pdbx_database_status.entry_id                        1YBN 
_pdbx_database_status.status_code                     REL 
_pdbx_database_status.recvd_initial_deposition_date   2004-12-21 
_pdbx_database_status.deposit_site                    RCSB 
_pdbx_database_status.process_site                    RCSB 
_pdbx_database_status.status_code_sf                  ? 
_pdbx_database_status.status_code_mr                  ? 
_pdbx_database_status.SG_entry                        N 
_pdbx_database_status.pdb_format_compatible           Y 
_pdbx_database_status.status_code_cs                  ? 
_pdbx_database_status.methods_development_category    ? 
_pdbx_database_status.status_code_nmr_data            ? 
# 
loop_
_pdbx_database_related.db_name 
_pdbx_database_related.db_id 
_pdbx_database_related.details 
_pdbx_database_related.content_type 
PDB 294D 'The X-ray structure of the same i-motif tetramer' unspecified 
PDB 1YBL 'i-motif, different sequence'                      unspecified 
PDB 1YBR 'i-motif, distinct topology, same sequence'        unspecified 
# 
loop_
_audit_author.name 
_audit_author.pdbx_ordinal 
'Esmaili, N.'  1 
'Leroy, J.-L.' 2 
# 
_citation.id                        primary 
_citation.title                     
'i-motif solution structure and dynamics of the d(AACCCC) and d(CCCCAA) tetrahymena telomeric repeats' 
_citation.journal_abbrev            'Nucleic Acids Res.' 
_citation.journal_volume            33 
_citation.page_first                213 
_citation.page_last                 224 
_citation.year                      2005 
_citation.journal_id_ASTM           NARHAD 
_citation.country                   UK 
_citation.journal_id_ISSN           0305-1048 
_citation.journal_id_CSD            0389 
_citation.book_publisher            ? 
_citation.pdbx_database_id_PubMed   15647504 
_citation.pdbx_database_id_DOI      10.1093/nar/gki160 
# 
loop_
_citation_author.citation_id 
_citation_author.name 
_citation_author.ordinal 
_citation_author.identifier_ORCID 
primary 'Esmaili, N.'  1 ? 
primary 'Leroy, J.-L.' 2 ? 
# 
_entity.id                         1 
_entity.type                       polymer 
_entity.src_method                 syn 
_entity.pdbx_description           "5'-D(*CP*CP*CP*CP*AP*A)-3'" 
_entity.formula_weight             1738.183 
_entity.pdbx_number_of_molecules   4 
_entity.pdbx_ec                    ? 
_entity.pdbx_mutation              ? 
_entity.pdbx_fragment              ? 
_entity.details                    'i-motif with a distinct topology' 
# 
_entity_poly.entity_id                      1 
_entity_poly.type                           polydeoxyribonucleotide 
_entity_poly.nstd_linkage                   no 
_entity_poly.nstd_monomer                   no 
_entity_poly.pdbx_seq_one_letter_code       '(DC)(DC)(DC)(DC)(DA)(DA)' 
_entity_poly.pdbx_seq_one_letter_code_can   CCCCAA 
_entity_poly.pdbx_strand_id                 A,B,C,D 
_entity_poly.pdbx_target_identifier         ? 
# 
loop_
_entity_poly_seq.entity_id 
_entity_poly_seq.num 
_entity_poly_seq.mon_id 
_entity_poly_seq.hetero 
1 1 DC n 
1 2 DC n 
1 3 DC n 
1 4 DC n 
1 5 DA n 
1 6 DA n 
# 
_pdbx_entity_src_syn.entity_id              1 
_pdbx_entity_src_syn.pdbx_src_id            1 
_pdbx_entity_src_syn.pdbx_alt_source_flag   sample 
_pdbx_entity_src_syn.pdbx_beg_seq_num       ? 
_pdbx_entity_src_syn.pdbx_end_seq_num       ? 
_pdbx_entity_src_syn.organism_scientific    'synthetic construct' 
_pdbx_entity_src_syn.organism_common_name   ? 
_pdbx_entity_src_syn.ncbi_taxonomy_id       32630 
_pdbx_entity_src_syn.details                ? 
# 
loop_
_chem_comp.id 
_chem_comp.type 
_chem_comp.mon_nstd_flag 
_chem_comp.name 
_chem_comp.pdbx_synonyms 
_chem_comp.formula 
_chem_comp.formula_weight 
DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 
DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE"  ? 'C9 H14 N3 O7 P'  307.197 
# 
loop_
_pdbx_poly_seq_scheme.asym_id 
_pdbx_poly_seq_scheme.entity_id 
_pdbx_poly_seq_scheme.seq_id 
_pdbx_poly_seq_scheme.mon_id 
_pdbx_poly_seq_scheme.ndb_seq_num 
_pdbx_poly_seq_scheme.pdb_seq_num 
_pdbx_poly_seq_scheme.auth_seq_num 
_pdbx_poly_seq_scheme.pdb_mon_id 
_pdbx_poly_seq_scheme.auth_mon_id 
_pdbx_poly_seq_scheme.pdb_strand_id 
_pdbx_poly_seq_scheme.pdb_ins_code 
_pdbx_poly_seq_scheme.hetero 
A 1 1 DC 1 1 1 DC C A . n 
A 1 2 DC 2 2 2 DC C A . n 
A 1 3 DC 3 3 3 DC C A . n 
A 1 4 DC 4 4 4 DC C A . n 
A 1 5 DA 5 5 5 DA A A . n 
A 1 6 DA 6 6 6 DA A A . n 
B 1 1 DC 1 1 1 DC C B . n 
B 1 2 DC 2 2 2 DC C B . n 
B 1 3 DC 3 3 3 DC C B . n 
B 1 4 DC 4 4 4 DC C B . n 
B 1 5 DA 5 5 5 DA A B . n 
B 1 6 DA 6 6 6 DA A B . n 
C 1 1 DC 1 1 1 DC C C . n 
C 1 2 DC 2 2 2 DC C C . n 
C 1 3 DC 3 3 3 DC C C . n 
C 1 4 DC 4 4 4 DC C C . n 
C 1 5 DA 5 5 5 DA A C . n 
C 1 6 DA 6 6 6 DA A C . n 
D 1 1 DC 1 1 1 DC C D . n 
D 1 2 DC 2 2 2 DC C D . n 
D 1 3 DC 3 3 3 DC C D . n 
D 1 4 DC 4 4 4 DC C D . n 
D 1 5 DA 5 5 5 DA A D . n 
D 1 6 DA 6 6 6 DA A D . n 
# 
_exptl.entry_id          1YBN 
_exptl.method            'SOLUTION NMR' 
_exptl.crystals_number   ? 
# 
_struct.entry_id                  1YBN 
_struct.title                     
;Solution structure of the 3'E topology of the i-motif tetramer of d(CCCCAA)
;
_struct.pdbx_model_details        ? 
_struct.pdbx_CASP_flag            ? 
_struct.pdbx_model_type_details   ? 
# 
_struct_keywords.entry_id        1YBN 
_struct_keywords.pdbx_keywords   DNA 
_struct_keywords.text            'DNA; i-motif; hemiprotonated cytidine; tetrahymena; telomer, DNA' 
# 
loop_
_struct_asym.id 
_struct_asym.pdbx_blank_PDB_chainid_flag 
_struct_asym.pdbx_modified 
_struct_asym.entity_id 
_struct_asym.details 
A N N 1 ? 
B N N 1 ? 
C N N 1 ? 
D N N 1 ? 
# 
_struct_ref.id                         1 
_struct_ref.entity_id                  1 
_struct_ref.db_name                    PDB 
_struct_ref.db_code                    1YBN 
_struct_ref.pdbx_db_accession          1YBN 
_struct_ref.pdbx_db_isoform            ? 
_struct_ref.pdbx_seq_one_letter_code   ? 
_struct_ref.pdbx_align_begin           ? 
# 
loop_
_struct_ref_seq.align_id 
_struct_ref_seq.ref_id 
_struct_ref_seq.pdbx_PDB_id_code 
_struct_ref_seq.pdbx_strand_id 
_struct_ref_seq.seq_align_beg 
_struct_ref_seq.pdbx_seq_align_beg_ins_code 
_struct_ref_seq.seq_align_end 
_struct_ref_seq.pdbx_seq_align_end_ins_code 
_struct_ref_seq.pdbx_db_accession 
_struct_ref_seq.db_align_beg 
_struct_ref_seq.pdbx_db_align_beg_ins_code 
_struct_ref_seq.db_align_end 
_struct_ref_seq.pdbx_db_align_end_ins_code 
_struct_ref_seq.pdbx_auth_seq_align_beg 
_struct_ref_seq.pdbx_auth_seq_align_end 
1 1 1YBN A 1 ? 6 ? 1YBN 1 ? 6 ? 1 6 
2 1 1YBN B 1 ? 6 ? 1YBN 1 ? 6 ? 1 6 
3 1 1YBN C 1 ? 6 ? 1YBN 1 ? 6 ? 1 6 
4 1 1YBN D 1 ? 6 ? 1YBN 1 ? 6 ? 1 6 
# 
_pdbx_struct_assembly.id                   1 
_pdbx_struct_assembly.details              author_defined_assembly 
_pdbx_struct_assembly.method_details       ? 
_pdbx_struct_assembly.oligomeric_details   tetrameric 
_pdbx_struct_assembly.oligomeric_count     4 
# 
loop_
_pdbx_struct_assembly_prop.biol_id 
_pdbx_struct_assembly_prop.type 
_pdbx_struct_assembly_prop.value 
_pdbx_struct_assembly_prop.details 
1 'ABSA (A^2)' 3770 ? 
1 MORE         13   ? 
1 'SSA (A^2)'  3670 ? 
# 
_pdbx_struct_assembly_gen.assembly_id       1 
_pdbx_struct_assembly_gen.oper_expression   1 
_pdbx_struct_assembly_gen.asym_id_list      A,B,C,D 
# 
_pdbx_struct_oper_list.id                   1 
_pdbx_struct_oper_list.type                 'identity operation' 
_pdbx_struct_oper_list.name                 1_555 
_pdbx_struct_oper_list.symmetry_operation   ? 
_pdbx_struct_oper_list.matrix[1][1]         1.0000000000 
_pdbx_struct_oper_list.matrix[1][2]         0.0000000000 
_pdbx_struct_oper_list.matrix[1][3]         0.0000000000 
_pdbx_struct_oper_list.vector[1]            0.0000000000 
_pdbx_struct_oper_list.matrix[2][1]         0.0000000000 
_pdbx_struct_oper_list.matrix[2][2]         1.0000000000 
_pdbx_struct_oper_list.matrix[2][3]         0.0000000000 
_pdbx_struct_oper_list.vector[2]            0.0000000000 
_pdbx_struct_oper_list.matrix[3][1]         0.0000000000 
_pdbx_struct_oper_list.matrix[3][2]         0.0000000000 
_pdbx_struct_oper_list.matrix[3][3]         1.0000000000 
_pdbx_struct_oper_list.vector[3]            0.0000000000 
# 
loop_
_struct_conn.id 
_struct_conn.conn_type_id 
_struct_conn.pdbx_leaving_atom_flag 
_struct_conn.pdbx_PDB_id 
_struct_conn.ptnr1_label_asym_id 
_struct_conn.ptnr1_label_comp_id 
_struct_conn.ptnr1_label_seq_id 
_struct_conn.ptnr1_label_atom_id 
_struct_conn.pdbx_ptnr1_label_alt_id 
_struct_conn.pdbx_ptnr1_PDB_ins_code 
_struct_conn.pdbx_ptnr1_standard_comp_id 
_struct_conn.ptnr1_symmetry 
_struct_conn.ptnr2_label_asym_id 
_struct_conn.ptnr2_label_comp_id 
_struct_conn.ptnr2_label_seq_id 
_struct_conn.ptnr2_label_atom_id 
_struct_conn.pdbx_ptnr2_label_alt_id 
_struct_conn.pdbx_ptnr2_PDB_ins_code 
_struct_conn.ptnr1_auth_asym_id 
_struct_conn.ptnr1_auth_comp_id 
_struct_conn.ptnr1_auth_seq_id 
_struct_conn.ptnr2_auth_asym_id 
_struct_conn.ptnr2_auth_comp_id 
_struct_conn.ptnr2_auth_seq_id 
_struct_conn.ptnr2_symmetry 
_struct_conn.pdbx_ptnr3_label_atom_id 
_struct_conn.pdbx_ptnr3_label_seq_id 
_struct_conn.pdbx_ptnr3_label_comp_id 
_struct_conn.pdbx_ptnr3_label_asym_id 
_struct_conn.pdbx_ptnr3_label_alt_id 
_struct_conn.pdbx_ptnr3_PDB_ins_code 
_struct_conn.details 
_struct_conn.pdbx_dist_value 
_struct_conn.pdbx_value_order 
_struct_conn.pdbx_role 
hydrog1  hydrog ? ? A DC 1 N4 ? ? ? 1_555 C DC 1 O2 ? ? A DC 1 C DC 1 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? 
hydrog2  hydrog ? ? A DC 1 O2 ? ? ? 1_555 C DC 1 N4 ? ? A DC 1 C DC 1 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? 
hydrog3  hydrog ? ? A DC 2 N4 ? ? ? 1_555 C DC 2 O2 ? ? A DC 2 C DC 2 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? 
hydrog4  hydrog ? ? A DC 2 O2 ? ? ? 1_555 C DC 2 N4 ? ? A DC 2 C DC 2 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? 
hydrog5  hydrog ? ? A DC 3 N4 ? ? ? 1_555 C DC 3 O2 ? ? A DC 3 C DC 3 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? 
hydrog6  hydrog ? ? A DC 3 O2 ? ? ? 1_555 C DC 3 N4 ? ? A DC 3 C DC 3 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? 
hydrog7  hydrog ? ? A DC 4 N4 ? ? ? 1_555 C DC 4 O2 ? ? A DC 4 C DC 4 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? 
hydrog8  hydrog ? ? A DC 4 O2 ? ? ? 1_555 C DC 4 N4 ? ? A DC 4 C DC 4 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? 
hydrog9  hydrog ? ? B DC 1 N4 ? ? ? 1_555 D DC 1 O2 ? ? B DC 1 D DC 1 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? 
hydrog10 hydrog ? ? B DC 1 O2 ? ? ? 1_555 D DC 1 N4 ? ? B DC 1 D DC 1 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? 
hydrog11 hydrog ? ? B DC 2 N4 ? ? ? 1_555 D DC 2 O2 ? ? B DC 2 D DC 2 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? 
hydrog12 hydrog ? ? B DC 2 O2 ? ? ? 1_555 D DC 2 N4 ? ? B DC 2 D DC 2 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? 
hydrog13 hydrog ? ? B DC 3 N4 ? ? ? 1_555 D DC 3 O2 ? ? B DC 3 D DC 3 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? 
hydrog14 hydrog ? ? B DC 3 O2 ? ? ? 1_555 D DC 3 N4 ? ? B DC 3 D DC 3 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? 
hydrog15 hydrog ? ? B DC 4 N4 ? ? ? 1_555 D DC 4 O2 ? ? B DC 4 D DC 4 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? 
hydrog16 hydrog ? ? B DC 4 O2 ? ? ? 1_555 D DC 4 N4 ? ? B DC 4 D DC 4 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? 
# 
_struct_conn_type.id          hydrog 
_struct_conn_type.criteria    ? 
_struct_conn_type.reference   ? 
# 
loop_
_pdbx_validate_rmsd_angle.id 
_pdbx_validate_rmsd_angle.PDB_model_num 
_pdbx_validate_rmsd_angle.auth_atom_id_1 
_pdbx_validate_rmsd_angle.auth_asym_id_1 
_pdbx_validate_rmsd_angle.auth_comp_id_1 
_pdbx_validate_rmsd_angle.auth_seq_id_1 
_pdbx_validate_rmsd_angle.PDB_ins_code_1 
_pdbx_validate_rmsd_angle.label_alt_id_1 
_pdbx_validate_rmsd_angle.auth_atom_id_2 
_pdbx_validate_rmsd_angle.auth_asym_id_2 
_pdbx_validate_rmsd_angle.auth_comp_id_2 
_pdbx_validate_rmsd_angle.auth_seq_id_2 
_pdbx_validate_rmsd_angle.PDB_ins_code_2 
_pdbx_validate_rmsd_angle.label_alt_id_2 
_pdbx_validate_rmsd_angle.auth_atom_id_3 
_pdbx_validate_rmsd_angle.auth_asym_id_3 
_pdbx_validate_rmsd_angle.auth_comp_id_3 
_pdbx_validate_rmsd_angle.auth_seq_id_3 
_pdbx_validate_rmsd_angle.PDB_ins_code_3 
_pdbx_validate_rmsd_angle.label_alt_id_3 
_pdbx_validate_rmsd_angle.angle_value 
_pdbx_validate_rmsd_angle.angle_target_value 
_pdbx_validate_rmsd_angle.angle_deviation 
_pdbx_validate_rmsd_angle.angle_standard_deviation 
_pdbx_validate_rmsd_angle.linker_flag 
1  1 "O4'" A DC 1 ? ? "C1'" A DC 1 ? ? N1 A DC 1 ? ? 111.56 108.30 3.26  0.30 N 
2  1 "O4'" A DC 2 ? ? "C1'" A DC 2 ? ? N1 A DC 2 ? ? 111.33 108.30 3.03  0.30 N 
3  1 "O4'" A DC 3 ? ? "C1'" A DC 3 ? ? N1 A DC 3 ? ? 110.61 108.30 2.31  0.30 N 
4  1 "O4'" A DC 4 ? ? "C1'" A DC 4 ? ? N1 A DC 4 ? ? 111.52 108.30 3.22  0.30 N 
5  1 N7    A DA 5 ? ? C8    A DA 5 ? ? N9 A DA 5 ? ? 117.71 113.80 3.91  0.50 N 
6  1 C8    A DA 5 ? ? N9    A DA 5 ? ? C4 A DA 5 ? ? 103.33 105.80 -2.47 0.40 N 
7  1 "O4'" A DA 6 ? ? "C1'" A DA 6 ? ? N9 A DA 6 ? ? 110.78 108.30 2.48  0.30 N 
8  1 N7    A DA 6 ? ? C8    A DA 6 ? ? N9 A DA 6 ? ? 117.44 113.80 3.64  0.50 N 
9  1 "O4'" B DC 1 ? ? "C1'" B DC 1 ? ? N1 B DC 1 ? ? 111.75 108.30 3.45  0.30 N 
10 1 "O4'" B DC 2 ? ? "C1'" B DC 2 ? ? N1 B DC 2 ? ? 110.94 108.30 2.64  0.30 N 
11 1 "O4'" B DC 3 ? ? "C1'" B DC 3 ? ? N1 B DC 3 ? ? 110.62 108.30 2.32  0.30 N 
12 1 "O4'" B DC 4 ? ? "C1'" B DC 4 ? ? N1 B DC 4 ? ? 111.36 108.30 3.06  0.30 N 
13 1 N7    B DA 5 ? ? C8    B DA 5 ? ? N9 B DA 5 ? ? 117.71 113.80 3.91  0.50 N 
14 1 C8    B DA 5 ? ? N9    B DA 5 ? ? C4 B DA 5 ? ? 103.36 105.80 -2.44 0.40 N 
15 1 "O4'" B DA 6 ? ? "C1'" B DA 6 ? ? N9 B DA 6 ? ? 110.74 108.30 2.44  0.30 N 
16 1 N7    B DA 6 ? ? C8    B DA 6 ? ? N9 B DA 6 ? ? 117.59 113.80 3.79  0.50 N 
17 1 "O4'" C DC 1 ? ? "C1'" C DC 1 ? ? N1 C DC 1 ? ? 111.84 108.30 3.54  0.30 N 
18 1 "O4'" C DC 2 ? ? "C1'" C DC 2 ? ? N1 C DC 2 ? ? 111.11 108.30 2.81  0.30 N 
19 1 "O4'" C DC 3 ? ? "C1'" C DC 3 ? ? N1 C DC 3 ? ? 110.58 108.30 2.28  0.30 N 
20 1 "O4'" C DC 4 ? ? "C1'" C DC 4 ? ? N1 C DC 4 ? ? 111.47 108.30 3.17  0.30 N 
21 1 N7    C DA 5 ? ? C8    C DA 5 ? ? N9 C DA 5 ? ? 117.69 113.80 3.89  0.50 N 
22 1 "O4'" C DA 6 ? ? "C1'" C DA 6 ? ? N9 C DA 6 ? ? 110.71 108.30 2.41  0.30 N 
23 1 N7    C DA 6 ? ? C8    C DA 6 ? ? N9 C DA 6 ? ? 117.47 113.80 3.67  0.50 N 
24 1 "O4'" D DC 1 ? ? "C1'" D DC 1 ? ? N1 D DC 1 ? ? 111.73 108.30 3.43  0.30 N 
25 1 "O4'" D DC 2 ? ? "C1'" D DC 2 ? ? N1 D DC 2 ? ? 110.99 108.30 2.69  0.30 N 
26 1 "O4'" D DC 3 ? ? "C1'" D DC 3 ? ? N1 D DC 3 ? ? 110.60 108.30 2.30  0.30 N 
27 1 "O4'" D DC 4 ? ? "C1'" D DC 4 ? ? N1 D DC 4 ? ? 111.66 108.30 3.36  0.30 N 
28 1 N7    D DA 5 ? ? C8    D DA 5 ? ? N9 D DA 5 ? ? 117.80 113.80 4.00  0.50 N 
29 1 C8    D DA 5 ? ? N9    D DA 5 ? ? C4 D DA 5 ? ? 103.33 105.80 -2.47 0.40 N 
30 1 "O4'" D DA 6 ? ? "C1'" D DA 6 ? ? N9 D DA 6 ? ? 110.85 108.30 2.55  0.30 N 
31 1 N7    D DA 6 ? ? C8    D DA 6 ? ? N9 D DA 6 ? ? 117.47 113.80 3.67  0.50 N 
# 
loop_
_pdbx_validate_planes.id 
_pdbx_validate_planes.PDB_model_num 
_pdbx_validate_planes.auth_comp_id 
_pdbx_validate_planes.auth_asym_id 
_pdbx_validate_planes.auth_seq_id 
_pdbx_validate_planes.PDB_ins_code 
_pdbx_validate_planes.label_alt_id 
_pdbx_validate_planes.rmsd 
_pdbx_validate_planes.type 
1 1 DC A 1 ? ? 0.060 'SIDE CHAIN' 
2 1 DC B 1 ? ? 0.061 'SIDE CHAIN' 
3 1 DC C 1 ? ? 0.062 'SIDE CHAIN' 
4 1 DC D 1 ? ? 0.059 'SIDE CHAIN' 
# 
_pdbx_nmr_ensemble.entry_id                                      1YBN 
_pdbx_nmr_ensemble.conformers_calculated_total_number            10 
_pdbx_nmr_ensemble.conformers_submitted_total_number             1 
_pdbx_nmr_ensemble.conformer_selection_criteria                  'back calculated data agree with experimental NOESY spectrum' 
_pdbx_nmr_ensemble.average_constraints_per_residue               ? 
_pdbx_nmr_ensemble.average_constraint_violations_per_residue     ? 
_pdbx_nmr_ensemble.maximum_distance_constraint_violation         ? 
_pdbx_nmr_ensemble.average_distance_constraint_violation         ? 
_pdbx_nmr_ensemble.maximum_upper_distance_constraint_violation   ? 
_pdbx_nmr_ensemble.maximum_lower_distance_constraint_violation   ? 
_pdbx_nmr_ensemble.distance_constraint_violation_method          ? 
_pdbx_nmr_ensemble.maximum_torsion_angle_constraint_violation    ? 
_pdbx_nmr_ensemble.average_torsion_angle_constraint_violation    ? 
_pdbx_nmr_ensemble.torsion_angle_constraint_violation_method     ? 
# 
_pdbx_nmr_representative.entry_id             1YBN 
_pdbx_nmr_representative.conformer_id         1 
_pdbx_nmr_representative.selection_criteria   'fewest violations' 
# 
_pdbx_nmr_sample_details.solution_id      1 
_pdbx_nmr_sample_details.contents         'pH 4.5' 
_pdbx_nmr_sample_details.solvent_system   H2O/D2O 
_pdbx_nmr_sample_details.label            ? 
_pdbx_nmr_sample_details.type             ? 
_pdbx_nmr_sample_details.details          ? 
# 
_pdbx_nmr_exptl_sample_conditions.conditions_id          1 
_pdbx_nmr_exptl_sample_conditions.temperature            273 
_pdbx_nmr_exptl_sample_conditions.pressure               normal 
_pdbx_nmr_exptl_sample_conditions.pH                     4.5 
_pdbx_nmr_exptl_sample_conditions.ionic_strength         'no added salt' 
_pdbx_nmr_exptl_sample_conditions.pressure_units         ? 
_pdbx_nmr_exptl_sample_conditions.temperature_units      K 
_pdbx_nmr_exptl_sample_conditions.label                  ? 
_pdbx_nmr_exptl_sample_conditions.pH_units               ? 
_pdbx_nmr_exptl_sample_conditions.ionic_strength_units   ? 
# 
loop_
_pdbx_nmr_exptl.experiment_id 
_pdbx_nmr_exptl.conditions_id 
_pdbx_nmr_exptl.type 
_pdbx_nmr_exptl.solution_id 
1 1 '2D NOESY' 1 
2 1 '2D TOCSY' 1 
3 1 HMBC       1 
# 
_pdbx_nmr_details.entry_id   1YBN 
_pdbx_nmr_details.text       'standard 2 D methods' 
# 
_pdbx_nmr_refine.entry_id           1YBN 
_pdbx_nmr_refine.method             'simulated annealing' 
_pdbx_nmr_refine.details            
'54 NOE-derived distance constraints and 12 distances constraints for H-bonding derived from proton exchange measurements' 
_pdbx_nmr_refine.software_ordinal   1 
# 
loop_
_pdbx_nmr_software.classification 
_pdbx_nmr_software.name 
_pdbx_nmr_software.version 
_pdbx_nmr_software.authors 
_pdbx_nmr_software.ordinal 
'structure solution' X-PLOR ? 'Brunger, A.T.' 1 
refinement           X-PLOR ? 'Brunger, A.T.' 2 
# 
loop_
_chem_comp_atom.comp_id 
_chem_comp_atom.atom_id 
_chem_comp_atom.type_symbol 
_chem_comp_atom.pdbx_aromatic_flag 
_chem_comp_atom.pdbx_stereo_config 
_chem_comp_atom.pdbx_ordinal 
DA OP3    O N N 1  
DA P      P N N 2  
DA OP1    O N N 3  
DA OP2    O N N 4  
DA "O5'"  O N N 5  
DA "C5'"  C N N 6  
DA "C4'"  C N R 7  
DA "O4'"  O N N 8  
DA "C3'"  C N S 9  
DA "O3'"  O N N 10 
DA "C2'"  C N N 11 
DA "C1'"  C N R 12 
DA N9     N Y N 13 
DA C8     C Y N 14 
DA N7     N Y N 15 
DA C5     C Y N 16 
DA C6     C Y N 17 
DA N6     N N N 18 
DA N1     N Y N 19 
DA C2     C Y N 20 
DA N3     N Y N 21 
DA C4     C Y N 22 
DA HOP3   H N N 23 
DA HOP2   H N N 24 
DA "H5'"  H N N 25 
DA "H5''" H N N 26 
DA "H4'"  H N N 27 
DA "H3'"  H N N 28 
DA "HO3'" H N N 29 
DA "H2'"  H N N 30 
DA "H2''" H N N 31 
DA "H1'"  H N N 32 
DA H8     H N N 33 
DA H61    H N N 34 
DA H62    H N N 35 
DA H2     H N N 36 
DC OP3    O N N 37 
DC P      P N N 38 
DC OP1    O N N 39 
DC OP2    O N N 40 
DC "O5'"  O N N 41 
DC "C5'"  C N N 42 
DC "C4'"  C N R 43 
DC "O4'"  O N N 44 
DC "C3'"  C N S 45 
DC "O3'"  O N N 46 
DC "C2'"  C N N 47 
DC "C1'"  C N R 48 
DC N1     N N N 49 
DC C2     C N N 50 
DC O2     O N N 51 
DC N3     N N N 52 
DC C4     C N N 53 
DC N4     N N N 54 
DC C5     C N N 55 
DC C6     C N N 56 
DC HOP3   H N N 57 
DC HOP2   H N N 58 
DC "H5'"  H N N 59 
DC "H5''" H N N 60 
DC "H4'"  H N N 61 
DC "H3'"  H N N 62 
DC "HO3'" H N N 63 
DC "H2'"  H N N 64 
DC "H2''" H N N 65 
DC "H1'"  H N N 66 
DC H41    H N N 67 
DC H42    H N N 68 
DC H5     H N N 69 
DC H6     H N N 70 
# 
loop_
_chem_comp_bond.comp_id 
_chem_comp_bond.atom_id_1 
_chem_comp_bond.atom_id_2 
_chem_comp_bond.value_order 
_chem_comp_bond.pdbx_aromatic_flag 
_chem_comp_bond.pdbx_stereo_config 
_chem_comp_bond.pdbx_ordinal 
DA OP3   P      sing N N 1  
DA OP3   HOP3   sing N N 2  
DA P     OP1    doub N N 3  
DA P     OP2    sing N N 4  
DA P     "O5'"  sing N N 5  
DA OP2   HOP2   sing N N 6  
DA "O5'" "C5'"  sing N N 7  
DA "C5'" "C4'"  sing N N 8  
DA "C5'" "H5'"  sing N N 9  
DA "C5'" "H5''" sing N N 10 
DA "C4'" "O4'"  sing N N 11 
DA "C4'" "C3'"  sing N N 12 
DA "C4'" "H4'"  sing N N 13 
DA "O4'" "C1'"  sing N N 14 
DA "C3'" "O3'"  sing N N 15 
DA "C3'" "C2'"  sing N N 16 
DA "C3'" "H3'"  sing N N 17 
DA "O3'" "HO3'" sing N N 18 
DA "C2'" "C1'"  sing N N 19 
DA "C2'" "H2'"  sing N N 20 
DA "C2'" "H2''" sing N N 21 
DA "C1'" N9     sing N N 22 
DA "C1'" "H1'"  sing N N 23 
DA N9    C8     sing Y N 24 
DA N9    C4     sing Y N 25 
DA C8    N7     doub Y N 26 
DA C8    H8     sing N N 27 
DA N7    C5     sing Y N 28 
DA C5    C6     sing Y N 29 
DA C5    C4     doub Y N 30 
DA C6    N6     sing N N 31 
DA C6    N1     doub Y N 32 
DA N6    H61    sing N N 33 
DA N6    H62    sing N N 34 
DA N1    C2     sing Y N 35 
DA C2    N3     doub Y N 36 
DA C2    H2     sing N N 37 
DA N3    C4     sing Y N 38 
DC OP3   P      sing N N 39 
DC OP3   HOP3   sing N N 40 
DC P     OP1    doub N N 41 
DC P     OP2    sing N N 42 
DC P     "O5'"  sing N N 43 
DC OP2   HOP2   sing N N 44 
DC "O5'" "C5'"  sing N N 45 
DC "C5'" "C4'"  sing N N 46 
DC "C5'" "H5'"  sing N N 47 
DC "C5'" "H5''" sing N N 48 
DC "C4'" "O4'"  sing N N 49 
DC "C4'" "C3'"  sing N N 50 
DC "C4'" "H4'"  sing N N 51 
DC "O4'" "C1'"  sing N N 52 
DC "C3'" "O3'"  sing N N 53 
DC "C3'" "C2'"  sing N N 54 
DC "C3'" "H3'"  sing N N 55 
DC "O3'" "HO3'" sing N N 56 
DC "C2'" "C1'"  sing N N 57 
DC "C2'" "H2'"  sing N N 58 
DC "C2'" "H2''" sing N N 59 
DC "C1'" N1     sing N N 60 
DC "C1'" "H1'"  sing N N 61 
DC N1    C2     sing N N 62 
DC N1    C6     sing N N 63 
DC C2    O2     doub N N 64 
DC C2    N3     sing N N 65 
DC N3    C4     doub N N 66 
DC C4    N4     sing N N 67 
DC C4    C5     sing N N 68 
DC N4    H41    sing N N 69 
DC N4    H42    sing N N 70 
DC C5    C6     doub N N 71 
DC C5    H5     sing N N 72 
DC C6    H6     sing N N 73 
# 
_ndb_struct_conf_na.entry_id   1YBN 
_ndb_struct_conf_na.feature    'double helix' 
# 
loop_
_ndb_struct_na_base_pair.model_number 
_ndb_struct_na_base_pair.i_label_asym_id 
_ndb_struct_na_base_pair.i_label_comp_id 
_ndb_struct_na_base_pair.i_label_seq_id 
_ndb_struct_na_base_pair.i_symmetry 
_ndb_struct_na_base_pair.j_label_asym_id 
_ndb_struct_na_base_pair.j_label_comp_id 
_ndb_struct_na_base_pair.j_label_seq_id 
_ndb_struct_na_base_pair.j_symmetry 
_ndb_struct_na_base_pair.shear 
_ndb_struct_na_base_pair.stretch 
_ndb_struct_na_base_pair.stagger 
_ndb_struct_na_base_pair.buckle 
_ndb_struct_na_base_pair.propeller 
_ndb_struct_na_base_pair.opening 
_ndb_struct_na_base_pair.pair_number 
_ndb_struct_na_base_pair.pair_name 
_ndb_struct_na_base_pair.i_auth_asym_id 
_ndb_struct_na_base_pair.i_auth_seq_id 
_ndb_struct_na_base_pair.i_PDB_ins_code 
_ndb_struct_na_base_pair.j_auth_asym_id 
_ndb_struct_na_base_pair.j_auth_seq_id 
_ndb_struct_na_base_pair.j_PDB_ins_code 
_ndb_struct_na_base_pair.hbond_type_28 
_ndb_struct_na_base_pair.hbond_type_12 
1 A DC 4 1_555 C DC 4 1_555 -2.083 -1.180 -0.056 -6.757  13.994 -179.323 1 A_DC4:DC4_C A 4 ? C 4 ? 15 2 
1 D DC 1 1_555 B DC 1 1_555 -2.078 -1.415 -0.024 -13.176 -8.201 -179.510 2 D_DC1:DC1_B D 1 ? B 1 ? 15 2 
1 A DC 3 1_555 C DC 3 1_555 -2.164 -1.771 -0.042 19.560  20.505 -179.272 3 A_DC3:DC3_C A 3 ? C 3 ? 15 2 
1 D DC 2 1_555 B DC 2 1_555 -1.967 -1.328 -0.010 9.062   -8.880 -179.511 4 D_DC2:DC2_B D 2 ? B 2 ? 15 2 
1 A DC 2 1_555 C DC 2 1_555 -1.976 -1.397 -0.042 9.303   -8.169 -179.686 5 A_DC2:DC2_C A 2 ? C 2 ? 15 2 
1 D DC 3 1_555 B DC 3 1_555 -2.151 -1.642 -0.023 18.971  20.105 -179.564 6 D_DC3:DC3_B D 3 ? B 3 ? 15 2 
1 A DC 1 1_555 C DC 1 1_555 -2.098 -1.470 -0.021 -12.996 -7.591 -179.351 7 A_DC1:DC1_C A 1 ? C 1 ? 15 2 
1 D DC 4 1_555 B DC 4 1_555 -2.040 -1.020 -0.018 -7.150  14.253 -179.597 8 D_DC4:DC4_B D 4 ? B 4 ? 15 2 
# 
loop_
_ndb_struct_na_base_pair_step.model_number 
_ndb_struct_na_base_pair_step.i_label_asym_id_1 
_ndb_struct_na_base_pair_step.i_label_comp_id_1 
_ndb_struct_na_base_pair_step.i_label_seq_id_1 
_ndb_struct_na_base_pair_step.i_symmetry_1 
_ndb_struct_na_base_pair_step.j_label_asym_id_1 
_ndb_struct_na_base_pair_step.j_label_comp_id_1 
_ndb_struct_na_base_pair_step.j_label_seq_id_1 
_ndb_struct_na_base_pair_step.j_symmetry_1 
_ndb_struct_na_base_pair_step.i_label_asym_id_2 
_ndb_struct_na_base_pair_step.i_label_comp_id_2 
_ndb_struct_na_base_pair_step.i_label_seq_id_2 
_ndb_struct_na_base_pair_step.i_symmetry_2 
_ndb_struct_na_base_pair_step.j_label_asym_id_2 
_ndb_struct_na_base_pair_step.j_label_comp_id_2 
_ndb_struct_na_base_pair_step.j_label_seq_id_2 
_ndb_struct_na_base_pair_step.j_symmetry_2 
_ndb_struct_na_base_pair_step.shift 
_ndb_struct_na_base_pair_step.slide 
_ndb_struct_na_base_pair_step.rise 
_ndb_struct_na_base_pair_step.tilt 
_ndb_struct_na_base_pair_step.roll 
_ndb_struct_na_base_pair_step.twist 
_ndb_struct_na_base_pair_step.x_displacement 
_ndb_struct_na_base_pair_step.y_displacement 
_ndb_struct_na_base_pair_step.helical_rise 
_ndb_struct_na_base_pair_step.inclination 
_ndb_struct_na_base_pair_step.tip 
_ndb_struct_na_base_pair_step.helical_twist 
_ndb_struct_na_base_pair_step.step_number 
_ndb_struct_na_base_pair_step.step_name 
_ndb_struct_na_base_pair_step.i_auth_asym_id_1 
_ndb_struct_na_base_pair_step.i_auth_seq_id_1 
_ndb_struct_na_base_pair_step.i_PDB_ins_code_1 
_ndb_struct_na_base_pair_step.j_auth_asym_id_1 
_ndb_struct_na_base_pair_step.j_auth_seq_id_1 
_ndb_struct_na_base_pair_step.j_PDB_ins_code_1 
_ndb_struct_na_base_pair_step.i_auth_asym_id_2 
_ndb_struct_na_base_pair_step.i_auth_seq_id_2 
_ndb_struct_na_base_pair_step.i_PDB_ins_code_2 
_ndb_struct_na_base_pair_step.j_auth_asym_id_2 
_ndb_struct_na_base_pair_step.j_auth_seq_id_2 
_ndb_struct_na_base_pair_step.j_PDB_ins_code_2 
1 A DC 4 1_555 C DC 4 1_555 D DC 1 1_555 B DC 1 1_555 -2.517 1.757  0.118  -107.924 -143.351 67.184   0.937  1.214  0.158  -71.776 
54.038 179.530  1 AD_DC4DC1:DC1DC4_BC A 4 ? C 4 ? D 1 ? B 1 ? 
1 D DC 1 1_555 B DC 1 1_555 A DC 3 1_555 C DC 3 1_555 -3.449 1.935  -0.137 83.213   159.257  -78.413  -0.901 -1.759 -0.178 -79.680 
41.633 -179.757 2 DA_DC1DC3:DC3DC1_CB D 1 ? B 1 ? A 3 ? C 3 ? 
1 A DC 3 1_555 C DC 3 1_555 D DC 2 1_555 B DC 2 1_555 -2.981 1.990  0.041  -106.716 -144.230 30.253   1.063  1.441  0.178  -72.288 
53.486 179.437  3 AD_DC3DC2:DC2DC3_BC A 3 ? C 3 ? D 2 ? B 2 ? 
1 D DC 2 1_555 B DC 2 1_555 A DC 2 1_555 C DC 2 1_555 -3.636 1.917  -0.063 75.717   162.558  -42.721  -0.873 -1.858 -0.211 -81.473 
37.949 -179.373 4 DA_DC2DC2:DC2DC2_CB D 2 ? B 2 ? A 2 ? C 2 ? 
1 A DC 2 1_555 C DC 2 1_555 D DC 3 1_555 B DC 3 1_555 -3.012 1.963  0.016  -106.834 -144.474 38.428   1.045  1.459  0.206  -72.322 
53.480 179.702  5 AD_DC2DC3:DC3DC2_BC A 2 ? C 2 ? D 3 ? B 3 ? 
1 D DC 3 1_555 B DC 3 1_555 A DC 1 1_555 C DC 1 1_555 3.473  -1.888 -0.210 -83.305  -159.089 174.676  -0.948 -1.734 -0.207 -79.545 
41.653 179.981  6 DA_DC3DC1:DC1DC3_CB D 3 ? B 3 ? A 1 ? C 1 ? 
1 A DC 1 1_555 C DC 1 1_555 D DC 4 1_555 B DC 4 1_555 2.511  -1.793 0.246  108.098  143.397  -157.430 0.878  1.270  0.225  -71.702 
54.051 -179.917 7 AD_DC1DC4:DC4DC1_BC A 1 ? C 1 ? D 4 ? B 4 ? 
# 
_pdbx_nmr_spectrometer.spectrometer_id   1 
_pdbx_nmr_spectrometer.model             INOVA 
_pdbx_nmr_spectrometer.manufacturer      Varian 
_pdbx_nmr_spectrometer.field_strength    500 
_pdbx_nmr_spectrometer.type              ? 
# 
_atom_sites.entry_id                    1YBN 
_atom_sites.fract_transf_matrix[1][1]   1.000000 
_atom_sites.fract_transf_matrix[1][2]   0.000000 
_atom_sites.fract_transf_matrix[1][3]   0.000000 
_atom_sites.fract_transf_matrix[2][1]   0.000000 
_atom_sites.fract_transf_matrix[2][2]   1.000000 
_atom_sites.fract_transf_matrix[2][3]   0.000000 
_atom_sites.fract_transf_matrix[3][1]   0.000000 
_atom_sites.fract_transf_matrix[3][2]   0.000000 
_atom_sites.fract_transf_matrix[3][3]   1.000000 
_atom_sites.fract_transf_vector[1]      0.00000 
_atom_sites.fract_transf_vector[2]      0.00000 
_atom_sites.fract_transf_vector[3]      0.00000 
# 
loop_
_atom_type.symbol 
C 
H 
N 
O 
P 
# 
loop_