data_1YB9
# 
_entry.id   1YB9 
# 
_audit_conform.dict_name       mmcif_pdbx.dic 
_audit_conform.dict_version    5.376 
_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   1YB9         pdb_00001yb9 10.2210/pdb1yb9/pdb 
NDB   AD0043       ?            ?                   
RCSB  RCSB031335   ?            ?                   
WWPDB D_1000031335 ?            ?                   
# 
loop_
_pdbx_database_related.db_name 
_pdbx_database_related.db_id 
_pdbx_database_related.details 
_pdbx_database_related.content_type 
PDB 1Y7F 
;Crystal structure of the A-DNA GCGTAT*CGC with a 2'-O-[2-[hydroxy(methyleneamino)oxy]ethyl] Thymidine (T*)
;
unspecified 
PDB 1Y84 
;Crystal structure of the A-DNA GCGTAT*CGC with a 2'-O-[2-(imidazolyl)ethyl] Thymidine (T*)
;
unspecified 
PDB 1Y86 
;Crystal structure of the A-DNA GCGTAT*CGC with a 2'-O-[2-(fluoro)ethyl] Thymidine (T*)
;
unspecified 
PDB 1Y8L 
;Crystal structure of the A-DNA GCGTAT*CGC with a 2'-O-[2-(trifluoro)ethyl] Thymidine (T*)
;
unspecified 
PDB 1Y8V 
;Crystal structure of the A-DNA GCGTAT*CGC with a 2'-O-propyl Thymidine (T*)
;
unspecified 
PDB 1WV5 
;X-RAY STRUCTURE OF THE A-DECAMER GCGTATACGC WITH A SINGLE 2'-O-BUTYL  THYMINE IN PLACE OF T6, MG-FORM
;
unspecified 
PDB 1WV6 
;X-RAY STRUCTURE OF THE A-DECAMER GCGTATACGC WITH A SINGLE 2'-O-BUTYL  THYMINE IN PLACE OF T6, SR-FORM
;
unspecified 
PDB 1Y9F 
;Crystal structure of the A-DNA GCGTAT*CGC with a 2'-O-allyl Thymidine (T*)
;
unspecified 
PDB 1Y9S 
;Crystal structure of the A-DNA GCGTAT*CGC with a 2'-O-propargyl Thymidine (T*)
;
unspecified 
PDB 1YBC 
;Crystal structure of the A-DNA GCGTAT*CGC with a 2'-O-[2-(benzyloxy)ethyl] Thymidine (T*)
;
unspecified 
# 
_pdbx_database_status.status_code                     REL 
_pdbx_database_status.entry_id                        1YB9 
_pdbx_database_status.recvd_initial_deposition_date   2004-12-20 
_pdbx_database_status.deposit_site                    RCSB 
_pdbx_database_status.process_site                    RCSB 
_pdbx_database_status.status_code_sf                  REL 
_pdbx_database_status.status_code_mr                  ? 
_pdbx_database_status.SG_entry                        ? 
_pdbx_database_status.pdb_format_compatible           Y 
_pdbx_database_status.status_code_cs                  ? 
_pdbx_database_status.status_code_nmr_data            ? 
_pdbx_database_status.methods_development_category    ? 
# 
loop_
_audit_author.name 
_audit_author.pdbx_ordinal 
'Egli, M.'      1  
'Minasov, G.'   2  
'Tereshko, V.'  3  
'Pallan, P.S.'  4  
'Teplova, M.'   5  
'Inamati, G.B.' 6  
'Lesnik, E.A.'  7  
'Owens, S.R.'   8  
'Ross, B.S.'    9  
'Prakash, T.P.' 10 
'Manoharan, M.' 11 
# 
_citation.id                        primary 
_citation.title                     
;Probing the Influence of Stereoelectronic Effects on the Biophysical Properties of Oligonucleotides: Comprehensive Analysis of the RNA Affinity, Nuclease Resistance, and Crystal Structure of Ten 2'-O-Ribonucleic Acid Modifications.
;
_citation.journal_abbrev            Biochemistry 
_citation.journal_volume            44 
_citation.page_first                9045 
_citation.page_last                 9057 
_citation.year                      2005 
_citation.journal_id_ASTM           BICHAW 
_citation.country                   US 
_citation.journal_id_ISSN           0006-2960 
_citation.journal_id_CSD            0033 
_citation.book_publisher            ? 
_citation.pdbx_database_id_PubMed   15966728 
_citation.pdbx_database_id_DOI      10.1021/bi050574m 
# 
loop_
_citation_author.citation_id 
_citation_author.name 
_citation_author.ordinal 
_citation_author.identifier_ORCID 
primary 'Egli, M.'      1  ? 
primary 'Minasov, G.'   2  ? 
primary 'Tereshko, V.'  3  ? 
primary 'Pallan, P.S.'  4  ? 
primary 'Teplova, M.'   5  ? 
primary 'Inamati, G.B.' 6  ? 
primary 'Lesnik, E.A.'  7  ? 
primary 'Owens, S.R.'   8  ? 
primary 'Ross, B.S.'    9  ? 
primary 'Prakash, T.P.' 10 ? 
primary 'Manoharan, M.' 11 ? 
# 
_cell.entry_id           1YB9 
_cell.length_a           24.840 
_cell.length_b           44.640 
_cell.length_c           45.180 
_cell.angle_alpha        90.00 
_cell.angle_beta         90.00 
_cell.angle_gamma        90.00 
_cell.Z_PDB              8 
_cell.pdbx_unique_axis   ? 
# 
_symmetry.entry_id                         1YB9 
_symmetry.space_group_name_H-M             'P 21 21 21' 
_symmetry.pdbx_full_space_group_name_H-M   ? 
_symmetry.cell_setting                     ? 
_symmetry.Int_Tables_number                19 
_symmetry.space_group_name_Hall            ? 
# 
loop_
_entity.id 
_entity.type 
_entity.src_method 
_entity.pdbx_description 
_entity.formula_weight 
_entity.pdbx_number_of_molecules 
_entity.pdbx_ec 
_entity.pdbx_mutation 
_entity.pdbx_fragment 
_entity.details 
1 polymer     syn "5'-D(*GP*CP*GP*TP*AP*(2OT)P*AP*CP*GP*C)-3')" 3148.125 2   ? ? ? ? 
2 non-polymer syn SPERMINE                                      202.340  1   ? ? ? ? 
3 water       nat water                                         18.015   124 ? ? ? ? 
# 
_entity_poly.entity_id                      1 
_entity_poly.type                           polydeoxyribonucleotide 
_entity_poly.nstd_linkage                   no 
_entity_poly.nstd_monomer                   yes 
_entity_poly.pdbx_seq_one_letter_code       '(DG)(DC)(DG)(DT)(DA)(2OT)(DA)(DC)(DG)(DC)' 
_entity_poly.pdbx_seq_one_letter_code_can   GCGTATACGC 
_entity_poly.pdbx_strand_id                 A,B 
_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  DG  n 
1 2  DC  n 
1 3  DG  n 
1 4  DT  n 
1 5  DA  n 
1 6  2OT n 
1 7  DA  n 
1 8  DC  n 
1 9  DG  n 
1 10 DC  n 
# 
_struct_ref.id                         1 
_struct_ref.entity_id                  1 
_struct_ref.db_name                    PDB 
_struct_ref.db_code                    1YB9 
_struct_ref.pdbx_db_accession          1YB9 
_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 1YB9 A 1 ? 10 ? 1YB9 1  ? 10 ? 1  10 
2 1 1YB9 B 1 ? 10 ? 1YB9 11 ? 20 ? 11 20 
# 
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 
2OT 'RNA linking' n 
;2'-O-[2-(N,N-DIMETHYLAMINOOXY)ETHYL] THYMIDINE-5'-MONOPHOSPHATE
;
? 'C14 H24 N3 O10 P' 425.328 
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 
DG  'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE"                              ? 'C10 H14 N5 O7 P'  347.221 
DT  'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE"                                      ? 'C10 H15 N2 O8 P'  322.208 
HOH non-polymer   . WATER                                                             ? 'H2 O'             18.015  
SPM non-polymer   . SPERMINE                                                          ? 'C10 H26 N4'       202.340 
# 
_exptl.entry_id          1YB9 
_exptl.method            'X-RAY DIFFRACTION' 
_exptl.crystals_number   1 
# 
_exptl_crystal.id                    1 
_exptl_crystal.density_meas          ? 
_exptl_crystal.density_Matthews      1.99 
_exptl_crystal.density_percent_sol   38.17 
_exptl_crystal.description           ? 
_exptl_crystal.F_000                 ? 
_exptl_crystal.preparation           ? 
# 
_exptl_crystal_grow.crystal_id      1 
_exptl_crystal_grow.method          'VAPOR DIFFUSION, HANGING DROP' 
_exptl_crystal_grow.temp            295 
_exptl_crystal_grow.temp_details    ? 
_exptl_crystal_grow.pH              6.0 
_exptl_crystal_grow.pdbx_details    
'10%MPD, 40mM Na-Cacodilate, 12 mM Spermine, 80mM NaCL, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K' 
_exptl_crystal_grow.pdbx_pH_range   . 
# 
loop_
_exptl_crystal_grow_comp.crystal_id 
_exptl_crystal_grow_comp.id 
_exptl_crystal_grow_comp.sol_id 
_exptl_crystal_grow_comp.name 
_exptl_crystal_grow_comp.volume 
_exptl_crystal_grow_comp.conc 
_exptl_crystal_grow_comp.details 
1 1 1 MPD           ? ? ? 
1 2 1 Na-Cacodilate ? ? ? 
1 3 1 Spermine      ? ? ? 
1 4 1 NaCL          ? ? ? 
1 5 1 H2O           ? ? ? 
1 6 2 MPD           ? ? ? 
1 7 2 Na-Cacodilate ? ? ? 
1 8 2 NaCL          ? ? ? 
# 
_diffrn.id                     1 
_diffrn.ambient_temp           110 
_diffrn.ambient_temp_details   ? 
_diffrn.crystal_id             1 
# 
_diffrn_detector.diffrn_id              1 
_diffrn_detector.detector               'IMAGE PLATE' 
_diffrn_detector.type                   'RIGAKU RAXIS IIC' 
_diffrn_detector.pdbx_collection_date   1999-08-03 
_diffrn_detector.details                Mirrors 
# 
_diffrn_radiation.diffrn_id                        1 
_diffrn_radiation.wavelength_id                    1 
_diffrn_radiation.pdbx_monochromatic_or_laue_m_l   M 
_diffrn_radiation.monochromator                    ? 
_diffrn_radiation.pdbx_diffrn_protocol             'SINGLE WAVELENGTH' 
_diffrn_radiation.pdbx_scattering_type             x-ray 
# 
_diffrn_radiation_wavelength.id           1 
_diffrn_radiation_wavelength.wavelength   1.5418 
_diffrn_radiation_wavelength.wt           1.0 
# 
_diffrn_source.diffrn_id                   1 
_diffrn_source.source                      'ROTATING ANODE' 
_diffrn_source.type                        'RIGAKU RU200' 
_diffrn_source.pdbx_synchrotron_site       ? 
_diffrn_source.pdbx_synchrotron_beamline   ? 
_diffrn_source.pdbx_wavelength             1.5418 
_diffrn_source.pdbx_wavelength_list        ? 
# 
_reflns.entry_id                     1YB9 
_reflns.observed_criterion_sigma_F   ? 
_reflns.observed_criterion_sigma_I   -3.0 
_reflns.d_resolution_high            1.65 
_reflns.d_resolution_low             20.0 
_reflns.number_all                   6146 
_reflns.number_obs                   6146 
_reflns.percent_possible_obs         95.4 
_reflns.pdbx_Rmerge_I_obs            0.102 
_reflns.pdbx_Rsym_value              ? 
_reflns.pdbx_netI_over_sigmaI        17.4 
_reflns.B_iso_Wilson_estimate        ? 
_reflns.pdbx_redundancy              6.5 
_reflns.R_free_details               ? 
_reflns.pdbx_chi_squared             ? 
_reflns.pdbx_scaling_rejects         ? 
_reflns.pdbx_diffrn_id               1 
_reflns.pdbx_ordinal                 1 
# 
_reflns_shell.d_res_high             1.65 
_reflns_shell.d_res_low              1.71 
_reflns_shell.percent_possible_all   70.7 
_reflns_shell.Rmerge_I_obs           0.175 
_reflns_shell.pdbx_Rsym_value        ? 
_reflns_shell.meanI_over_sigI_obs    6.1 
_reflns_shell.pdbx_redundancy        2.7 
_reflns_shell.percent_possible_obs   ? 
_reflns_shell.number_unique_all      442 
_reflns_shell.number_measured_all    ? 
_reflns_shell.number_measured_obs    ? 
_reflns_shell.number_unique_obs      ? 
_reflns_shell.pdbx_chi_squared       ? 
_reflns_shell.pdbx_diffrn_id         ? 
_reflns_shell.pdbx_ordinal           1 
# 
_refine.entry_id                                 1YB9 
_refine.ls_d_res_high                            1.65 
_refine.ls_d_res_low                             20.0 
_refine.pdbx_ls_sigma_F                          0.0 
_refine.pdbx_ls_sigma_I                          ? 
_refine.ls_number_reflns_all                     6099 
_refine.ls_number_reflns_obs                     6099 
_refine.ls_number_reflns_R_free                  672 
_refine.ls_percent_reflns_obs                    94.9 
_refine.ls_R_factor_all                          ? 
_refine.ls_R_factor_obs                          ? 
_refine.ls_R_factor_R_work                       0.1632 
_refine.ls_R_factor_R_free                       0.1906 
_refine.ls_redundancy_reflns_obs                 ? 
_refine.pdbx_data_cutoff_high_absF               ? 
_refine.pdbx_data_cutoff_low_absF                ? 
_refine.ls_number_parameters                     ? 
_refine.ls_number_restraints                     ? 
_refine.ls_percent_reflns_R_free                 ? 
_refine.ls_R_factor_R_free_error                 ? 
_refine.ls_R_factor_R_free_error_details         ? 
_refine.pdbx_method_to_determine_struct          'MOLECULAR REPLACEMENT' 
_refine.pdbx_starting_model                      'pdb entry 410D' 
_refine.pdbx_ls_cross_valid_method               THROUGHOUT 
_refine.pdbx_R_Free_selection_details            Random 
_refine.pdbx_stereochem_target_val_spec_case     ? 
_refine.pdbx_stereochemistry_target_values       ? 
_refine.solvent_model_details                    ? 
_refine.solvent_model_param_bsol                 ? 
_refine.solvent_model_param_ksol                 ? 
_refine.occupancy_max                            ? 
_refine.occupancy_min                            ? 
_refine.pdbx_isotropic_thermal_model             Isotropic 
_refine.B_iso_mean                               19.0 
_refine.aniso_B[1][1]                            -0.559 
_refine.aniso_B[1][2]                            0.000 
_refine.aniso_B[1][3]                            0.000 
_refine.aniso_B[2][2]                            1.014 
_refine.aniso_B[2][3]                            0.000 
_refine.aniso_B[3][3]                            -0.456 
_refine.details                                  'Conjugate gradient refinement using maximum likelihood target for amplitudes' 
_refine.correlation_coeff_Fo_to_Fc               ? 
_refine.correlation_coeff_Fo_to_Fc_free          ? 
_refine.pdbx_solvent_vdw_probe_radii             ? 
_refine.pdbx_solvent_ion_probe_radii             ? 
_refine.pdbx_solvent_shrinkage_radii             ? 
_refine.overall_SU_R_Cruickshank_DPI             ? 
_refine.overall_SU_R_free                        ? 
_refine.overall_SU_B                             ? 
_refine.overall_SU_ML                            ? 
_refine.pdbx_overall_ESU_R                       ? 
_refine.pdbx_overall_ESU_R_Free                  ? 
_refine.pdbx_data_cutoff_high_rms_absF           ? 
_refine.ls_wR_factor_R_free                      ? 
_refine.ls_wR_factor_R_work                      ? 
_refine.overall_FOM_free_R_set                   ? 
_refine.overall_FOM_work_R_set                   ? 
_refine.pdbx_refine_id                           'X-RAY DIFFRACTION' 
_refine.pdbx_diffrn_id                           1 
_refine.pdbx_TLS_residual_ADP_flag               ? 
_refine.pdbx_overall_phase_error                 ? 
_refine.pdbx_overall_SU_R_free_Cruickshank_DPI   ? 
_refine.pdbx_overall_SU_R_Blow_DPI               ? 
_refine.pdbx_overall_SU_R_free_Blow_DPI          ? 
# 
_refine_analyze.entry_id                        1YB9 
_refine_analyze.Luzzati_coordinate_error_obs    0.16 
_refine_analyze.Luzzati_sigma_a_obs             0.04 
_refine_analyze.Luzzati_d_res_low_obs           5.0 
_refine_analyze.Luzzati_coordinate_error_free   0.19 
_refine_analyze.Luzzati_sigma_a_free            0.09 
_refine_analyze.Luzzati_d_res_low_free          ? 
_refine_analyze.number_disordered_residues      ? 
_refine_analyze.occupancy_sum_non_hydrogen      ? 
_refine_analyze.occupancy_sum_hydrogen          ? 
_refine_analyze.pdbx_refine_id                  'X-RAY DIFFRACTION' 
# 
_refine_hist.pdbx_refine_id                   'X-RAY DIFFRACTION' 
_refine_hist.cycle_id                         LAST 
_refine_hist.pdbx_number_atoms_protein        0 
_refine_hist.pdbx_number_atoms_nucleic_acid   418 
_refine_hist.pdbx_number_atoms_ligand         18 
_refine_hist.number_atoms_solvent             131 
_refine_hist.number_atoms_total               567 
_refine_hist.d_res_high                       1.65 
_refine_hist.d_res_low                        20.0 
# 
loop_
_refine_ls_restr.type 
_refine_ls_restr.dev_ideal 
_refine_ls_restr.dev_ideal_target 
_refine_ls_restr.weight 
_refine_ls_restr.number 
_refine_ls_restr.pdbx_refine_id 
_refine_ls_restr.pdbx_restraint_function 
c_bond_d           0.008 ? ? ? 'X-RAY DIFFRACTION' ? 
c_angle_deg        1.20  ? ? ? 'X-RAY DIFFRACTION' ? 
c_dihedral_angle_d 26.8  ? ? ? 'X-RAY DIFFRACTION' ? 
c_improper_angle_d 1.53  ? ? ? 'X-RAY DIFFRACTION' ? 
# 
_refine_ls_shell.pdbx_total_number_of_bins_used   ? 
_refine_ls_shell.d_res_high                       1.65 
_refine_ls_shell.d_res_low                        1.71 
_refine_ls_shell.number_reflns_R_work             ? 
_refine_ls_shell.R_factor_R_work                  0.2042 
_refine_ls_shell.percent_reflns_obs               67.46 
_refine_ls_shell.R_factor_R_free                  0.2389 
_refine_ls_shell.R_factor_R_free_error            ? 
_refine_ls_shell.percent_reflns_R_free            ? 
_refine_ls_shell.number_reflns_R_free             55 
_refine_ls_shell.redundancy_reflns_obs            ? 
_refine_ls_shell.pdbx_refine_id                   'X-RAY DIFFRACTION' 
_refine_ls_shell.number_reflns_all                ? 
_refine_ls_shell.R_factor_all                     ? 
# 
_struct.entry_id                  1YB9 
_struct.title                     
;Crystal structure of the A-DNA GCGTAT*CGC with a 2'-O-[2-(N,N-dimethylaminooxy)ethyl] Thymidine (T*)
;
_struct.pdbx_model_details        ? 
_struct.pdbx_CASP_flag            ? 
_struct.pdbx_model_type_details   ? 
# 
_struct_keywords.entry_id        1YB9 
_struct_keywords.pdbx_keywords   DNA 
_struct_keywords.text            
;A-DNA, O2'-modification, decamer, 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 2 ? 
D N N 3 ? 
E N N 3 ? 
# 
_struct_biol.id                    1 
_struct_biol.details               'Chains A and B form duplex' 
_struct_biol.pdbx_parent_biol_id   ? 
# 
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 
covale1  covale both ? A DA  5  "O3'" ? ? ? 1_555 A 2OT 6  P  ? ? A DA  5  A 2OT 6  1_555 ? ? ? ? ? ? ?            1.600 ? ? 
covale2  covale both ? A 2OT 6  "O3'" ? ? ? 1_555 A DA  7  P  ? ? A 2OT 6  A DA  7  1_555 ? ? ? ? ? ? ?            1.613 ? ? 
covale3  covale both ? B DA  5  "O3'" ? ? ? 1_555 B 2OT 6  P  ? ? B DA  15 B 2OT 16 1_555 ? ? ? ? ? ? ?            1.604 ? ? 
covale4  covale both ? B 2OT 6  "O3'" ? ? ? 1_555 B DA  7  P  ? ? B 2OT 16 B DA  17 1_555 ? ? ? ? ? ? ?            1.603 ? ? 
hydrog1  hydrog ?    ? A DG  1  N1    ? ? ? 1_555 B DC  10 N3 ? ? A DG  1  B DC  20 1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog2  hydrog ?    ? A DG  1  N2    ? ? ? 1_555 B DC  10 O2 ? ? A DG  1  B DC  20 1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog3  hydrog ?    ? A DG  1  O6    ? ? ? 1_555 B DC  10 N4 ? ? A DG  1  B DC  20 1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog4  hydrog ?    ? A DC  2  N3    ? ? ? 1_555 B DG  9  N1 ? ? A DC  2  B DG  19 1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog5  hydrog ?    ? A DC  2  N4    ? ? ? 1_555 B DG  9  O6 ? ? A DC  2  B DG  19 1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog6  hydrog ?    ? A DC  2  O2    ? ? ? 1_555 B DG  9  N2 ? ? A DC  2  B DG  19 1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog7  hydrog ?    ? A DG  3  N1    ? ? ? 1_555 B DC  8  N3 ? ? A DG  3  B DC  18 1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog8  hydrog ?    ? A DG  3  N2    ? ? ? 1_555 B DC  8  O2 ? ? A DG  3  B DC  18 1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog9  hydrog ?    ? A DG  3  O6    ? ? ? 1_555 B DC  8  N4 ? ? A DG  3  B DC  18 1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog10 hydrog ?    ? A DT  4  N3    ? ? ? 1_555 B DA  7  N1 ? ? A DT  4  B DA  17 1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog11 hydrog ?    ? A DT  4  O4    ? ? ? 1_555 B DA  7  N6 ? ? A DT  4  B DA  17 1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog12 hydrog ?    ? A DA  5  N1    ? ? ? 1_555 B 2OT 6  N3 ? ? A DA  5  B 2OT 16 1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog13 hydrog ?    ? A DA  5  N6    ? ? ? 1_555 B 2OT 6  O4 ? ? A DA  5  B 2OT 16 1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog14 hydrog ?    ? A 2OT 6  N3    ? ? ? 1_555 B DA  5  N1 ? ? A 2OT 6  B DA  15 1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog15 hydrog ?    ? A 2OT 6  O4    ? ? ? 1_555 B DA  5  N6 ? ? A 2OT 6  B DA  15 1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog16 hydrog ?    ? A DA  7  N1    ? ? ? 1_555 B DT  4  N3 ? ? A DA  7  B DT  14 1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog17 hydrog ?    ? A DA  7  N6    ? ? ? 1_555 B DT  4  O4 ? ? A DA  7  B DT  14 1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog18 hydrog ?    ? A DC  8  N3    ? ? ? 1_555 B DG  3  N1 ? ? A DC  8  B DG  13 1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog19 hydrog ?    ? A DC  8  N4    ? ? ? 1_555 B DG  3  O6 ? ? A DC  8  B DG  13 1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog20 hydrog ?    ? A DC  8  O2    ? ? ? 1_555 B DG  3  N2 ? ? A DC  8  B DG  13 1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog21 hydrog ?    ? A DG  9  N1    ? ? ? 1_555 B DC  2  N3 ? ? A DG  9  B DC  12 1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog22 hydrog ?    ? A DG  9  N2    ? ? ? 1_555 B DC  2  O2 ? ? A DG  9  B DC  12 1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog23 hydrog ?    ? A DG  9  O6    ? ? ? 1_555 B DC  2  N4 ? ? A DG  9  B DC  12 1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog24 hydrog ?    ? A DC  10 N3    ? ? ? 1_555 B DG  1  N1 ? ? A DC  10 B DG  11 1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog25 hydrog ?    ? A DC  10 N4    ? ? ? 1_555 B DG  1  O6 ? ? A DC  10 B DG  11 1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog26 hydrog ?    ? A DC  10 O2    ? ? ? 1_555 B DG  1  N2 ? ? A DC  10 B DG  11 1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
# 
loop_
_struct_conn_type.id 
_struct_conn_type.criteria 
_struct_conn_type.reference 
covale ? ? 
hydrog ? ? 
# 
_struct_site.id                   AC1 
_struct_site.pdbx_evidence_code   Software 
_struct_site.pdbx_auth_asym_id    B 
_struct_site.pdbx_auth_comp_id    SPM 
_struct_site.pdbx_auth_seq_id     100 
_struct_site.pdbx_auth_ins_code   ? 
_struct_site.pdbx_num_residues    14 
_struct_site.details              'BINDING SITE FOR RESIDUE SPM B 100' 
# 
loop_
_struct_site_gen.id 
_struct_site_gen.site_id 
_struct_site_gen.pdbx_num_res 
_struct_site_gen.label_comp_id 
_struct_site_gen.label_asym_id 
_struct_site_gen.label_seq_id 
_struct_site_gen.pdbx_auth_ins_code 
_struct_site_gen.auth_comp_id 
_struct_site_gen.auth_asym_id 
_struct_site_gen.auth_seq_id 
_struct_site_gen.label_atom_id 
_struct_site_gen.label_alt_id 
_struct_site_gen.symmetry 
_struct_site_gen.details 
1  AC1 14 DG  A 9  ? DG  A 9   . ? 2_555 ? 
2  AC1 14 DC  A 10 ? DC  A 10  . ? 2_555 ? 
3  AC1 14 HOH D .  ? HOH A 139 . ? 1_655 ? 
4  AC1 14 HOH D .  ? HOH A 160 . ? 2_555 ? 
5  AC1 14 HOH D .  ? HOH A 167 . ? 4_556 ? 
6  AC1 14 DT  B 4  ? DT  B 14  . ? 3_655 ? 
7  AC1 14 DA  B 5  ? DA  B 15  . ? 3_655 ? 
8  AC1 14 DG  B 9  ? DG  B 19  . ? 1_555 ? 
9  AC1 14 DC  B 10 ? DC  B 20  . ? 1_555 ? 
10 AC1 14 HOH E .  ? HOH B 124 . ? 3_655 ? 
11 AC1 14 HOH E .  ? HOH B 140 . ? 1_555 ? 
12 AC1 14 HOH E .  ? HOH B 166 . ? 1_555 ? 
13 AC1 14 HOH E .  ? HOH B 187 . ? 1_555 ? 
14 AC1 14 HOH E .  ? HOH B 200 . ? 1_555 ? 
# 
_database_PDB_matrix.entry_id          1YB9 
_database_PDB_matrix.origx[1][1]       1.000000 
_database_PDB_matrix.origx[1][2]       0.000000 
_database_PDB_matrix.origx[1][3]       0.000000 
_database_PDB_matrix.origx[2][1]       0.000000 
_database_PDB_matrix.origx[2][2]       1.000000 
_database_PDB_matrix.origx[2][3]       0.000000 
_database_PDB_matrix.origx[3][1]       0.000000 
_database_PDB_matrix.origx[3][2]       0.000000 
_database_PDB_matrix.origx[3][3]       1.000000 
_database_PDB_matrix.origx_vector[1]   0.00000 
_database_PDB_matrix.origx_vector[2]   0.00000 
_database_PDB_matrix.origx_vector[3]   0.00000 
# 
_atom_sites.entry_id                    1YB9 
_atom_sites.fract_transf_matrix[1][1]   0.040258 
_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]   0.022401 
_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]   0.022134 
_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 
N 
O 
P 
# 
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  DG  1  1  1  DG  G   A . n 
A 1 2  DC  2  2  2  DC  C   A . n 
A 1 3  DG  3  3  3  DG  G   A . n 
A 1 4  DT  4  4  4  DT  T   A . n 
A 1 5  DA  5  5  5  DA  A   A . n 
A 1 6  2OT 6  6  6  2OT DMA A . n 
A 1 7  DA  7  7  7  DA  A   A . n 
A 1 8  DC  8  8  8  DC  C   A . n 
A 1 9  DG  9  9  9  DG  G   A . n 
A 1 10 DC  10 10 10 DC  C   A . n 
B 1 1  DG  1  11 11 DG  G   B . n 
B 1 2  DC  2  12 12 DC  C   B . n 
B 1 3  DG  3  13 13 DG  G   B . n 
B 1 4  DT  4  14 14 DT  T   B . n 
B 1 5  DA  5  15 15 DA  A   B . n 
B 1 6  2OT 6  16 16 2OT DMA B . n 
B 1 7  DA  7  17 17 DA  A   B . n 
B 1 8  DC  8  18 18 DC  C   B . n 
B 1 9  DG  9  19 19 DG  G   B . n 
B 1 10 DC  10 20 20 DC  C   B . n 
# 
loop_
_pdbx_nonpoly_scheme.asym_id 
_pdbx_nonpoly_scheme.entity_id 
_pdbx_nonpoly_scheme.mon_id 
_pdbx_nonpoly_scheme.ndb_seq_num 
_pdbx_nonpoly_scheme.pdb_seq_num 
_pdbx_nonpoly_scheme.auth_seq_num 
_pdbx_nonpoly_scheme.pdb_mon_id 
_pdbx_nonpoly_scheme.auth_mon_id 
_pdbx_nonpoly_scheme.pdb_strand_id 
_pdbx_nonpoly_scheme.pdb_ins_code 
C 2 SPM 1  100 100 SPM SPM B . 
D 3 HOH 1  101 101 HOH HOH A . 
D 3 HOH 2  102 102 HOH HOH A . 
D 3 HOH 3  104 104 HOH HOH A . 
D 3 HOH 4  107 107 HOH HOH A . 
D 3 HOH 5  109 109 HOH HOH A . 
D 3 HOH 6  110 110 HOH HOH A . 
D 3 HOH 7  111 111 HOH HOH A . 
D 3 HOH 8  116 116 HOH HOH A . 
D 3 HOH 9  117 117 HOH HOH A . 
D 3 HOH 10 118 118 HOH HOH A . 
D 3 HOH 11 119 119 HOH HOH A . 
D 3 HOH 12 121 121 HOH HOH A . 
D 3 HOH 13 123 123 HOH HOH A . 
D 3 HOH 14 125 125 HOH HOH A . 
D 3 HOH 15 128 128 HOH HOH A . 
D 3 HOH 16 132 132 HOH HOH A . 
D 3 HOH 17 133 133 HOH HOH A . 
D 3 HOH 18 134 134 HOH HOH A . 
D 3 HOH 19 135 135 HOH HOH A . 
D 3 HOH 20 136 136 HOH HOH A . 
D 3 HOH 21 137 137 HOH HOH A . 
D 3 HOH 22 139 139 HOH HOH A . 
D 3 HOH 23 141 141 HOH HOH A . 
D 3 HOH 24 142 142 HOH HOH A . 
D 3 HOH 25 145 145 HOH HOH A . 
D 3 HOH 26 146 146 HOH HOH A . 
D 3 HOH 27 147 147 HOH HOH A . 
D 3 HOH 28 149 149 HOH HOH A . 
D 3 HOH 29 151 151 HOH HOH A . 
D 3 HOH 30 152 152 HOH HOH A . 
D 3 HOH 31 157 157 HOH HOH A . 
D 3 HOH 32 158 158 HOH HOH A . 
D 3 HOH 33 160 160 HOH HOH A . 
D 3 HOH 34 164 164 HOH HOH A . 
D 3 HOH 35 167 167 HOH HOH A . 
D 3 HOH 36 168 168 HOH HOH A . 
D 3 HOH 37 172 172 HOH HOH A . 
D 3 HOH 38 173 173 HOH HOH A . 
D 3 HOH 39 174 174 HOH HOH A . 
D 3 HOH 40 176 176 HOH HOH A . 
D 3 HOH 41 177 177 HOH HOH A . 
D 3 HOH 42 178 178 HOH HOH A . 
D 3 HOH 43 180 180 HOH HOH A . 
D 3 HOH 44 183 183 HOH HOH A . 
D 3 HOH 45 185 185 HOH HOH A . 
D 3 HOH 46 186 186 HOH HOH A . 
D 3 HOH 47 189 189 HOH HOH A . 
D 3 HOH 48 190 190 HOH HOH A . 
D 3 HOH 49 194 194 HOH HOH A . 
D 3 HOH 50 196 196 HOH HOH A . 
D 3 HOH 51 197 197 HOH HOH A . 
D 3 HOH 52 198 198 HOH HOH A . 
D 3 HOH 53 201 201 HOH HOH A . 
D 3 HOH 54 204 204 HOH HOH A . 
D 3 HOH 55 205 205 HOH HOH A . 
D 3 HOH 56 207 207 HOH HOH A . 
D 3 HOH 57 208 208 HOH HOH A . 
D 3 HOH 58 209 209 HOH HOH A . 
D 3 HOH 59 211 211 HOH HOH A . 
D 3 HOH 60 212 212 HOH HOH A . 
D 3 HOH 61 215 215 HOH HOH A . 
D 3 HOH 62 216 216 HOH HOH A . 
D 3 HOH 63 217 217 HOH HOH A . 
D 3 HOH 64 218 218 HOH HOH A . 
D 3 HOH 65 221 221 HOH HOH A . 
D 3 HOH 66 223 223 HOH HOH A . 
D 3 HOH 67 224 224 HOH HOH A . 
E 3 HOH 1  103 103 HOH HOH B . 
E 3 HOH 2  105 105 HOH HOH B . 
E 3 HOH 3  106 106 HOH HOH B . 
E 3 HOH 4  108 108 HOH HOH B . 
E 3 HOH 5  112 112 HOH HOH B . 
E 3 HOH 6  113 113 HOH HOH B . 
E 3 HOH 7  114 114 HOH HOH B . 
E 3 HOH 8  115 115 HOH HOH B . 
E 3 HOH 9  120 120 HOH HOH B . 
E 3 HOH 10 122 122 HOH HOH B . 
E 3 HOH 11 124 124 HOH HOH B . 
E 3 HOH 12 126 126 HOH HOH B . 
E 3 HOH 13 127 127 HOH HOH B . 
E 3 HOH 14 129 129 HOH HOH B . 
E 3 HOH 15 130 130 HOH HOH B . 
E 3 HOH 16 131 131 HOH HOH B . 
E 3 HOH 17 138 138 HOH HOH B . 
E 3 HOH 18 140 140 HOH HOH B . 
E 3 HOH 19 143 143 HOH HOH B . 
E 3 HOH 20 144 144 HOH HOH B . 
E 3 HOH 21 148 148 HOH HOH B . 
E 3 HOH 22 150 150 HOH HOH B . 
E 3 HOH 23 153 153 HOH HOH B . 
E 3 HOH 24 154 154 HOH HOH B . 
E 3 HOH 25 155 155 HOH HOH B . 
E 3 HOH 26 156 156 HOH HOH B . 
E 3 HOH 27 159 159 HOH HOH B . 
E 3 HOH 28 161 161 HOH HOH B . 
E 3 HOH 29 162 162 HOH HOH B . 
E 3 HOH 30 163 163 HOH HOH B . 
E 3 HOH 31 165 165 HOH HOH B . 
E 3 HOH 32 166 166 HOH HOH B . 
E 3 HOH 33 169 169 HOH HOH B . 
E 3 HOH 34 170 170 HOH HOH B . 
E 3 HOH 35 171 171 HOH HOH B . 
E 3 HOH 36 175 175 HOH HOH B . 
E 3 HOH 37 179 179 HOH HOH B . 
E 3 HOH 38 181 181 HOH HOH B . 
E 3 HOH 39 182 182 HOH HOH B . 
E 3 HOH 40 184 184 HOH HOH B . 
E 3 HOH 41 187 187 HOH HOH B . 
E 3 HOH 42 188 188 HOH HOH B . 
E 3 HOH 43 191 191 HOH HOH B . 
E 3 HOH 44 192 192 HOH HOH B . 
E 3 HOH 45 193 193 HOH HOH B . 
E 3 HOH 46 195 195 HOH HOH B . 
E 3 HOH 47 199 199 HOH HOH B . 
E 3 HOH 48 200 200 HOH HOH B . 
E 3 HOH 49 202 202 HOH HOH B . 
E 3 HOH 50 203 203 HOH HOH B . 
E 3 HOH 51 206 206 HOH HOH B . 
E 3 HOH 52 210 210 HOH HOH B . 
E 3 HOH 53 213 213 HOH HOH B . 
E 3 HOH 54 214 214 HOH HOH B . 
E 3 HOH 55 219 219 HOH HOH B . 
E 3 HOH 56 220 220 HOH HOH B . 
E 3 HOH 57 222 222 HOH HOH B . 
# 
loop_
_pdbx_struct_mod_residue.id 
_pdbx_struct_mod_residue.label_asym_id 
_pdbx_struct_mod_residue.label_comp_id 
_pdbx_struct_mod_residue.label_seq_id 
_pdbx_struct_mod_residue.auth_asym_id 
_pdbx_struct_mod_residue.auth_comp_id 
_pdbx_struct_mod_residue.auth_seq_id 
_pdbx_struct_mod_residue.PDB_ins_code 
_pdbx_struct_mod_residue.parent_comp_id 
_pdbx_struct_mod_residue.details 
1 A 2OT 6 A 2OT 6  ? DT ? 
2 B 2OT 6 B 2OT 16 ? DT ? 
# 
_pdbx_struct_assembly.id                   1 
_pdbx_struct_assembly.details              author_defined_assembly 
_pdbx_struct_assembly.method_details       ? 
_pdbx_struct_assembly.oligomeric_details   dimeric 
_pdbx_struct_assembly.oligomeric_count     2 
# 
_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,E 
# 
_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   x,y,z 
_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_
_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 2005-06-28 
2 'Structure model' 1 1 2008-04-30 
3 'Structure model' 1 2 2011-07-13 
4 'Structure model' 1 3 2023-08-23 
# 
_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' 'Database references'       
5 4 'Structure model' 'Derived calculations'      
6 4 'Structure model' 'Refinement description'    
# 
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' chem_comp_atom                
2 4 'Structure model' chem_comp_bond                
3 4 'Structure model' database_2                    
4 4 'Structure model' pdbx_initial_refinement_model 
5 4 'Structure model' struct_conn                   
6 4 'Structure model' struct_site                   
# 
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' '_database_2.pdbx_DOI'                
2 4 'Structure model' '_database_2.pdbx_database_accession' 
3 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 
4 4 'Structure model' '_struct_site.pdbx_auth_asym_id'      
5 4 'Structure model' '_struct_site.pdbx_auth_comp_id'      
6 4 'Structure model' '_struct_site.pdbx_auth_seq_id'       
# 
loop_
_software.name 
_software.classification 
_software.version 
_software.citation_id 
_software.pdbx_ordinal 
DENZO     'data reduction' . ? 1 
SCALEPACK 'data scaling'   . ? 2 
AMoRE     phasing          . ? 3 
CNS       refinement       . ? 4 
# 
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 
2OT P      P N N 1   
2OT OP1    O N N 2   
2OT OP2    O N N 3   
2OT "O5'"  O N N 4   
2OT "C5'"  C N N 5   
2OT "C4'"  C N R 6   
2OT "O4'"  O N N 7   
2OT "C1'"  C N R 8   
2OT N1     N N N 9   
2OT C6     C N N 10  
2OT C2     C N N 11  
2OT O2     O N N 12  
2OT N3     N N N 13  
2OT C4     C N N 14  
2OT O4     O N N 15  
2OT C5     C N N 16  
2OT C5M    C N N 17  
2OT "C2'"  C N R 18  
2OT "O2'"  O N N 19  
2OT "CB'"  C N N 20  
2OT "CC'"  C N N 21  
2OT "OD'"  O N N 22  
2OT "NE'"  N N N 23  
2OT "CF'"  C N N 24  
2OT "CG'"  C N N 25  
2OT "C3'"  C N R 26  
2OT "O3'"  O N N 27  
2OT OP3    O N N 28  
2OT HOP2   H N N 29  
2OT "H5'"  H N N 30  
2OT "H5''" H N N 31  
2OT "H4'"  H N N 32  
2OT "H1'"  H N N 33  
2OT H6     H N N 34  
2OT HN3    H N N 35  
2OT H71    H N N 36  
2OT H72    H N N 37  
2OT H73    H N N 38  
2OT "H2'"  H N N 39  
2OT "HB'1" H N N 40  
2OT "HB'2" H N N 41  
2OT "HC'1" H N N 42  
2OT "HC'2" H N N 43  
2OT "HF'1" H N N 44  
2OT "HF'2" H N N 45  
2OT "HF'3" H N N 46  
2OT "HG'1" H N N 47  
2OT "HG'2" H N N 48  
2OT "HG'3" H N N 49  
2OT "H3'"  H N N 50  
2OT "HO3'" H N N 51  
2OT HOP3   H N N 52  
DA  OP3    O N N 53  
DA  P      P N N 54  
DA  OP1    O N N 55  
DA  OP2    O N N 56  
DA  "O5'"  O N N 57  
DA  "C5'"  C N N 58  
DA  "C4'"  C N R 59  
DA  "O4'"  O N N 60  
DA  "C3'"  C N S 61  
DA  "O3'"  O N N 62  
DA  "C2'"  C N N 63  
DA  "C1'"  C N R 64  
DA  N9     N Y N 65  
DA  C8     C Y N 66  
DA  N7     N Y N 67  
DA  C5     C Y N 68  
DA  C6     C Y N 69  
DA  N6     N N N 70  
DA  N1     N Y N 71  
DA  C2     C Y N 72  
DA  N3     N Y N 73  
DA  C4     C Y N 74  
DA  HOP3   H N N 75  
DA  HOP2   H N N 76  
DA  "H5'"  H N N 77  
DA  "H5''" H N N 78  
DA  "H4'"  H N N 79  
DA  "H3'"  H N N 80  
DA  "HO3'" H N N 81  
DA  "H2'"  H N N 82  
DA  "H2''" H N N 83  
DA  "H1'"  H N N 84  
DA  H8     H N N 85  
DA  H61    H N N 86  
DA  H62    H N N 87  
DA  H2     H N N 88  
DC  OP3    O N N 89  
DC  P      P N N 90  
DC  OP1    O N N 91  
DC  OP2    O N N 92  
DC  "O5'"  O N N 93  
DC  "C5'"  C N N 94  
DC  "C4'"  C N R 95  
DC  "O4'"  O N N 96  
DC  "C3'"  C N S 97  
DC  "O3'"  O N N 98  
DC  "C2'"  C N N 99  
DC  "C1'"  C N R 100 
DC  N1     N N N 101 
DC  C2     C N N 102 
DC  O2     O N N 103 
DC  N3     N N N 104 
DC  C4     C N N 105 
DC  N4     N N N 106 
DC  C5     C N N 107 
DC  C6     C N N 108 
DC  HOP3   H N N 109 
DC  HOP2   H N N 110 
DC  "H5'"  H N N 111 
DC  "H5''" H N N 112 
DC  "H4'"  H N N 113 
DC  "H3'"  H N N 114 
DC  "HO3'" H N N 115 
DC  "H2'"  H N N 116 
DC  "H2''" H N N 117 
DC  "H1'"  H N N 118 
DC  H41    H N N 119 
DC  H42    H N N 120 
DC  H5     H N N 121 
DC  H6     H N N 122 
DG  OP3    O N N 123 
DG  P      P N N 124 
DG  OP1    O N N 125 
DG  OP2    O N N 126 
DG  "O5'"  O N N 127 
DG  "C5'"  C N N 128 
DG  "C4'"  C N R 129 
DG  "O4'"  O N N 130 
DG  "C3'"  C N S 131 
DG  "O3'"  O N N 132 
DG  "C2'"  C N N 133 
DG  "C1'"  C N R 134 
DG  N9     N Y N 135 
DG  C8     C Y N 136 
DG  N7     N Y N 137 
DG  C5     C Y N 138 
DG  C6     C N N 139 
DG  O6     O N N 140 
DG  N1     N N N 141 
DG  C2     C N N 142 
DG  N2     N N N 143 
DG  N3     N N N 144 
DG  C4     C Y N 145 
DG  HOP3   H N N 146 
DG  HOP2   H N N 147 
DG  "H5'"  H N N 148 
DG  "H5''" H N N 149 
DG  "H4'"  H N N 150 
DG  "H3'"  H N N 151 
DG  "HO3'" H N N 152 
DG  "H2'"  H N N 153 
DG  "H2''" H N N 154 
DG  "H1'"  H N N 155 
DG  H8     H N N 156 
DG  H1     H N N 157 
DG  H21    H N N 158 
DG  H22    H N N 159 
DT  OP3    O N N 160 
DT  P      P N N 161 
DT  OP1    O N N 162 
DT  OP2    O N N 163 
DT  "O5'"  O N N 164 
DT  "C5'"  C N N 165 
DT  "C4'"  C N R 166 
DT  "O4'"  O N N 167 
DT  "C3'"  C N S 168 
DT  "O3'"  O N N 169 
DT  "C2'"  C N N 170 
DT  "C1'"  C N R 171 
DT  N1     N N N 172 
DT  C2     C N N 173 
DT  O2     O N N 174 
DT  N3     N N N 175 
DT  C4     C N N 176 
DT  O4     O N N 177 
DT  C5     C N N 178 
DT  C7     C N N 179 
DT  C6     C N N 180 
DT  HOP3   H N N 181 
DT  HOP2   H N N 182 
DT  "H5'"  H N N 183 
DT  "H5''" H N N 184 
DT  "H4'"  H N N 185 
DT  "H3'"  H N N 186 
DT  "HO3'" H N N 187 
DT  "H2'"  H N N 188 
DT  "H2''" H N N 189 
DT  "H1'"  H N N 190 
DT  H3     H N N 191 
DT  H71    H N N 192 
DT  H72    H N N 193 
DT  H73    H N N 194 
DT  H6     H N N 195 
HOH O      O N N 196 
HOH H1     H N N 197 
HOH H2     H N N 198 
SPM N1     N N N 199 
SPM C2     C N N 200 
SPM C3     C N N 201 
SPM C4     C N N 202 
SPM N5     N N N 203 
SPM C6     C N N 204 
SPM C7     C N N 205 
SPM C8     C N N 206 
SPM C9     C N N 207 
SPM N10    N N N 208 
SPM C11    C N N 209 
SPM C12    C N N 210 
SPM C13    C N N 211 
SPM N14    N N N 212 
SPM HN11   H N N 213 
SPM HN12   H N N 214 
SPM H21    H N N 215 
SPM H22    H N N 216 
SPM H31    H N N 217 
SPM H32    H N N 218 
SPM H41    H N N 219 
SPM H42    H N N 220 
SPM HN5    H N N 221 
SPM H61    H N N 222 
SPM H62    H N N 223 
SPM H71    H N N 224 
SPM H72    H N N 225 
SPM H81    H N N 226 
SPM H82    H N N 227 
SPM H91    H N N 228 
SPM H92    H N N 229 
SPM HN0    H N N 230 
SPM H111   H N N 231 
SPM H112   H N N 232 
SPM H121   H N N 233 
SPM H122   H N N 234 
SPM H131   H N N 235 
SPM H132   H N N 236 
SPM HN41   H N N 237 
SPM HN42   H N N 238 
# 
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 
2OT P     OP1    doub N N 1   
2OT P     OP2    sing N N 2   
2OT P     "O5'"  sing N N 3   
2OT P     OP3    sing N N 4   
2OT OP2   HOP2   sing N N 5   
2OT "O5'" "C5'"  sing N N 6   
2OT "C5'" "C4'"  sing N N 7   
2OT "C5'" "H5'"  sing N N 8   
2OT "C5'" "H5''" sing N N 9   
2OT "C4'" "O4'"  sing N N 10  
2OT "C4'" "C3'"  sing N N 11  
2OT "C4'" "H4'"  sing N N 12  
2OT "O4'" "C1'"  sing N N 13  
2OT "C1'" N1     sing N N 14  
2OT "C1'" "C2'"  sing N N 15  
2OT "C1'" "H1'"  sing N N 16  
2OT N1    C6     sing N N 17  
2OT N1    C2     sing N N 18  
2OT C6    C5     doub N N 19  
2OT C6    H6     sing N N 20  
2OT C2    O2     doub N N 21  
2OT C2    N3     sing N N 22  
2OT N3    C4     sing N N 23  
2OT N3    HN3    sing N N 24  
2OT C4    O4     doub N N 25  
2OT C4    C5     sing N N 26  
2OT C5    C5M    sing N N 27  
2OT C5M   H71    sing N N 28  
2OT C5M   H72    sing N N 29  
2OT C5M   H73    sing N N 30  
2OT "C2'" "O2'"  sing N N 31  
2OT "C2'" "C3'"  sing N N 32  
2OT "C2'" "H2'"  sing N N 33  
2OT "O2'" "CB'"  sing N N 34  
2OT "CB'" "CC'"  sing N N 35  
2OT "CB'" "HB'1" sing N N 36  
2OT "CB'" "HB'2" sing N N 37  
2OT "CC'" "OD'"  sing N N 38  
2OT "CC'" "HC'1" sing N N 39  
2OT "CC'" "HC'2" sing N N 40  
2OT "OD'" "NE'"  sing N N 41  
2OT "NE'" "CF'"  sing N N 42  
2OT "NE'" "CG'"  sing N N 43  
2OT "CF'" "HF'1" sing N N 44  
2OT "CF'" "HF'2" sing N N 45  
2OT "CF'" "HF'3" sing N N 46  
2OT "CG'" "HG'1" sing N N 47  
2OT "CG'" "HG'2" sing N N 48  
2OT "CG'" "HG'3" sing N N 49  
2OT "C3'" "O3'"  sing N N 50  
2OT "C3'" "H3'"  sing N N 51  
2OT "O3'" "HO3'" sing N N 52  
2OT OP3   HOP3   sing N N 53  
DA  OP3   P      sing N N 54  
DA  OP3   HOP3   sing N N 55  
DA  P     OP1    doub N N 56  
DA  P     OP2    sing N N 57  
DA  P     "O5'"  sing N N 58  
DA  OP2   HOP2   sing N N 59  
DA  "O5'" "C5'"  sing N N 60  
DA  "C5'" "C4'"  sing N N 61  
DA  "C5'" "H5'"  sing N N 62  
DA  "C5'" "H5''" sing N N 63  
DA  "C4'" "O4'"  sing N N 64  
DA  "C4'" "C3'"  sing N N 65  
DA  "C4'" "H4'"  sing N N 66  
DA  "O4'" "C1'"  sing N N 67  
DA  "C3'" "O3'"  sing N N 68  
DA  "C3'" "C2'"  sing N N 69  
DA  "C3'" "H3'"  sing N N 70  
DA  "O3'" "HO3'" sing N N 71  
DA  "C2'" "C1'"  sing N N 72  
DA  "C2'" "H2'"  sing N N 73  
DA  "C2'" "H2''" sing N N 74  
DA  "C1'" N9     sing N N 75  
DA  "C1'" "H1'"  sing N N 76  
DA  N9    C8     sing Y N 77  
DA  N9    C4     sing Y N 78  
DA  C8    N7     doub Y N 79  
DA  C8    H8     sing N N 80  
DA  N7    C5     sing Y N 81  
DA  C5    C6     sing Y N 82  
DA  C5    C4     doub Y N 83  
DA  C6    N6     sing N N 84  
DA  C6    N1     doub Y N 85  
DA  N6    H61    sing N N 86  
DA  N6    H62    sing N N 87  
DA  N1    C2     sing Y N 88  
DA  C2    N3     doub Y N 89  
DA  C2    H2     sing N N 90  
DA  N3    C4     sing Y N 91  
DC  OP3   P      sing N N 92  
DC  OP3   HOP3   sing N N 93  
DC  P     OP1    doub N N 94  
DC  P     OP2    sing N N 95  
DC  P     "O5'"  sing N N 96  
DC  OP2   HOP2   sing N N 97  
DC  "O5'" "C5'"  sing N N 98  
DC  "C5'" "C4'"  sing N N 99  
DC  "C5'" "H5'"  sing N N 100 
DC  "C5'" "H5''" sing N N 101 
DC  "C4'" "O4'"  sing N N 102 
DC  "C4'" "C3'"  sing N N 103 
DC  "C4'" "H4'"  sing N N 104 
DC  "O4'" "C1'"  sing N N 105 
DC  "C3'" "O3'"  sing N N 106 
DC  "C3'" "C2'"  sing N N 107 
DC  "C3'" "H3'"  sing N N 108 
DC  "O3'" "HO3'" sing N N 109 
DC  "C2'" "C1'"  sing N N 110 
DC  "C2'" "H2'"  sing N N 111 
DC  "C2'" "H2''" sing N N 112 
DC  "C1'" N1     sing N N 113 
DC  "C1'" "H1'"  sing N N 114 
DC  N1    C2     sing N N 115 
DC  N1    C6     sing N N 116 
DC  C2    O2     doub N N 117 
DC  C2    N3     sing N N 118 
DC  N3    C4     doub N N 119 
DC  C4    N4     sing N N 120 
DC  C4    C5     sing N N 121 
DC  N4    H41    sing N N 122 
DC  N4    H42    sing N N 123 
DC  C5    C6     doub N N 124 
DC  C5    H5     sing N N 125 
DC  C6    H6     sing N N 126 
DG  OP3   P      sing N N 127 
DG  OP3   HOP3   sing N N 128 
DG  P     OP1    doub N N 129 
DG  P     OP2    sing N N 130 
DG  P     "O5'"  sing N N 131 
DG  OP2   HOP2   sing N N 132 
DG  "O5'" "C5'"  sing N N 133 
DG  "C5'" "C4'"  sing N N 134 
DG  "C5'" "H5'"  sing N N 135 
DG  "C5'" "H5''" sing N N 136 
DG  "C4'" "O4'"  sing N N 137 
DG  "C4'" "C3'"  sing N N 138 
DG  "C4'" "H4'"  sing N N 139 
DG  "O4'" "C1'"  sing N N 140 
DG  "C3'" "O3'"  sing N N 141 
DG  "C3'" "C2'"  sing N N 142 
DG  "C3'" "H3'"  sing N N 143 
DG  "O3'" "HO3'" sing N N 144 
DG  "C2'" "C1'"  sing N N 145 
DG  "C2'" "H2'"  sing N N 146 
DG  "C2'" "H2''" sing N N 147 
DG  "C1'" N9     sing N N 148 
DG  "C1'" "H1'"  sing N N 149 
DG  N9    C8     sing Y N 150 
DG  N9    C4     sing Y N 151 
DG  C8    N7     doub Y N 152 
DG  C8    H8     sing N N 153 
DG  N7    C5     sing Y N 154 
DG  C5    C6     sing N N 155 
DG  C5    C4     doub Y N 156 
DG  C6    O6     doub N N 157 
DG  C6    N1     sing N N 158 
DG  N1    C2     sing N N 159 
DG  N1    H1     sing N N 160 
DG  C2    N2     sing N N 161 
DG  C2    N3     doub N N 162 
DG  N2    H21    sing N N 163 
DG  N2    H22    sing N N 164 
DG  N3    C4     sing N N 165 
DT  OP3   P      sing N N 166 
DT  OP3   HOP3   sing N N 167 
DT  P     OP1    doub N N 168 
DT  P     OP2    sing N N 169 
DT  P     "O5'"  sing N N 170 
DT  OP2   HOP2   sing N N 171 
DT  "O5'" "C5'"  sing N N 172 
DT  "C5'" "C4'"  sing N N 173 
DT  "C5'" "H5'"  sing N N 174 
DT  "C5'" "H5''" sing N N 175 
DT  "C4'" "O4'"  sing N N 176 
DT  "C4'" "C3'"  sing N N 177 
DT  "C4'" "H4'"  sing N N 178 
DT  "O4'" "C1'"  sing N N 179 
DT  "C3'" "O3'"  sing N N 180 
DT  "C3'" "C2'"  sing N N 181 
DT  "C3'" "H3'"  sing N N 182 
DT  "O3'" "HO3'" sing N N 183 
DT  "C2'" "C1'"  sing N N 184 
DT  "C2'" "H2'"  sing N N 185 
DT  "C2'" "H2''" sing N N 186 
DT  "C1'" N1     sing N N 187 
DT  "C1'" "H1'"  sing N N 188 
DT  N1    C2     sing N N 189 
DT  N1    C6     sing N N 190 
DT  C2    O2     doub N N 191 
DT  C2    N3     sing N N 192 
DT  N3    C4     sing N N 193 
DT  N3    H3     sing N N 194 
DT  C4    O4     doub N N 195 
DT  C4    C5     sing N N 196 
DT  C5    C7     sing N N 197 
DT  C5    C6     doub N N 198 
DT  C7    H71    sing N N 199 
DT  C7    H72    sing N N 200 
DT  C7    H73    sing N N 201 
DT  C6    H6     sing N N 202 
HOH O     H1     sing N N 203 
HOH O     H2     sing N N 204 
SPM N1    C2     sing N N 205 
SPM N1    HN11   sing N N 206 
SPM N1    HN12   sing N N 207 
SPM C2    C3     sing N N 208 
SPM C2    H21    sing N N 209 
SPM C2    H22    sing N N 210 
SPM C3    C4     sing N N 211 
SPM C3    H31    sing N N 212 
SPM C3    H32    sing N N 213 
SPM C4    N5     sing N N 214 
SPM C4    H41    sing N N 215 
SPM C4    H42    sing N N 216 
SPM N5    C6     sing N N 217 
SPM N5    HN5    sing N N 218 
SPM C6    C7     sing N N 219 
SPM C6    H61    sing N N 220 
SPM C6    H62    sing N N 221 
SPM C7    C8     sing N N 222 
SPM C7    H71    sing N N 223 
SPM C7    H72    sing N N 224 
SPM C8    C9     sing N N 225 
SPM C8    H81    sing N N 226 
SPM C8    H82    sing N N 227 
SPM C9    N10    sing N N 228 
SPM C9    H91    sing N N 229 
SPM C9    H92    sing N N 230 
SPM N10   C11    sing N N 231 
SPM N10   HN0    sing N N 232 
SPM C11   C12    sing N N 233 
SPM C11   H111   sing N N 234 
SPM C11   H112   sing N N 235 
SPM C12   C13    sing N N 236 
SPM C12   H121   sing N N 237 
SPM C12   H122   sing N N 238 
SPM C13   N14    sing N N 239 
SPM C13   H131   sing N N 240 
SPM C13   H132   sing N N 241 
SPM N14   HN41   sing N N 242 
SPM N14   HN42   sing N N 243 
# 
_ndb_struct_conf_na.entry_id   1YB9 
_ndb_struct_conf_na.feature    'a-form 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 DG  1  1_555 B DC  10 1_555 -0.255 -0.268 0.173  -0.174 -5.672  -2.453 1  A_DG1:DC20_B  A 1  ? B 20 ? 19 1 
1 A DC  2  1_555 B DG  9  1_555 0.169  -0.056 0.074  3.416  -11.197 2.105  2  A_DC2:DG19_B  A 2  ? B 19 ? 19 1 
1 A DG  3  1_555 B DC  8  1_555 -0.334 -0.130 -0.017 -7.807 -14.752 0.743  3  A_DG3:DC18_B  A 3  ? B 18 ? 19 1 
1 A DT  4  1_555 B DA  7  1_555 -0.064 -0.121 -0.018 -4.650 -17.496 1.643  4  A_DT4:DA17_B  A 4  ? B 17 ? 20 1 
1 A DA  5  1_555 B 2OT 6  1_555 0.262  -0.119 0.143  -3.596 -13.943 -2.569 5  A_DA5:2OT16_B A 5  ? B 16 ? 20 1 
1 A 2OT 6  1_555 B DA  5  1_555 0.008  -0.095 0.207  2.616  -14.303 6.651  6  A_2OT6:DA15_B A 6  ? B 15 ? 20 1 
1 A DA  7  1_555 B DT  4  1_555 0.078  -0.158 0.097  6.225  -11.167 1.160  7  A_DA7:DT14_B  A 7  ? B 14 ? 20 1 
1 A DC  8  1_555 B DG  3  1_555 0.154  -0.176 -0.097 8.021  -14.091 1.260  8  A_DC8:DG13_B  A 8  ? B 13 ? 19 1 
1 A DG  9  1_555 B DC  2  1_555 -0.109 -0.159 0.063  -7.862 -10.059 1.004  9  A_DG9:DC12_B  A 9  ? B 12 ? 19 1 
1 A DC  10 1_555 B DG  1  1_555 0.217  -0.107 -0.034 -2.235 5.346   0.237  10 A_DC10:DG11_B A 10 ? B 11 ? 19 1 
# 
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 DG  1 1_555 B DC  10 1_555 A DC  2  1_555 B DG  9 1_555 0.282  -1.696 3.189 1.738  1.157  39.735 -2.622 -0.220 3.149 1.701  
-2.554 39.788 1 AA_DG1DC2:DG19DC20_BB   A 1 ? B 20 ? A 2  ? B 19 ? 
1 A DC  2 1_555 B DG  9  1_555 A DG  3  1_555 B DC  8 1_555 0.125  -2.301 3.474 1.307  8.436  23.893 -7.552 0.073  2.529 19.592 
-3.036 25.351 2 AA_DC2DG3:DC18DG19_BB   A 2 ? B 19 ? A 3  ? B 18 ? 
1 A DG  3 1_555 B DC  8  1_555 A DT  4  1_555 B DA  7 1_555 -1.109 -1.517 3.143 -1.757 5.338  36.479 -3.073 1.529  2.948 8.465  
2.786  36.895 3 AA_DG3DT4:DA17DC18_BB   A 3 ? B 18 ? A 4  ? B 17 ? 
1 A DT  4 1_555 B DA  7  1_555 A DA  5  1_555 B 2OT 6 1_555 0.507  -1.610 3.171 1.456  19.639 26.179 -5.655 -0.695 1.625 37.363 
-2.770 32.655 4 AA_DT4DA5:2OT16DA17_BB  A 4 ? B 17 ? A 5  ? B 16 ? 
1 A DA  5 1_555 B 2OT 6  1_555 A 2OT 6  1_555 B DA  5 1_555 0.627  -1.280 3.106 1.191  6.009  31.903 -3.256 -0.929 2.844 10.807 
-2.142 32.471 5 AA_DA52OT6:DA152OT16_BB A 5 ? B 16 ? A 6  ? B 15 ? 
1 A 2OT 6 1_555 B DA  5  1_555 A DA  7  1_555 B DT  4 1_555 -0.292 -1.232 3.029 0.214  13.925 30.344 -4.118 0.539  2.260 25.014 
-0.384 33.319 6 AA_2OT6DA7:DT14DA15_BB  A 6 ? B 15 ? A 7  ? B 14 ? 
1 A DA  7 1_555 B DT  4  1_555 A DC  8  1_555 B DG  3 1_555 0.390  -1.715 3.294 1.795  2.858  31.154 -3.708 -0.388 3.145 5.302  
-3.330 31.332 7 AA_DA7DC8:DG13DT14_BB   A 7 ? B 14 ? A 8  ? B 13 ? 
1 A DC  8 1_555 B DG  3  1_555 A DG  9  1_555 B DC  2 1_555 -0.263 -1.992 3.551 -1.310 13.155 29.860 -5.761 0.249  2.485 24.099 
2.400  32.595 8 AA_DC8DG9:DC12DG13_BB   A 8 ? B 13 ? A 9  ? B 12 ? 
1 A DG  9 1_555 B DC  2  1_555 A DC  10 1_555 B DG  1 1_555 0.190  -1.696 3.268 2.254  -0.270 34.026 -2.849 0.036  3.287 -0.462 
-3.847 34.100 9 AA_DG9DC10:DG11DC12_BB  A 9 ? B 12 ? A 10 ? B 11 ? 
# 
loop_
_pdbx_entity_nonpoly.entity_id 
_pdbx_entity_nonpoly.name 
_pdbx_entity_nonpoly.comp_id 
2 SPERMINE SPM 
3 water    HOH 
# 
_pdbx_initial_refinement_model.id               1 
_pdbx_initial_refinement_model.entity_id_list   ? 
_pdbx_initial_refinement_model.type             'experimental model' 
_pdbx_initial_refinement_model.source_name      PDB 
_pdbx_initial_refinement_model.accession_code   410D 
_pdbx_initial_refinement_model.details          'pdb entry 410D' 
#