data_4E87
# 
_entry.id   4E87 
# 
_audit_conform.dict_name       mmcif_pdbx.dic 
_audit_conform.dict_version    5.280 
_audit_conform.dict_location   http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 
# 
loop_
_database_2.database_id 
_database_2.database_code 
PDB   4E87         
NDB   NA1693       
RCSB  RCSB071291   
WWPDB D_1000071291 
# 
_pdbx_database_PDB_obs_spr.id               OBSLTE 
_pdbx_database_PDB_obs_spr.date             2013-04-24 
_pdbx_database_PDB_obs_spr.pdb_id           4JD8 
_pdbx_database_PDB_obs_spr.replace_pdb_id   4E87 
_pdbx_database_PDB_obs_spr.details          ? 
# 
loop_
_pdbx_database_related.db_name 
_pdbx_database_related.db_id 
_pdbx_database_related.details 
_pdbx_database_related.content_type 
PDB 4DX4 'Lower resolution model' unspecified 
PDB 4E7Y .                        unspecified 
PDB 4E8S .                        unspecified 
PDB 4E8X .                        unspecified 
PDB 4E95 .                        unspecified 
# 
_pdbx_database_status.status_code                     OBS 
_pdbx_database_status.entry_id                        4E87 
_pdbx_database_status.recvd_initial_deposition_date   2012-03-19 
_pdbx_database_status.deposit_site                    RCSB 
_pdbx_database_status.process_site                    RCSB 
_pdbx_database_status.status_code_sf                  OBS 
_pdbx_database_status.status_code_mr                  ? 
_pdbx_database_status.SG_entry                        ? 
_pdbx_database_status.status_code_cs                  ? 
_pdbx_database_status.methods_development_category    ? 
_pdbx_database_status.pdb_format_compatible           Y 
# 
loop_
_audit_author.name 
_audit_author.pdbx_ordinal 
'Hall, J.P.'     1 
'Ruiz-Morte, S.' 2 
'Winter, G'      3 
'Cardin, C.J.'   4 
# 
_citation.id                        primary 
_citation.title                     'Cooperativity in the DNA binding of ruthenium light switch complexes' 
_citation.journal_abbrev            'To be Published' 
_citation.journal_volume            ? 
_citation.page_first                ? 
_citation.page_last                 ? 
_citation.year                      ? 
_citation.journal_id_ASTM           ? 
_citation.country                   ? 
_citation.journal_id_ISSN           ? 
_citation.journal_id_CSD            0353 
_citation.book_publisher            ? 
_citation.pdbx_database_id_PubMed   ? 
_citation.pdbx_database_id_DOI      ? 
# 
loop_
_citation_author.citation_id 
_citation_author.name 
_citation_author.ordinal 
primary 'Hall, J.P.'     1 
primary 'Winter, G.'     2 
primary 'Ruiz-Morte, S.' 3 
primary 'Kelly, J.'      4 
primary 'Cardin, C.J.'   5 
# 
_cell.entry_id           4E87 
_cell.length_a           37.370 
_cell.length_b           37.370 
_cell.length_c           53.020 
_cell.angle_alpha        90.00 
_cell.angle_beta         90.00 
_cell.angle_gamma        120.00 
_cell.Z_PDB              12 
_cell.pdbx_unique_axis   ? 
_cell.length_a_esd       ? 
_cell.length_b_esd       ? 
_cell.length_c_esd       ? 
_cell.angle_alpha_esd    ? 
_cell.angle_beta_esd     ? 
_cell.angle_gamma_esd    ? 
# 
_symmetry.entry_id                         4E87 
_symmetry.space_group_name_H-M             'P 31 2 1' 
_symmetry.pdbx_full_space_group_name_H-M   ? 
_symmetry.cell_setting                     ? 
_symmetry.Int_Tables_number                152 
_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(*AP*TP*GP*CP*AP*T)-3'"    1808.229 2  ? ? ? ? 
2 non-polymer syn 'Delta-Ru(phen)2(dppz) complex' 743.779  2  ? ? ? ? 
3 water       nat water                           18.015   40 ? ? ? ? 
# 
_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       '(DA)(DT)(DG)(DC)(DA)(DT)' 
_entity_poly.pdbx_seq_one_letter_code_can   ATGCAT 
_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 DA n 
1 2 DT n 
1 3 DG n 
1 4 DC n 
1 5 DA n 
1 6 DT 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    ? 
_pdbx_entity_src_syn.organism_common_name   ? 
_pdbx_entity_src_syn.ncbi_taxonomy_id       ? 
_pdbx_entity_src_syn.details                'DNA Purchased from ATDBio' 
# 
_struct_ref.id                         1 
_struct_ref.db_name                    PDB 
_struct_ref.db_code                    4E87 
_struct_ref.pdbx_db_accession          4E87 
_struct_ref.entity_id                  1 
_struct_ref.pdbx_align_begin           ? 
_struct_ref.pdbx_seq_one_letter_code   ATGCAT 
_struct_ref.pdbx_db_isoform            ? 
# 
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 4E87 A 1 ? 6 ? 4E87 1 ? 6 ? 1 6 
2 1 4E87 B 1 ? 6 ? 4E87 1 ? 6 ? 1 6 
# 
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 
0TN non-polymer   . 'Delta-Ru(phen)2(dppz) complex'      ? 'C42 H26 N8 Ru'   743.779 
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  
# 
_exptl.entry_id          4E87 
_exptl.method            'X-RAY DIFFRACTION' 
_exptl.crystals_number   1 
# 
_exptl_crystal.id                    1 
_exptl_crystal.density_meas          ? 
_exptl_crystal.density_Matthews      2.96 
_exptl_crystal.density_percent_sol   58.38 
_exptl_crystal.description           ? 
_exptl_crystal.F_000                 ? 
_exptl_crystal.preparation           ? 
# 
_exptl_crystal_grow.crystal_id      1 
_exptl_crystal_grow.method          'VAPOR DIFFUSION, SITTING DROP' 
_exptl_crystal_grow.temp            298 
_exptl_crystal_grow.temp_details    ? 
_exptl_crystal_grow.pH              6.3 
_exptl_crystal_grow.pdbx_details    
;1ul 4mM rac-Ru(phen)2(dppz).Cl2, 1ul 2mM oligonucleotide, 8ul 40mM Sodium cacodylate, 12mM Spermine-HCl, 20mM BaCl2, 2% 2-methyl-2,4-pentanediol, 80mM NaCl, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 298K
;
_exptl_crystal_grow.pdbx_pH_range   ? 
# 
_diffrn.id                     1 
_diffrn.ambient_temp           100 
_diffrn.ambient_temp_details   ? 
_diffrn.crystal_id             1 
# 
_diffrn_detector.diffrn_id              1 
_diffrn_detector.detector               CCD 
_diffrn_detector.type                   'ADSC QUANTUM 315r' 
_diffrn_detector.pdbx_collection_date   2012-02-08 
_diffrn_detector.details                ? 
# 
_diffrn_radiation.diffrn_id                        1 
_diffrn_radiation.wavelength_id                    1 
_diffrn_radiation.pdbx_monochromatic_or_laue_m_l   M 
_diffrn_radiation.monochromator                    'Dual crystal Si(111)' 
_diffrn_radiation.pdbx_diffrn_protocol             'SINGLE WAVELENGTH' 
_diffrn_radiation.pdbx_scattering_type             x-ray 
# 
_diffrn_radiation_wavelength.id           1 
_diffrn_radiation_wavelength.wavelength   1.6531 
_diffrn_radiation_wavelength.wt           1.0 
# 
_diffrn_source.diffrn_id                   1 
_diffrn_source.source                      SYNCHROTRON 
_diffrn_source.type                        'DIAMOND BEAMLINE I04' 
_diffrn_source.pdbx_synchrotron_site       Diamond 
_diffrn_source.pdbx_synchrotron_beamline   I04 
_diffrn_source.pdbx_wavelength             ? 
_diffrn_source.pdbx_wavelength_list        1.6531 
# 
_reflns.entry_id                     4E87 
_reflns.observed_criterion_sigma_I   ? 
_reflns.observed_criterion_sigma_F   ? 
_reflns.d_resolution_low             27.63 
_reflns.d_resolution_high            1.94 
_reflns.number_obs                   3397 
_reflns.number_all                   3417 
_reflns.percent_possible_obs         99.4 
_reflns.pdbx_Rmerge_I_obs            ? 
_reflns.pdbx_Rsym_value              ? 
_reflns.pdbx_netI_over_sigmaI        ? 
_reflns.B_iso_Wilson_estimate        ? 
_reflns.pdbx_redundancy              ? 
_reflns.R_free_details               ? 
_reflns.limit_h_max                  ? 
_reflns.limit_h_min                  ? 
_reflns.limit_k_max                  ? 
_reflns.limit_k_min                  ? 
_reflns.limit_l_max                  ? 
_reflns.limit_l_min                  ? 
_reflns.observed_criterion_F_max     ? 
_reflns.observed_criterion_F_min     ? 
_reflns.pdbx_chi_squared             ? 
_reflns.pdbx_scaling_rejects         ? 
_reflns.pdbx_ordinal                 1 
_reflns.pdbx_diffrn_id               1 
# 
_reflns_shell.d_res_high             1.94 
_reflns_shell.d_res_low              1.99 
_reflns_shell.percent_possible_all   96.9 
_reflns_shell.Rmerge_I_obs           ? 
_reflns_shell.pdbx_Rsym_value        ? 
_reflns_shell.meanI_over_sigI_obs    ? 
_reflns_shell.pdbx_redundancy        ? 
_reflns_shell.percent_possible_obs   ? 
_reflns_shell.number_unique_all      ? 
_reflns_shell.number_measured_all    ? 
_reflns_shell.number_measured_obs    ? 
_reflns_shell.number_unique_obs      ? 
_reflns_shell.pdbx_chi_squared       ? 
_reflns_shell.pdbx_ordinal           1 
_reflns_shell.pdbx_diffrn_id         1 
# 
_refine.entry_id                                 4E87 
_refine.ls_number_reflns_obs                     2868 
_refine.ls_number_reflns_all                     3018 
_refine.pdbx_ls_sigma_I                          ? 
_refine.pdbx_ls_sigma_F                          . 
_refine.pdbx_data_cutoff_high_absF               ? 
_refine.pdbx_data_cutoff_low_absF                ? 
_refine.pdbx_data_cutoff_high_rms_absF           ? 
_refine.ls_d_res_low                             27.63 
_refine.ls_d_res_high                            1.95 
_refine.ls_percent_reflns_obs                    95.74 
_refine.ls_R_factor_obs                          0.18199 
_refine.ls_R_factor_all                          0.17854 
_refine.ls_R_factor_R_work                       0.1785 
_refine.ls_R_factor_R_free                       0.20888 
_refine.ls_R_factor_R_free_error                 ? 
_refine.ls_R_factor_R_free_error_details         ? 
_refine.ls_percent_reflns_R_free                 10.8 
_refine.ls_number_reflns_R_free                  347 
_refine.ls_number_parameters                     ? 
_refine.ls_number_restraints                     ? 
_refine.occupancy_min                            ? 
_refine.occupancy_max                            ? 
_refine.correlation_coeff_Fo_to_Fc               0.957 
_refine.correlation_coeff_Fo_to_Fc_free          0.945 
_refine.B_iso_mean                               24.401 
_refine.aniso_B[1][1]                            -0.26 
_refine.aniso_B[2][2]                            -0.26 
_refine.aniso_B[3][3]                            0.39 
_refine.aniso_B[1][2]                            -0.13 
_refine.aniso_B[1][3]                            0.00 
_refine.aniso_B[2][3]                            0.00 
_refine.solvent_model_details                    MASK 
_refine.solvent_model_param_ksol                 ? 
_refine.solvent_model_param_bsol                 ? 
_refine.pdbx_solvent_vdw_probe_radii             1.20 
_refine.pdbx_solvent_ion_probe_radii             0.80 
_refine.pdbx_solvent_shrinkage_radii             0.80 
_refine.pdbx_ls_cross_valid_method               THROUGHOUT 
_refine.details                                  'HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT' 
_refine.pdbx_starting_model                      ? 
_refine.pdbx_method_to_determine_struct          SAD 
_refine.pdbx_isotropic_thermal_model             ? 
_refine.pdbx_stereochemistry_target_values       'MAXIMUM LIKELIHOOD WITH PHASES' 
_refine.pdbx_stereochem_target_val_spec_case     ? 
_refine.pdbx_R_Free_selection_details            RANDOM 
_refine.pdbx_overall_ESU_R                       0.196 
_refine.pdbx_overall_ESU_R_Free                  0.157 
_refine.overall_SU_ML                            0.095 
_refine.pdbx_overall_phase_error                 ? 
_refine.overall_SU_B                             3.333 
_refine.overall_SU_R_Cruickshank_DPI             ? 
_refine.ls_redundancy_reflns_obs                 ? 
_refine.B_iso_min                                ? 
_refine.B_iso_max                                ? 
_refine.overall_SU_R_free                        ? 
_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_diffrn_id                           1 
_refine.pdbx_refine_id                           'X-RAY DIFFRACTION' 
_refine.pdbx_TLS_residual_ADP_flag               ? 
_refine.pdbx_overall_SU_R_free_Cruickshank_DPI   ? 
_refine.pdbx_overall_SU_R_Blow_DPI               ? 
_refine.pdbx_overall_SU_R_free_Blow_DPI          ? 
# 
_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   240 
_refine_hist.pdbx_number_atoms_ligand         102 
_refine_hist.number_atoms_solvent             40 
_refine_hist.number_atoms_total               382 
_refine_hist.d_res_high                       1.95 
_refine_hist.d_res_low                        27.63 
# 
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_restraint_function 
_refine_ls_restr.pdbx_refine_id 
r_bond_refined_d             0.024 0.014 ? 396 ? 'X-RAY DIFFRACTION' 
r_bond_other_d               ?     ?     ? ?   ? 'X-RAY DIFFRACTION' 
r_angle_refined_deg          3.161 1.917 ? 628 ? 'X-RAY DIFFRACTION' 
r_angle_other_deg            ?     ?     ? ?   ? 'X-RAY DIFFRACTION' 
r_dihedral_angle_1_deg       ?     ?     ? ?   ? 'X-RAY DIFFRACTION' 
r_dihedral_angle_2_deg       ?     ?     ? ?   ? 'X-RAY DIFFRACTION' 
r_dihedral_angle_3_deg       ?     ?     ? ?   ? 'X-RAY DIFFRACTION' 
r_dihedral_angle_4_deg       ?     ?     ? ?   ? 'X-RAY DIFFRACTION' 
r_chiral_restr               0.088 0.200 ? 36  ? 'X-RAY DIFFRACTION' 
r_gen_planes_refined         0.031 0.020 ? 232 ? 'X-RAY DIFFRACTION' 
r_gen_planes_other           ?     ?     ? ?   ? 'X-RAY DIFFRACTION' 
r_nbd_refined                ?     ?     ? ?   ? 'X-RAY DIFFRACTION' 
r_nbd_other                  ?     ?     ? ?   ? 'X-RAY DIFFRACTION' 
r_nbtor_refined              ?     ?     ? ?   ? 'X-RAY DIFFRACTION' 
r_nbtor_other                ?     ?     ? ?   ? 'X-RAY DIFFRACTION' 
r_xyhbond_nbd_refined        ?     ?     ? ?   ? 'X-RAY DIFFRACTION' 
r_xyhbond_nbd_other          ?     ?     ? ?   ? 'X-RAY DIFFRACTION' 
r_metal_ion_refined          ?     ?     ? ?   ? 'X-RAY DIFFRACTION' 
r_metal_ion_other            ?     ?     ? ?   ? 'X-RAY DIFFRACTION' 
r_symmetry_vdw_refined       ?     ?     ? ?   ? 'X-RAY DIFFRACTION' 
r_symmetry_vdw_other         ?     ?     ? ?   ? 'X-RAY DIFFRACTION' 
r_symmetry_hbond_refined     ?     ?     ? ?   ? 'X-RAY DIFFRACTION' 
r_symmetry_hbond_other       ?     ?     ? ?   ? 'X-RAY DIFFRACTION' 
r_symmetry_metal_ion_refined ?     ?     ? ?   ? 'X-RAY DIFFRACTION' 
r_symmetry_metal_ion_other   ?     ?     ? ?   ? 'X-RAY DIFFRACTION' 
r_mcbond_it                  ?     ?     ? ?   ? 'X-RAY DIFFRACTION' 
r_mcbond_other               ?     ?     ? ?   ? 'X-RAY DIFFRACTION' 
r_mcangle_it                 ?     ?     ? ?   ? 'X-RAY DIFFRACTION' 
r_scbond_it                  ?     ?     ? ?   ? 'X-RAY DIFFRACTION' 
r_scangle_it                 ?     ?     ? ?   ? 'X-RAY DIFFRACTION' 
r_rigid_bond_restr           ?     ?     ? ?   ? 'X-RAY DIFFRACTION' 
r_sphericity_free            ?     ?     ? ?   ? 'X-RAY DIFFRACTION' 
r_sphericity_bonded          ?     ?     ? ?   ? 'X-RAY DIFFRACTION' 
# 
_refine_ls_shell.pdbx_total_number_of_bins_used   20 
_refine_ls_shell.d_res_high                       1.950 
_refine_ls_shell.d_res_low                        2.001 
_refine_ls_shell.number_reflns_R_work             153 
_refine_ls_shell.R_factor_R_work                  0.238 
_refine_ls_shell.percent_reflns_obs               81.55 
_refine_ls_shell.R_factor_R_free                  0.302 
_refine_ls_shell.R_factor_R_free_error            ? 
_refine_ls_shell.percent_reflns_R_free            ? 
_refine_ls_shell.number_reflns_R_free             15 
_refine_ls_shell.number_reflns_all                ? 
_refine_ls_shell.R_factor_all                     ? 
_refine_ls_shell.number_reflns_obs                ? 
_refine_ls_shell.redundancy_reflns_obs            ? 
_refine_ls_shell.pdbx_refine_id                   'X-RAY DIFFRACTION' 
# 
_struct.entry_id                  4E87 
_struct.title                     'Racemic-[Ru(phen)2(dppz)]2+ bound to synthetic DNA' 
_struct.pdbx_descriptor           "5'-D(*AP*TP*GP*CP*AP*T)-3'" 
_struct.pdbx_model_details        ? 
_struct.pdbx_CASP_flag            ? 
_struct.pdbx_model_type_details   ? 
# 
_struct_keywords.entry_id        4E87 
_struct_keywords.pdbx_keywords   DNA 
_struct_keywords.text            'Intercalation, DNA, racemic-[Ru(phen)2(dppz)]2+, Delta-[Ru(phen)2(dppz)]2+' 
# 
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 2 ? 
E N N 3 ? 
F N N 3 ? 
# 
_struct_biol.id        1 
_struct_biol.details   ? 
# 
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 
hydrog1  hydrog ? ? A DA 1 N1 ? ? ? 1_555 B DT 6 N3 ? ? A DA 1 B DT 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? 
hydrog2  hydrog ? ? A DA 1 N6 ? ? ? 1_555 B DT 6 O4 ? ? A DA 1 B DT 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? 
hydrog3  hydrog ? ? A DT 2 N3 ? ? ? 1_555 B DA 5 N1 ? ? A DT 2 B DA 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? 
hydrog4  hydrog ? ? A DT 2 O4 ? ? ? 1_555 B DA 5 N6 ? ? A DT 2 B DA 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? 
hydrog5  hydrog ? ? A DG 3 N1 ? ? ? 1_555 B DC 4 N3 ? ? A DG 3 B DC 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? 
hydrog6  hydrog ? ? A DG 3 N2 ? ? ? 1_555 B DC 4 O2 ? ? A DG 3 B DC 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? 
hydrog7  hydrog ? ? A DG 3 O6 ? ? ? 1_555 B DC 4 N4 ? ? A DG 3 B DC 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? 
hydrog8  hydrog ? ? A DC 4 N3 ? ? ? 1_555 B DG 3 N1 ? ? A DC 4 B DG 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? 
hydrog9  hydrog ? ? A DC 4 N4 ? ? ? 1_555 B DG 3 O6 ? ? A DC 4 B DG 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? 
hydrog10 hydrog ? ? A DC 4 O2 ? ? ? 1_555 B DG 3 N2 ? ? A DC 4 B DG 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? 
hydrog11 hydrog ? ? A DA 5 N1 ? ? ? 1_555 B DT 2 N3 ? ? A DA 5 B DT 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? 
hydrog12 hydrog ? ? A DA 5 N6 ? ? ? 1_555 B DT 2 O4 ? ? A DA 5 B DT 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? 
hydrog13 hydrog ? ? A DT 6 N3 ? ? ? 1_555 B DA 1 N1 ? ? A DT 6 B DA 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? 
hydrog14 hydrog ? ? A DT 6 O4 ? ? ? 1_555 B DA 1 N6 ? ? A DT 6 B DA 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? 
# 
_struct_conn_type.id          hydrog 
_struct_conn_type.criteria    ? 
_struct_conn_type.reference   ? 
# 
loop_
_struct_site.id 
_struct_site.pdbx_evidence_code 
_struct_site.pdbx_auth_asym_id 
_struct_site.pdbx_auth_comp_id 
_struct_site.pdbx_auth_seq_id 
_struct_site.pdbx_auth_ins_code 
_struct_site.pdbx_num_residues 
_struct_site.details 
AC1 Software ? ? ? ? 9 'BINDING SITE FOR RESIDUE 0TN A 101' 
AC2 Software ? ? ? ? 7 'BINDING SITE FOR RESIDUE 0TN B 101' 
# 
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 9 DT A 2 ? DT A 2 . ? 1_555 ? 
2  AC1 9 DG A 3 ? DG A 3 . ? 1_555 ? 
3  AC1 9 DC A 4 ? DC A 4 . ? 1_555 ? 
4  AC1 9 DA A 5 ? DA A 5 . ? 6_665 ? 
5  AC1 9 DT A 6 ? DT A 6 . ? 6_665 ? 
6  AC1 9 DA B 1 ? DA B 1 . ? 6_665 ? 
7  AC1 9 DC B 4 ? DC B 4 . ? 1_555 ? 
8  AC1 9 DA B 5 ? DA B 5 . ? 1_555 ? 
9  AC1 9 DT B 6 ? DT B 6 . ? 1_555 ? 
10 AC2 7 DA A 1 ? DA A 1 . ? 2_665 ? 
11 AC2 7 DC A 4 ? DC A 4 . ? 1_555 ? 
12 AC2 7 DA A 5 ? DA A 5 . ? 1_555 ? 
13 AC2 7 DT A 6 ? DT A 6 . ? 1_555 ? 
14 AC2 7 DT B 2 ? DT B 2 . ? 1_555 ? 
15 AC2 7 DG B 3 ? DG B 3 . ? 1_555 ? 
16 AC2 7 DT B 6 ? DT B 6 . ? 2_665 ? 
# 
_database_PDB_matrix.entry_id          4E87 
_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                    4E87 
_atom_sites.fract_transf_matrix[1][1]   0.026759 
_atom_sites.fract_transf_matrix[1][2]   0.015450 
_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]   0.030899 
_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]   0.018861 
_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  
RU 
# 
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 DA 1 1 1 DA DA A . n 
A 1 2 DT 2 2 2 DT DT A . n 
A 1 3 DG 3 3 3 DG DG A . n 
A 1 4 DC 4 4 4 DC DC A . n 
A 1 5 DA 5 5 5 DA DA A . n 
A 1 6 DT 6 6 6 DT DT A . n 
B 1 1 DA 1 1 1 DA DA B . n 
B 1 2 DT 2 2 2 DT DT B . n 
B 1 3 DG 3 3 3 DG DG B . n 
B 1 4 DC 4 4 4 DC DC B . n 
B 1 5 DA 5 5 5 DA DA B . n 
B 1 6 DT 6 6 6 DT DT 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 0TN 1  101 1  0TN KPD A . 
D 2 0TN 1  101 1  0TN RKP B . 
E 3 HOH 1  201 1  HOH HOH A . 
E 3 HOH 2  202 2  HOH HOH A . 
E 3 HOH 3  203 3  HOH HOH A . 
E 3 HOH 4  204 4  HOH HOH A . 
E 3 HOH 5  205 6  HOH HOH A . 
E 3 HOH 6  206 7  HOH HOH A . 
E 3 HOH 7  207 10 HOH HOH A . 
E 3 HOH 8  208 13 HOH HOH A . 
E 3 HOH 9  209 16 HOH HOH A . 
E 3 HOH 10 210 17 HOH HOH A . 
E 3 HOH 11 211 19 HOH HOH A . 
E 3 HOH 12 212 20 HOH HOH A . 
E 3 HOH 13 213 22 HOH HOH A . 
E 3 HOH 14 214 24 HOH HOH A . 
E 3 HOH 15 215 28 HOH HOH A . 
E 3 HOH 16 216 29 HOH HOH A . 
E 3 HOH 17 217 31 HOH HOH A . 
E 3 HOH 18 218 35 HOH HOH A . 
E 3 HOH 19 219 36 HOH HOH A . 
E 3 HOH 20 220 37 HOH HOH A . 
E 3 HOH 21 221 38 HOH HOH A . 
E 3 HOH 22 222 40 HOH HOH A . 
F 3 HOH 1  201 23 HOH HOH B . 
F 3 HOH 2  202 5  HOH HOH B . 
F 3 HOH 3  203 8  HOH HOH B . 
F 3 HOH 4  204 9  HOH HOH B . 
F 3 HOH 5  205 11 HOH HOH B . 
F 3 HOH 6  206 12 HOH HOH B . 
F 3 HOH 7  207 14 HOH HOH B . 
F 3 HOH 8  208 15 HOH HOH B . 
F 3 HOH 9  209 18 HOH HOH B . 
F 3 HOH 10 210 21 HOH HOH B . 
F 3 HOH 11 211 25 HOH HOH B . 
F 3 HOH 12 212 26 HOH HOH B . 
F 3 HOH 13 213 27 HOH HOH B . 
F 3 HOH 14 214 30 HOH HOH B . 
F 3 HOH 15 215 32 HOH HOH B . 
F 3 HOH 16 216 33 HOH HOH B . 
F 3 HOH 17 217 34 HOH HOH B . 
F 3 HOH 18 218 39 HOH HOH B . 
# 
_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,F 
# 
_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 2013-03-20 
2 'Structure model' 1 1 2013-04-24 
# 
loop_
_pdbx_audit_revision_details.ordinal 
_pdbx_audit_revision_details.revision_ordinal 
_pdbx_audit_revision_details.data_content_type 
_pdbx_audit_revision_details.provider 
_pdbx_audit_revision_details.type 
_pdbx_audit_revision_details.description 
1 1 'Structure model' repository 'Initial release' ? 
2 2 'Structure model' repository Obsolete          ? 
# 
loop_
_software.name 
_software.classification 
_software.version 
_software.citation_id 
_software.pdbx_ordinal 
GDA        'data collection' .        ? 1 
SHELXC/D/E 'model building'  .        ? 2 
REFMAC     refinement        5.6.0117 ? 3 
XDS        'data reduction'  .        ? 4 
SCALA      'data scaling'    .        ? 5 
SHELXC/D/E phasing           .        ? 6 
# 
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 "O3'" A DG 3 ? ? P     A DC 4 ? ? OP2   A DC 4 ? ? 117.33 110.50 6.83  1.10 Y 
2 1 "C1'" A DT 6 ? ? "O4'" A DT 6 ? ? "C4'" A DT 6 ? ? 103.46 110.10 -6.64 1.00 N 
# 
_ndb_struct_conf_na.entry_id   4E87 
_ndb_struct_conf_na.feature    'b-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 DA 1 1_555 B DT 6 1_555 0.099  -0.151 0.097  -9.276  0.830  1.158  1 A_DA1:DT6_B A 1 ? B 6 ? 20 1 
1 A DT 2 1_555 B DA 5 1_555 -0.026 -0.100 0.080  14.568  9.307  3.094  2 A_DT2:DA5_B A 2 ? B 5 ? 20 1 
1 A DG 3 1_555 B DC 4 1_555 -0.392 -0.088 -0.291 -1.341  9.876  -0.512 3 A_DG3:DC4_B A 3 ? B 4 ? 19 1 
1 A DC 4 1_555 B DG 3 1_555 0.377  -0.190 -0.322 16.778  2.099  -1.101 4 A_DC4:DG3_B A 4 ? B 3 ? 19 1 
1 A DA 5 1_555 B DT 2 1_555 0.179  -0.103 -0.028 -11.617 16.125 7.960  5 A_DA5:DT2_B A 5 ? B 2 ? 20 1 
1 A DT 6 1_555 B DA 1 1_555 -0.140 -0.125 -0.427 12.854  8.046  3.817  6 A_DT6:DA1_B A 6 ? B 1 ? 20 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 DA 1 1_555 B DT 6 1_555 A DT 2 1_555 B DA 5 1_555 1.024  0.224 2.869 0.403   3.123 28.757 -0.162 -1.972 2.891 6.265  -0.808  
28.926 1 AA_DA1DT2:DA5DT6_BB A 1 ? B 6 ? A 2 ? B 5 ? 
1 A DT 2 1_555 B DA 5 1_555 A DG 3 1_555 B DC 4 1_555 0.767  1.921 6.875 12.674  2.835 25.625 2.476  4.723  6.676 5.932  -26.514 
28.679 2 AA_DT2DG3:DC4DA5_BB A 2 ? B 5 ? A 3 ? B 4 ? 
1 A DG 3 1_555 B DC 4 1_555 A DC 4 1_555 B DG 3 1_555 -0.208 0.016 2.914 1.499   6.161 22.873 -1.774 0.947  2.802 15.165 -3.690  
23.724 3 AA_DG3DC4:DG3DC4_BB A 3 ? B 4 ? A 4 ? B 3 ? 
1 A DC 4 1_555 B DG 3 1_555 A DA 5 1_555 B DT 2 1_555 -1.758 1.860 6.874 -11.292 5.460 22.232 0.622  -3.446 7.171 12.921 26.723  
25.488 4 AA_DC4DA5:DT2DG3_BB A 4 ? B 3 ? A 5 ? B 2 ? 
1 A DA 5 1_555 B DT 2 1_555 A DT 6 1_555 B DA 1 1_555 -0.619 0.119 2.819 4.091   6.428 14.574 -3.343 4.559  2.395 23.368 -14.872 
16.436 5 AA_DA5DT6:DA1DT2_BB A 5 ? B 2 ? A 6 ? B 1 ? 
# 
loop_
_pdbx_entity_nonpoly.entity_id 
_pdbx_entity_nonpoly.name 
_pdbx_entity_nonpoly.comp_id 
2 'Delta-Ru(phen)2(dppz) complex' 0TN 
3 water                           HOH 
#