data_165D
# 
_entry.id   165D 
# 
_audit_conform.dict_name       mmcif_pdbx.dic 
_audit_conform.dict_version    5.385 
_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   165D         pdb_0000165d 10.2210/pdb165d/pdb 
RCSB  AHIB53       ?            ?                   
WWPDB D_1000170146 ?            ?                   
# 
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 1994-08-31 
2 'Structure model' 1 1 2008-05-22 
3 'Structure model' 1 2 2011-07-13 
4 'Structure model' 1 3 2018-04-18 
5 'Structure model' 1 4 2024-02-07 
# 
_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 5 'Structure model' 'Data collection'           
5 5 'Structure model' 'Database references'       
6 5 'Structure model' 'Derived calculations'      
# 
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' diffrn_detector              
2 5 'Structure model' chem_comp_atom               
3 5 'Structure model' chem_comp_bond               
4 5 'Structure model' database_2                   
5 5 'Structure model' pdbx_struct_special_symmetry 
6 5 'Structure model' struct_conn                  
7 5 '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' '_diffrn_detector.detector'           
2 5 'Structure model' '_database_2.pdbx_DOI'                
3 5 'Structure model' '_database_2.pdbx_database_accession' 
4 5 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 
5 5 'Structure model' '_struct_site.pdbx_auth_asym_id'      
6 5 'Structure model' '_struct_site.pdbx_auth_comp_id'      
7 5 'Structure model' '_struct_site.pdbx_auth_seq_id'       
# 
_pdbx_database_status.status_code                     REL 
_pdbx_database_status.entry_id                        165D 
_pdbx_database_status.recvd_initial_deposition_date   1994-03-21 
_pdbx_database_status.deposit_site                    BNL 
_pdbx_database_status.process_site                    NDB 
_pdbx_database_status.SG_entry                        . 
_pdbx_database_status.pdb_format_compatible           Y 
_pdbx_database_status.status_code_mr                  ? 
_pdbx_database_status.status_code_sf                  ? 
_pdbx_database_status.status_code_cs                  ? 
_pdbx_database_status.methods_development_category    ? 
_pdbx_database_status.status_code_nmr_data            ? 
# 
loop_
_audit_author.name 
_audit_author.pdbx_ordinal 
'Cruse, W.'      1 
'Saludjian, P.'  2 
'Biala, E.'      3 
'Strazewski, P.' 4 
'Prange, T.'     5 
'Kennard, O.'    6 
# 
_citation.id                        primary 
_citation.title                     
'Structure of a mispaired RNA double helix at 1.6-A resolution and implications for the prediction of RNA secondary structure.' 
_citation.journal_abbrev            Proc.Natl.Acad.Sci.USA 
_citation.journal_volume            91 
_citation.page_first                4160 
_citation.page_last                 4164 
_citation.year                      1994 
_citation.journal_id_ASTM           PNASA6 
_citation.country                   US 
_citation.journal_id_ISSN           0027-8424 
_citation.journal_id_CSD            0040 
_citation.book_publisher            ? 
_citation.pdbx_database_id_PubMed   7514296 
_citation.pdbx_database_id_DOI      10.1073/pnas.91.10.4160 
# 
loop_
_citation_author.citation_id 
_citation_author.name 
_citation_author.ordinal 
_citation_author.identifier_ORCID 
primary 'Cruse, W.B.'    1 ? 
primary 'Saludjian, P.'  2 ? 
primary 'Biala, E.'      3 ? 
primary 'Strazewski, P.' 4 ? 
primary 'Prange, T.'     5 ? 
primary 'Kennard, O.'    6 ? 
# 
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 
;DNA/RNA (5'-R(*GP*CP*UP*UP*CP*GP*GP*CP*)-D(*(BRU))-3')
;
2887.600 2  ? ? ? ? 
2 non-polymer syn 'RHODIUM HEXAMINE ION'                                   205.089  4  ? ? ? ? 
3 water       nat water                                                    18.015   54 ? ? ? ? 
# 
_entity_poly.entity_id                      1 
_entity_poly.type                           polyribonucleotide 
_entity_poly.nstd_linkage                   no 
_entity_poly.nstd_monomer                   yes 
_entity_poly.pdbx_seq_one_letter_code       'GCUUCGGC(BRU)' 
_entity_poly.pdbx_seq_one_letter_code_can   GCUUCGGCU 
_entity_poly.pdbx_strand_id                 A,B 
_entity_poly.pdbx_target_identifier         ? 
# 
loop_
_pdbx_entity_nonpoly.entity_id 
_pdbx_entity_nonpoly.name 
_pdbx_entity_nonpoly.comp_id 
2 'RHODIUM HEXAMINE ION' RHD 
3 water                  HOH 
# 
loop_
_entity_poly_seq.entity_id 
_entity_poly_seq.num 
_entity_poly_seq.mon_id 
_entity_poly_seq.hetero 
1 1 G   n 
1 2 C   n 
1 3 U   n 
1 4 U   n 
1 5 C   n 
1 6 G   n 
1 7 G   n 
1 8 C   n 
1 9 BRU n 
# 
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 
BRU 'DNA linking' n "5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE" ? 'C9 H12 Br N2 O8 P' 387.078 
C   'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE"                ? 'C9 H14 N3 O8 P'    323.197 
G   'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE"               ? 'C10 H14 N5 O8 P'   363.221 
HOH non-polymer   . WATER                                      ? 'H2 O'              18.015  
RHD non-polymer   . 'RHODIUM HEXAMINE ION'                     ? 'H18 N6 Rh 3'       205.089 
U   'RNA linking' y "URIDINE-5'-MONOPHOSPHATE"                 ? 'C9 H13 N2 O9 P'    324.181 
# 
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 G   1 1  1  G   G  A . n 
A 1 2 C   2 2  2  C   C  A . n 
A 1 3 U   3 3  3  U   U  A . n 
A 1 4 U   4 4  4  U   U  A . n 
A 1 5 C   5 5  5  C   C  A . n 
A 1 6 G   6 6  6  G   G  A . n 
A 1 7 G   7 7  7  G   G  A . n 
A 1 8 C   8 8  8  C   C  A . n 
A 1 9 BRU 9 9  9  BRU +U A . n 
B 1 1 G   1 10 10 G   G  B . n 
B 1 2 C   2 11 11 C   C  B . n 
B 1 3 U   3 12 12 U   U  B . n 
B 1 4 U   4 13 13 U   U  B . n 
B 1 5 C   5 14 14 C   C  B . n 
B 1 6 G   6 15 15 G   G  B . n 
B 1 7 G   7 16 16 G   G  B . n 
B 1 8 C   8 17 17 C   C  B . n 
B 1 9 BRU 9 18 18 BRU +U 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 RHD 1  19 19 RHD RHD A . 
D 2 RHD 1  20 20 RHD RHD A . 
E 2 RHD 1  22 22 RHD RHD A . 
F 2 RHD 1  21 21 RHD RHD B . 
G 3 HOH 1  23 23 HOH HOH A . 
G 3 HOH 2  25 25 HOH HOH A . 
G 3 HOH 3  26 26 HOH HOH A . 
G 3 HOH 4  27 27 HOH HOH A . 
G 3 HOH 5  28 28 HOH HOH A . 
G 3 HOH 6  29 29 HOH HOH A . 
G 3 HOH 7  30 30 HOH HOH A . 
G 3 HOH 8  31 31 HOH HOH A . 
G 3 HOH 9  33 33 HOH HOH A . 
G 3 HOH 10 35 35 HOH HOH A . 
G 3 HOH 11 36 36 HOH HOH A . 
G 3 HOH 12 37 37 HOH HOH A . 
G 3 HOH 13 38 38 HOH HOH A . 
G 3 HOH 14 41 41 HOH HOH A . 
G 3 HOH 15 43 43 HOH HOH A . 
G 3 HOH 16 47 47 HOH HOH A . 
G 3 HOH 17 48 48 HOH HOH A . 
G 3 HOH 18 51 51 HOH HOH A . 
G 3 HOH 19 53 53 HOH HOH A . 
G 3 HOH 20 54 54 HOH HOH A . 
G 3 HOH 21 56 56 HOH HOH A . 
G 3 HOH 22 57 57 HOH HOH A . 
G 3 HOH 23 59 59 HOH HOH A . 
G 3 HOH 24 60 60 HOH HOH A . 
G 3 HOH 25 61 61 HOH HOH A . 
G 3 HOH 26 63 63 HOH HOH A . 
G 3 HOH 27 64 64 HOH HOH A . 
G 3 HOH 28 65 65 HOH HOH A . 
G 3 HOH 29 66 66 HOH HOH A . 
G 3 HOH 30 73 73 HOH HOH A . 
G 3 HOH 31 74 74 HOH HOH A . 
H 3 HOH 1  24 24 HOH HOH B . 
H 3 HOH 2  32 32 HOH HOH B . 
H 3 HOH 3  34 34 HOH HOH B . 
H 3 HOH 4  39 39 HOH HOH B . 
H 3 HOH 5  40 40 HOH HOH B . 
H 3 HOH 6  42 42 HOH HOH B . 
H 3 HOH 7  44 44 HOH HOH B . 
H 3 HOH 8  45 45 HOH HOH B . 
H 3 HOH 9  46 46 HOH HOH B . 
H 3 HOH 10 49 49 HOH HOH B . 
H 3 HOH 11 50 50 HOH HOH B . 
H 3 HOH 12 52 52 HOH HOH B . 
H 3 HOH 13 55 55 HOH HOH B . 
H 3 HOH 14 58 58 HOH HOH B . 
H 3 HOH 15 62 62 HOH HOH B . 
H 3 HOH 16 67 67 HOH HOH B . 
H 3 HOH 17 68 68 HOH HOH B . 
H 3 HOH 18 69 69 HOH HOH B . 
H 3 HOH 19 70 70 HOH HOH B . 
H 3 HOH 20 71 71 HOH HOH B . 
H 3 HOH 21 72 72 HOH HOH B . 
H 3 HOH 22 75 75 HOH HOH B . 
H 3 HOH 23 76 76 HOH HOH B . 
# 
_software.name             X-PLOR 
_software.classification   refinement 
_software.version          . 
_software.citation_id      ? 
_software.pdbx_ordinal     1 
# 
_cell.entry_id           165D 
_cell.length_a           53.800 
_cell.length_b           19.400 
_cell.length_c           50.140 
_cell.angle_alpha        90.00 
_cell.angle_beta         109.90 
_cell.angle_gamma        90.00 
_cell.Z_PDB              8 
_cell.pdbx_unique_axis   ? 
# 
_symmetry.entry_id                         165D 
_symmetry.space_group_name_H-M             'C 1 2 1' 
_symmetry.pdbx_full_space_group_name_H-M   ? 
_symmetry.cell_setting                     ? 
_symmetry.Int_Tables_number                5 
# 
_exptl.entry_id          165D 
_exptl.method            'X-RAY DIFFRACTION' 
_exptl.crystals_number   ? 
# 
_exptl_crystal.id                    1 
_exptl_crystal.density_meas          ? 
_exptl_crystal.density_Matthews      2.13 
_exptl_crystal.density_percent_sol   42.26 
_exptl_crystal.description           ? 
# 
_exptl_crystal_grow.crystal_id      1 
_exptl_crystal_grow.method          'VAPOR DIFFUSION, SITTING DROP' 
_exptl_crystal_grow.temp            277.00 
_exptl_crystal_grow.temp_details    ? 
_exptl_crystal_grow.pH              6.30 
_exptl_crystal_grow.pdbx_details    'pH 6.30, VAPOR DIFFUSION, SITTING DROP, temperature 277.00K' 
_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 WATER           ? ? ? 
1 2 1 'LI CACODYLATE' ? ? ? 
1 3 1 '[RH(NH3)6]CL3' ? ? ? 
# 
loop_
_diffrn.id 
_diffrn.crystal_id 
_diffrn.ambient_temp 
_diffrn.ambient_temp_details 
1 1 ? ? 
2 1 ? ? 
# 
loop_
_diffrn_detector.diffrn_id 
_diffrn_detector.detector 
_diffrn_detector.type 
_diffrn_detector.pdbx_collection_date 
_diffrn_detector.details 
1 'IMAGE PLATE'  MARRESEARCH         ? ? 
2 DIFFRACTOMETER 'ENRAF-NONIUS FAST' ? ? 
# 
loop_
_diffrn_radiation.diffrn_id 
_diffrn_radiation.wavelength_id 
_diffrn_radiation.pdbx_monochromatic_or_laue_m_l 
_diffrn_radiation.monochromator 
_diffrn_radiation.pdbx_diffrn_protocol 
_diffrn_radiation.pdbx_scattering_type 
1 1 M ? ? x-ray 
2 2 M ? ? x-ray 
# 
loop_
_diffrn_radiation_wavelength.id 
_diffrn_radiation_wavelength.wavelength 
_diffrn_radiation_wavelength.wt 
1 . 1.0 
2 . 1.0 
# 
loop_
_diffrn_source.diffrn_id 
_diffrn_source.source 
_diffrn_source.type 
_diffrn_source.pdbx_synchrotron_site 
_diffrn_source.pdbx_synchrotron_beamline 
_diffrn_source.pdbx_wavelength 
_diffrn_source.pdbx_wavelength_list 
1 SYNCHROTRON LURE LURE ? ? ? 
2 ?           ?    ?    ? ? ? 
# 
_reflns.entry_id                     165D 
_reflns.observed_criterion_sigma_I   ? 
_reflns.observed_criterion_sigma_F   2.000 
_reflns.d_resolution_low             ? 
_reflns.d_resolution_high            1.600 
_reflns.number_obs                   6093 
_reflns.number_all                   ? 
_reflns.percent_possible_obs         ? 
_reflns.pdbx_Rmerge_I_obs            ? 
_reflns.pdbx_Rsym_value              ? 
_reflns.pdbx_netI_over_sigmaI        ? 
_reflns.B_iso_Wilson_estimate        ? 
_reflns.pdbx_redundancy              ? 
_reflns.pdbx_diffrn_id               1,2 
_reflns.pdbx_ordinal                 1 
# 
_refine.entry_id                                 165D 
_refine.ls_number_reflns_obs                     6098 
_refine.ls_number_reflns_all                     ? 
_refine.pdbx_ls_sigma_I                          ? 
_refine.pdbx_ls_sigma_F                          2.000 
_refine.pdbx_data_cutoff_high_absF               ? 
_refine.pdbx_data_cutoff_low_absF                ? 
_refine.pdbx_data_cutoff_high_rms_absF           ? 
_refine.ls_d_res_low                             10.000 
_refine.ls_d_res_high                            1.550 
_refine.ls_percent_reflns_obs                    ? 
_refine.ls_R_factor_obs                          0.18 
_refine.ls_R_factor_all                          ? 
_refine.ls_R_factor_R_work                       0.18 
_refine.ls_R_factor_R_free                       ? 
_refine.ls_R_factor_R_free_error                 ? 
_refine.ls_R_factor_R_free_error_details         ? 
_refine.ls_percent_reflns_R_free                 ? 
_refine.ls_number_reflns_R_free                  ? 
_refine.ls_number_parameters                     ? 
_refine.ls_number_restraints                     ? 
_refine.occupancy_min                            ? 
_refine.occupancy_max                            ? 
_refine.B_iso_mean                               ? 
_refine.aniso_B[1][1]                            ? 
_refine.aniso_B[2][2]                            ? 
_refine.aniso_B[3][3]                            ? 
_refine.aniso_B[1][2]                            ? 
_refine.aniso_B[1][3]                            ? 
_refine.aniso_B[2][3]                            ? 
_refine.solvent_model_details                    ? 
_refine.solvent_model_param_ksol                 ? 
_refine.solvent_model_param_bsol                 ? 
_refine.pdbx_ls_cross_valid_method               ? 
_refine.details                                  ? 
_refine.pdbx_starting_model                      ? 
_refine.pdbx_method_to_determine_struct          ? 
_refine.pdbx_isotropic_thermal_model             ? 
_refine.pdbx_stereochemistry_target_values       ? 
_refine.pdbx_stereochem_target_val_spec_case     ? 
_refine.pdbx_R_Free_selection_details            ? 
_refine.pdbx_overall_ESU_R                       ? 
_refine.pdbx_overall_ESU_R_Free                  ? 
_refine.overall_SU_ML                            ? 
_refine.overall_SU_B                             ? 
_refine.pdbx_refine_id                           'X-RAY DIFFRACTION' 
_refine.pdbx_diffrn_id                           1 
_refine.pdbx_TLS_residual_ADP_flag               ? 
_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.pdbx_overall_phase_error                 ? 
_refine.overall_SU_R_Cruickshank_DPI             ? 
_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   389 
_refine_hist.pdbx_number_atoms_ligand         31 
_refine_hist.number_atoms_solvent             54 
_refine_hist.number_atoms_total               474 
_refine_hist.d_res_high                       1.550 
_refine_hist.d_res_low                        10.000 
# 
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 
x_bond_d                0.017 ? ? ? 'X-RAY DIFFRACTION' ? 
x_bond_d_na             ?     ? ? ? 'X-RAY DIFFRACTION' ? 
x_bond_d_prot           ?     ? ? ? 'X-RAY DIFFRACTION' ? 
x_angle_d               0.030 ? ? ? 'X-RAY DIFFRACTION' ? 
x_angle_d_na            ?     ? ? ? 'X-RAY DIFFRACTION' ? 
x_angle_d_prot          ?     ? ? ? 'X-RAY DIFFRACTION' ? 
x_angle_deg             2.10  ? ? ? 'X-RAY DIFFRACTION' ? 
x_angle_deg_na          ?     ? ? ? 'X-RAY DIFFRACTION' ? 
x_angle_deg_prot        ?     ? ? ? 'X-RAY DIFFRACTION' ? 
x_dihedral_angle_d      ?     ? ? ? 'X-RAY DIFFRACTION' ? 
x_dihedral_angle_d_na   ?     ? ? ? 'X-RAY DIFFRACTION' ? 
x_dihedral_angle_d_prot ?     ? ? ? 'X-RAY DIFFRACTION' ? 
x_improper_angle_d      ?     ? ? ? 'X-RAY DIFFRACTION' ? 
x_improper_angle_d_na   ?     ? ? ? 'X-RAY DIFFRACTION' ? 
x_improper_angle_d_prot ?     ? ? ? 'X-RAY DIFFRACTION' ? 
x_mcbond_it             ?     ? ? ? 'X-RAY DIFFRACTION' ? 
x_mcangle_it            ?     ? ? ? 'X-RAY DIFFRACTION' ? 
x_scbond_it             ?     ? ? ? 'X-RAY DIFFRACTION' ? 
x_scangle_it            ?     ? ? ? 'X-RAY DIFFRACTION' ? 
# 
_database_PDB_matrix.entry_id          165D 
_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 
# 
_struct.entry_id                  165D 
_struct.title                     
;THE STRUCTURE OF A MISPAIRED RNA DOUBLE HELIX AT 1.6 ANGSTROMS RESOLUTION AND IMPLICATIONS FOR THE PREDICTION OF RNA SECONDARY STRUCTURE
;
_struct.pdbx_model_details        ? 
_struct.pdbx_CASP_flag            ? 
_struct.pdbx_model_type_details   ? 
# 
_struct_keywords.entry_id        165D 
_struct_keywords.pdbx_keywords   'DNA-RNA HYBRID' 
_struct_keywords.text            'A-DNA/RNA, DOUBLE HELIX, OVERHANGING BASES, MODIFIED, MISMATCHED, DNA-RNA HYBRID' 
# 
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 2 ? 
F N N 2 ? 
G N N 3 ? 
H N N 3 ? 
# 
_struct_ref.id                         1 
_struct_ref.entity_id                  1 
_struct_ref.db_name                    PDB 
_struct_ref.db_code                    165D 
_struct_ref.pdbx_db_accession          165D 
_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 165D A 1 ? 9 ? 165D 1  ? 9  ? 1  9  
2 1 165D B 1 ? 9 ? 165D 10 ? 18 ? 10 18 
# 
_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,G,H 
# 
_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 
# 
_struct_biol.id   1 
# 
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 C 8 "O3'" ? ? ? 1_555 A BRU 9 P  ? ? A C 8  A BRU 9  1_555 ? ? ? ? ? ? ?             1.584 ? ? 
covale2  covale both ? B C 8 "O3'" ? ? ? 1_555 B BRU 9 P  A ? B C 17 B BRU 18 1_555 ? ? ? ? ? ? ?             1.617 ? ? 
covale3  covale both ? B C 8 "O3'" ? ? ? 1_555 B BRU 9 P  B ? B C 17 B BRU 18 1_555 ? ? ? ? ? ? ?             1.632 ? ? 
hydrog1  hydrog ?    ? A G 1 N1    ? ? ? 1_555 B C   8 N3 ? ? A G 1  B C   17 1_555 ? ? ? ? ? ? WATSON-CRICK  ?     ? ? 
hydrog2  hydrog ?    ? A G 1 N2    ? ? ? 1_555 B C   8 O2 ? ? A G 1  B C   17 1_555 ? ? ? ? ? ? WATSON-CRICK  ?     ? ? 
hydrog3  hydrog ?    ? A G 1 O6    ? ? ? 1_555 B C   8 N4 ? ? A G 1  B C   17 1_555 ? ? ? ? ? ? WATSON-CRICK  ?     ? ? 
hydrog4  hydrog ?    ? A C 2 N3    ? ? ? 1_555 B G   7 N1 ? ? A C 2  B G   16 1_555 ? ? ? ? ? ? WATSON-CRICK  ?     ? ? 
hydrog5  hydrog ?    ? A C 2 N4    ? ? ? 1_555 B G   7 O6 ? ? A C 2  B G   16 1_555 ? ? ? ? ? ? WATSON-CRICK  ?     ? ? 
hydrog6  hydrog ?    ? A C 2 O2    ? ? ? 1_555 B G   7 N2 ? ? A C 2  B G   16 1_555 ? ? ? ? ? ? WATSON-CRICK  ?     ? ? 
hydrog7  hydrog ?    ? A U 3 N3    ? ? ? 1_555 B G   6 O6 ? ? A U 3  B G   15 1_555 ? ? ? ? ? ? TYPE_28_PAIR  ?     ? ? 
hydrog8  hydrog ?    ? A U 3 O2    ? ? ? 1_555 B G   6 N1 ? ? A U 3  B G   15 1_555 ? ? ? ? ? ? TYPE_28_PAIR  ?     ? ? 
hydrog9  hydrog ?    ? A U 4 O4    ? ? ? 1_555 B C   5 N4 ? ? A U 4  B C   14 1_555 ? ? ? ? ? ? 'U-C MISPAIR' ?     ? ? 
hydrog10 hydrog ?    ? A C 5 N4    ? ? ? 1_555 B U   4 O4 ? ? A C 5  B U   13 1_555 ? ? ? ? ? ? 'C-U MISPAIR' ?     ? ? 
hydrog11 hydrog ?    ? A G 6 N1    ? ? ? 1_555 B U   3 O2 ? ? A G 6  B U   12 1_555 ? ? ? ? ? ? TYPE_28_PAIR  ?     ? ? 
hydrog12 hydrog ?    ? A G 6 O6    ? ? ? 1_555 B U   3 N3 ? ? A G 6  B U   12 1_555 ? ? ? ? ? ? TYPE_28_PAIR  ?     ? ? 
hydrog13 hydrog ?    ? A G 7 N1    ? ? ? 1_555 B C   2 N3 ? ? A G 7  B C   11 1_555 ? ? ? ? ? ? WATSON-CRICK  ?     ? ? 
hydrog14 hydrog ?    ? A G 7 N2    ? ? ? 1_555 B C   2 O2 ? ? A G 7  B C   11 1_555 ? ? ? ? ? ? WATSON-CRICK  ?     ? ? 
hydrog15 hydrog ?    ? A G 7 O6    ? ? ? 1_555 B C   2 N4 ? ? A G 7  B C   11 1_555 ? ? ? ? ? ? WATSON-CRICK  ?     ? ? 
hydrog16 hydrog ?    ? A C 8 N3    ? ? ? 1_555 B G   1 N1 ? ? A C 8  B G   10 1_555 ? ? ? ? ? ? WATSON-CRICK  ?     ? ? 
hydrog17 hydrog ?    ? A C 8 N4    ? ? ? 1_555 B G   1 O6 ? ? A C 8  B G   10 1_555 ? ? ? ? ? ? WATSON-CRICK  ?     ? ? 
hydrog18 hydrog ?    ? A C 8 O2    ? ? ? 1_555 B G   1 N2 ? ? A C 8  B G   10 1_555 ? ? ? ? ? ? WATSON-CRICK  ?     ? ? 
# 
loop_
_struct_conn_type.id 
_struct_conn_type.criteria 
_struct_conn_type.reference 
covale ? ? 
hydrog ? ? 
# 
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 A RHD 19 ? 5 'BINDING SITE FOR RESIDUE RHD A 19' 
AC2 Software A RHD 20 ? 5 'BINDING SITE FOR RESIDUE RHD A 20' 
AC3 Software B RHD 21 ? 5 'BINDING SITE FOR RESIDUE RHD B 21' 
AC4 Software A RHD 22 ? 6 'BINDING SITE FOR RESIDUE RHD A 22' 
# 
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 5 C   A 5 ? C   A 5  . ? 1_555 ? 
2  AC1 5 G   A 6 ? G   A 6  . ? 1_555 ? 
3  AC1 5 G   A 7 ? G   A 7  . ? 1_555 ? 
4  AC1 5 HOH G . ? HOH A 26 . ? 1_555 ? 
5  AC1 5 HOH H . ? HOH B 72 . ? 1_555 ? 
6  AC2 5 C   A 5 ? C   A 5  . ? 4_546 ? 
7  AC2 5 G   A 7 ? G   A 7  . ? 1_545 ? 
8  AC2 5 C   A 8 ? C   A 8  . ? 1_545 ? 
9  AC2 5 C   B 5 ? C   B 14 . ? 4_546 ? 
10 AC2 5 HOH H . ? HOH B 45 . ? 4_546 ? 
11 AC3 5 U   A 3 ? U   A 3  . ? 1_555 ? 
12 AC3 5 G   B 6 ? G   B 15 . ? 1_555 ? 
13 AC3 5 G   B 7 ? G   B 16 . ? 1_555 ? 
14 AC3 5 HOH H . ? HOH B 34 . ? 1_555 ? 
15 AC3 5 HOH H . ? HOH B 46 . ? 1_555 ? 
16 AC4 6 C   A 2 ? C   A 2  . ? 2_566 ? 
17 AC4 6 U   A 3 ? U   A 3  . ? 2_566 ? 
18 AC4 6 BRU A 9 ? BRU A 9  . ? 1_555 ? 
19 AC4 6 C   B 2 ? C   B 11 . ? 2_556 ? 
20 AC4 6 U   B 3 ? U   B 12 . ? 2_556 ? 
21 AC4 6 HOH H . ? HOH B 32 . ? 2_556 ? 
# 
loop_
_pdbx_validate_close_contact.id 
_pdbx_validate_close_contact.PDB_model_num 
_pdbx_validate_close_contact.auth_atom_id_1 
_pdbx_validate_close_contact.auth_asym_id_1 
_pdbx_validate_close_contact.auth_comp_id_1 
_pdbx_validate_close_contact.auth_seq_id_1 
_pdbx_validate_close_contact.PDB_ins_code_1 
_pdbx_validate_close_contact.label_alt_id_1 
_pdbx_validate_close_contact.auth_atom_id_2 
_pdbx_validate_close_contact.auth_asym_id_2 
_pdbx_validate_close_contact.auth_comp_id_2 
_pdbx_validate_close_contact.auth_seq_id_2 
_pdbx_validate_close_contact.PDB_ins_code_2 
_pdbx_validate_close_contact.label_alt_id_2 
_pdbx_validate_close_contact.dist 
1 1 O A HOH 51 ? ? O A HOH 61 ? ? 1.43 
2 1 O B HOH 50 ? ? O B HOH 71 ? ? 2.05 
# 
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 N3    A U 3  ? ? C2    A U   3  ? ? O2    A U   3  ? ? 117.83 122.20 -4.37  0.70 N 
2 1 "O3'" A U 3  ? ? P     A U   4  ? ? OP2   A U   4  ? ? 117.53 110.50 7.03   1.10 Y 
3 1 "O4'" B U 13 ? ? "C1'" B U   13 ? ? N1    B U   13 ? ? 113.52 108.50 5.02   0.70 N 
4 1 "O3'" B C 14 ? ? P     B G   15 ? ? "O5'" B G   15 ? ? 92.37  104.00 -11.63 1.90 Y 
5 1 "O3'" B C 14 ? ? P     B G   15 ? ? OP2   B G   15 ? ? 128.59 110.50 18.09  1.10 Y 
6 1 "O3'" B G 15 ? ? P     B G   16 ? ? OP2   B G   16 ? ? 117.24 110.50 6.74   1.10 Y 
7 1 "O3'" B C 17 ? ? P     B BRU 18 ? A OP2   B BRU 18 ? A 123.90 110.50 13.40  1.10 Y 
8 1 "O3'" B C 17 ? ? P     B BRU 18 ? B OP2   B BRU 18 ? B 76.48  105.20 -28.72 2.20 Y 
9 1 "O3'" B C 17 ? ? P     B BRU 18 ? B OP1   B BRU 18 ? B 127.17 110.50 16.67  1.10 Y 
# 
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 G A 1  ? ? 0.075 'SIDE CHAIN' 
2 1 G A 7  ? ? 0.073 'SIDE CHAIN' 
3 1 C B 11 ? ? 0.072 'SIDE CHAIN' 
# 
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 BRU 9 A BRU 9  ? DU ? 
2 B BRU 9 B BRU 18 ? DU ? 
# 
_pdbx_struct_special_symmetry.id              1 
_pdbx_struct_special_symmetry.PDB_model_num   1 
_pdbx_struct_special_symmetry.auth_asym_id    B 
_pdbx_struct_special_symmetry.auth_comp_id    BRU 
_pdbx_struct_special_symmetry.auth_seq_id     18 
_pdbx_struct_special_symmetry.PDB_ins_code    ? 
_pdbx_struct_special_symmetry.label_asym_id   B 
_pdbx_struct_special_symmetry.label_comp_id   BRU 
_pdbx_struct_special_symmetry.label_seq_id    9 
# 
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 
BRU N1     N  N N 1   
BRU C2     C  N N 2   
BRU N3     N  N N 3   
BRU C4     C  N N 4   
BRU C5     C  N N 5   
BRU C6     C  N N 6   
BRU O2     O  N N 7   
BRU O4     O  N N 8   
BRU BR     BR N N 9   
BRU "C1'"  C  N R 10  
BRU "C2'"  C  N N 11  
BRU "C3'"  C  N S 12  
BRU "C4'"  C  N R 13  
BRU "O3'"  O  N N 14  
BRU "O4'"  O  N N 15  
BRU "C5'"  C  N N 16  
BRU "O5'"  O  N N 17  
BRU P      P  N N 18  
BRU OP1    O  N N 19  
BRU OP2    O  N N 20  
BRU OP3    O  N N 21  
BRU HN3    H  N N 22  
BRU H6     H  N N 23  
BRU "H1'"  H  N N 24  
BRU "H2'"  H  N N 25  
BRU "H2''" H  N N 26  
BRU "H3'"  H  N N 27  
BRU "H4'"  H  N N 28  
BRU "HO3'" H  N N 29  
BRU "H5'"  H  N N 30  
BRU "H5''" H  N N 31  
BRU HOP2   H  N N 32  
BRU HOP3   H  N N 33  
C   OP3    O  N N 34  
C   P      P  N N 35  
C   OP1    O  N N 36  
C   OP2    O  N N 37  
C   "O5'"  O  N N 38  
C   "C5'"  C  N N 39  
C   "C4'"  C  N R 40  
C   "O4'"  O  N N 41  
C   "C3'"  C  N S 42  
C   "O3'"  O  N N 43  
C   "C2'"  C  N R 44  
C   "O2'"  O  N N 45  
C   "C1'"  C  N R 46  
C   N1     N  N N 47  
C   C2     C  N N 48  
C   O2     O  N N 49  
C   N3     N  N N 50  
C   C4     C  N N 51  
C   N4     N  N N 52  
C   C5     C  N N 53  
C   C6     C  N N 54  
C   HOP3   H  N N 55  
C   HOP2   H  N N 56  
C   "H5'"  H  N N 57  
C   "H5''" H  N N 58  
C   "H4'"  H  N N 59  
C   "H3'"  H  N N 60  
C   "HO3'" H  N N 61  
C   "H2'"  H  N N 62  
C   "HO2'" H  N N 63  
C   "H1'"  H  N N 64  
C   H41    H  N N 65  
C   H42    H  N N 66  
C   H5     H  N N 67  
C   H6     H  N N 68  
G   OP3    O  N N 69  
G   P      P  N N 70  
G   OP1    O  N N 71  
G   OP2    O  N N 72  
G   "O5'"  O  N N 73  
G   "C5'"  C  N N 74  
G   "C4'"  C  N R 75  
G   "O4'"  O  N N 76  
G   "C3'"  C  N S 77  
G   "O3'"  O  N N 78  
G   "C2'"  C  N R 79  
G   "O2'"  O  N N 80  
G   "C1'"  C  N R 81  
G   N9     N  Y N 82  
G   C8     C  Y N 83  
G   N7     N  Y N 84  
G   C5     C  Y N 85  
G   C6     C  N N 86  
G   O6     O  N N 87  
G   N1     N  N N 88  
G   C2     C  N N 89  
G   N2     N  N N 90  
G   N3     N  N N 91  
G   C4     C  Y N 92  
G   HOP3   H  N N 93  
G   HOP2   H  N N 94  
G   "H5'"  H  N N 95  
G   "H5''" H  N N 96  
G   "H4'"  H  N N 97  
G   "H3'"  H  N N 98  
G   "HO3'" H  N N 99  
G   "H2'"  H  N N 100 
G   "HO2'" H  N N 101 
G   "H1'"  H  N N 102 
G   H8     H  N N 103 
G   H1     H  N N 104 
G   H21    H  N N 105 
G   H22    H  N N 106 
HOH O      O  N N 107 
HOH H1     H  N N 108 
HOH H2     H  N N 109 
RHD RH     RH N N 110 
RHD N1     N  N N 111 
RHD N2     N  N N 112 
RHD N3     N  N N 113 
RHD N4     N  N N 114 
RHD N5     N  N N 115 
RHD N6     N  N N 116 
RHD HN11   H  N N 117 
RHD HN12   H  N N 118 
RHD HN13   H  N N 119 
RHD HN21   H  N N 120 
RHD HN22   H  N N 121 
RHD HN23   H  N N 122 
RHD HN31   H  N N 123 
RHD HN32   H  N N 124 
RHD HN33   H  N N 125 
RHD HN41   H  N N 126 
RHD HN42   H  N N 127 
RHD HN43   H  N N 128 
RHD HN51   H  N N 129 
RHD HN52   H  N N 130 
RHD HN53   H  N N 131 
RHD HN61   H  N N 132 
RHD HN62   H  N N 133 
RHD HN63   H  N N 134 
U   OP3    O  N N 135 
U   P      P  N N 136 
U   OP1    O  N N 137 
U   OP2    O  N N 138 
U   "O5'"  O  N N 139 
U   "C5'"  C  N N 140 
U   "C4'"  C  N R 141 
U   "O4'"  O  N N 142 
U   "C3'"  C  N S 143 
U   "O3'"  O  N N 144 
U   "C2'"  C  N R 145 
U   "O2'"  O  N N 146 
U   "C1'"  C  N R 147 
U   N1     N  N N 148 
U   C2     C  N N 149 
U   O2     O  N N 150 
U   N3     N  N N 151 
U   C4     C  N N 152 
U   O4     O  N N 153 
U   C5     C  N N 154 
U   C6     C  N N 155 
U   HOP3   H  N N 156 
U   HOP2   H  N N 157 
U   "H5'"  H  N N 158 
U   "H5''" H  N N 159 
U   "H4'"  H  N N 160 
U   "H3'"  H  N N 161 
U   "HO3'" H  N N 162 
U   "H2'"  H  N N 163 
U   "HO2'" H  N N 164 
U   "H1'"  H  N N 165 
U   H3     H  N N 166 
U   H5     H  N N 167 
U   H6     H  N N 168 
# 
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 
BRU N1    C2     sing N N 1   
BRU N1    C6     sing N N 2   
BRU N1    "C1'"  sing N N 3   
BRU C2    N3     sing N N 4   
BRU C2    O2     doub N N 5   
BRU N3    C4     sing N N 6   
BRU N3    HN3    sing N N 7   
BRU C4    C5     sing N N 8   
BRU C4    O4     doub N N 9   
BRU C5    C6     doub N N 10  
BRU C5    BR     sing N N 11  
BRU C6    H6     sing N N 12  
BRU "C1'" "C2'"  sing N N 13  
BRU "C1'" "O4'"  sing N N 14  
BRU "C1'" "H1'"  sing N N 15  
BRU "C2'" "C3'"  sing N N 16  
BRU "C2'" "H2'"  sing N N 17  
BRU "C2'" "H2''" sing N N 18  
BRU "C3'" "C4'"  sing N N 19  
BRU "C3'" "O3'"  sing N N 20  
BRU "C3'" "H3'"  sing N N 21  
BRU "C4'" "O4'"  sing N N 22  
BRU "C4'" "C5'"  sing N N 23  
BRU "C4'" "H4'"  sing N N 24  
BRU "O3'" "HO3'" sing N N 25  
BRU "C5'" "O5'"  sing N N 26  
BRU "C5'" "H5'"  sing N N 27  
BRU "C5'" "H5''" sing N N 28  
BRU "O5'" P      sing N N 29  
BRU P     OP1    doub N N 30  
BRU P     OP2    sing N N 31  
BRU P     OP3    sing N N 32  
BRU OP2   HOP2   sing N N 33  
BRU OP3   HOP3   sing N N 34  
C   OP3   P      sing N N 35  
C   OP3   HOP3   sing N N 36  
C   P     OP1    doub N N 37  
C   P     OP2    sing N N 38  
C   P     "O5'"  sing N N 39  
C   OP2   HOP2   sing N N 40  
C   "O5'" "C5'"  sing N N 41  
C   "C5'" "C4'"  sing N N 42  
C   "C5'" "H5'"  sing N N 43  
C   "C5'" "H5''" sing N N 44  
C   "C4'" "O4'"  sing N N 45  
C   "C4'" "C3'"  sing N N 46  
C   "C4'" "H4'"  sing N N 47  
C   "O4'" "C1'"  sing N N 48  
C   "C3'" "O3'"  sing N N 49  
C   "C3'" "C2'"  sing N N 50  
C   "C3'" "H3'"  sing N N 51  
C   "O3'" "HO3'" sing N N 52  
C   "C2'" "O2'"  sing N N 53  
C   "C2'" "C1'"  sing N N 54  
C   "C2'" "H2'"  sing N N 55  
C   "O2'" "HO2'" sing N N 56  
C   "C1'" N1     sing N N 57  
C   "C1'" "H1'"  sing N N 58  
C   N1    C2     sing N N 59  
C   N1    C6     sing N N 60  
C   C2    O2     doub N N 61  
C   C2    N3     sing N N 62  
C   N3    C4     doub N N 63  
C   C4    N4     sing N N 64  
C   C4    C5     sing N N 65  
C   N4    H41    sing N N 66  
C   N4    H42    sing N N 67  
C   C5    C6     doub N N 68  
C   C5    H5     sing N N 69  
C   C6    H6     sing N N 70  
G   OP3   P      sing N N 71  
G   OP3   HOP3   sing N N 72  
G   P     OP1    doub N N 73  
G   P     OP2    sing N N 74  
G   P     "O5'"  sing N N 75  
G   OP2   HOP2   sing N N 76  
G   "O5'" "C5'"  sing N N 77  
G   "C5'" "C4'"  sing N N 78  
G   "C5'" "H5'"  sing N N 79  
G   "C5'" "H5''" sing N N 80  
G   "C4'" "O4'"  sing N N 81  
G   "C4'" "C3'"  sing N N 82  
G   "C4'" "H4'"  sing N N 83  
G   "O4'" "C1'"  sing N N 84  
G   "C3'" "O3'"  sing N N 85  
G   "C3'" "C2'"  sing N N 86  
G   "C3'" "H3'"  sing N N 87  
G   "O3'" "HO3'" sing N N 88  
G   "C2'" "O2'"  sing N N 89  
G   "C2'" "C1'"  sing N N 90  
G   "C2'" "H2'"  sing N N 91  
G   "O2'" "HO2'" sing N N 92  
G   "C1'" N9     sing N N 93  
G   "C1'" "H1'"  sing N N 94  
G   N9    C8     sing Y N 95  
G   N9    C4     sing Y N 96  
G   C8    N7     doub Y N 97  
G   C8    H8     sing N N 98  
G   N7    C5     sing Y N 99  
G   C5    C6     sing N N 100 
G   C5    C4     doub Y N 101 
G   C6    O6     doub N N 102 
G   C6    N1     sing N N 103 
G   N1    C2     sing N N 104 
G   N1    H1     sing N N 105 
G   C2    N2     sing N N 106 
G   C2    N3     doub N N 107 
G   N2    H21    sing N N 108 
G   N2    H22    sing N N 109 
G   N3    C4     sing N N 110 
HOH O     H1     sing N N 111 
HOH O     H2     sing N N 112 
RHD RH    N1     sing N N 113 
RHD RH    N2     sing N N 114 
RHD RH    N3     sing N N 115 
RHD RH    N4     sing N N 116 
RHD RH    N5     sing N N 117 
RHD RH    N6     sing N N 118 
RHD N1    HN11   sing N N 119 
RHD N1    HN12   sing N N 120 
RHD N1    HN13   sing N N 121 
RHD N2    HN21   sing N N 122 
RHD N2    HN22   sing N N 123 
RHD N2    HN23   sing N N 124 
RHD N3    HN31   sing N N 125 
RHD N3    HN32   sing N N 126 
RHD N3    HN33   sing N N 127 
RHD N4    HN41   sing N N 128 
RHD N4    HN42   sing N N 129 
RHD N4    HN43   sing N N 130 
RHD N5    HN51   sing N N 131 
RHD N5    HN52   sing N N 132 
RHD N5    HN53   sing N N 133 
RHD N6    HN61   sing N N 134 
RHD N6    HN62   sing N N 135 
RHD N6    HN63   sing N N 136 
U   OP3   P      sing N N 137 
U   OP3   HOP3   sing N N 138 
U   P     OP1    doub N N 139 
U   P     OP2    sing N N 140 
U   P     "O5'"  sing N N 141 
U   OP2   HOP2   sing N N 142 
U   "O5'" "C5'"  sing N N 143 
U   "C5'" "C4'"  sing N N 144 
U   "C5'" "H5'"  sing N N 145 
U   "C5'" "H5''" sing N N 146 
U   "C4'" "O4'"  sing N N 147 
U   "C4'" "C3'"  sing N N 148 
U   "C4'" "H4'"  sing N N 149 
U   "O4'" "C1'"  sing N N 150 
U   "C3'" "O3'"  sing N N 151 
U   "C3'" "C2'"  sing N N 152 
U   "C3'" "H3'"  sing N N 153 
U   "O3'" "HO3'" sing N N 154 
U   "C2'" "O2'"  sing N N 155 
U   "C2'" "C1'"  sing N N 156 
U   "C2'" "H2'"  sing N N 157 
U   "O2'" "HO2'" sing N N 158 
U   "C1'" N1     sing N N 159 
U   "C1'" "H1'"  sing N N 160 
U   N1    C2     sing N N 161 
U   N1    C6     sing N N 162 
U   C2    O2     doub N N 163 
U   C2    N3     sing N N 164 
U   N3    C4     sing N N 165 
U   N3    H3     sing N N 166 
U   C4    O4     doub N N 167 
U   C4    C5     sing N N 168 
U   C5    C6     doub N N 169 
U   C5    H5     sing N N 170 
U   C6    H6     sing N N 171 
# 
loop_
_ndb_struct_conf_na.entry_id 
_ndb_struct_conf_na.feature 
165D 'double helix'         
165D 'a-form double helix'  
165D 'mismatched base pair' 
# 
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 G 1 1_555 B C 8 1_555 -0.507 -0.379 -0.271 0.915  -13.439 1.089   1 A_G1:C17_B A 1 ? B 17 ? 19 1 
1 A C 2 1_555 B G 7 1_555 0.162  -0.263 -0.027 5.509  -11.964 1.106   2 A_C2:G16_B A 2 ? B 16 ? 19 1 
1 A U 3 1_555 B G 6 1_555 2.233  -0.490 -0.124 4.776  -10.255 -1.858  3 A_U3:G15_B A 3 ? B 15 ? 28 ? 
1 A U 4 1_555 B C 5 1_555 -0.638 0.206  0.220  2.026  2.784   -40.981 4 A_U4:C14_B A 4 ? B 14 ? ?  ? 
1 A C 5 1_555 B U 4 1_555 0.733  0.119  -0.397 7.013  -3.734  -39.828 5 A_C5:U13_B A 5 ? B 13 ? ?  ? 
1 A G 6 1_555 B U 3 1_555 -2.244 -0.601 -0.180 -0.232 -12.882 -1.239  6 A_G6:U12_B A 6 ? B 12 ? 28 1 
1 A G 7 1_555 B C 2 1_555 -0.178 -0.118 -0.160 -4.817 -12.774 1.012   7 A_G7:C11_B A 7 ? B 11 ? 19 1 
1 A C 8 1_555 B G 1 1_555 0.445  -0.195 0.090  -3.779 -6.718  -0.871  8 A_C8:G10_B A 8 ? B 10 ? 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 G 1 1_555 B C 8 1_555 A C 2 1_555 B G 7 1_555 -0.228 -1.669 3.238 -2.718 4.640  35.602 -3.335 -0.002 3.012 7.535  4.415  
35.993 1 AA_G1C2:G16C17_BB A 1 ? B 17 ? A 2 ? B 16 ? 
1 A C 2 1_555 B G 7 1_555 A U 3 1_555 B G 6 1_555 -0.023 -1.320 3.377 2.142  5.349  37.904 -2.684 0.305  3.163 8.177  -3.275 
38.323 2 AA_C2U3:G15G16_BB A 2 ? B 16 ? A 3 ? B 15 ? 
1 A U 3 1_555 B G 6 1_555 A U 4 1_555 B C 5 1_555 -3.926 -1.958 3.406 -5.163 6.663  20.686 -7.783 8.032  3.479 17.641 13.668 
22.320 3 AA_U3U4:C14G15_BB A 3 ? B 15 ? A 4 ? B 14 ? 
1 A U 4 1_555 B C 5 1_555 A C 5 1_555 B U 4 1_555 0.004  -1.867 3.489 2.016  6.124  38.655 -3.536 0.241  3.164 9.174  -3.019 
39.169 4 AA_U4C5:U13C14_BB A 4 ? B 14 ? A 5 ? B 13 ? 
1 A C 5 1_555 B U 4 1_555 A G 6 1_555 B U 3 1_555 3.202  -1.635 3.434 -0.651 12.018 25.252 -6.047 -6.779 2.344 25.709 1.393  
27.932 5 AA_C5G6:U12U13_BB A 5 ? B 13 ? A 6 ? B 12 ? 
1 A G 6 1_555 B U 3 1_555 A G 7 1_555 B C 2 1_555 0.186  -1.616 3.456 -0.690 7.573  39.522 -3.219 -0.350 3.103 11.075 1.009  
40.218 6 AA_G6G7:C11U12_BB A 6 ? B 12 ? A 7 ? B 11 ? 
1 A G 7 1_555 B C 2 1_555 A C 8 1_555 B G 1 1_555 0.107  -1.732 3.462 -0.073 -0.759 35.338 -2.734 -0.187 3.497 -1.251 0.121  
35.346 7 AA_G7C8:G10C11_BB A 7 ? B 11 ? A 8 ? B 10 ? 
# 
_atom_sites.entry_id                    165D 
_atom_sites.fract_transf_matrix[1][1]   0.018587 
_atom_sites.fract_transf_matrix[1][2]   0.000000 
_atom_sites.fract_transf_matrix[1][3]   0.006729 
_atom_sites.fract_transf_matrix[2][1]   0.000000 
_atom_sites.fract_transf_matrix[2][2]   0.051546 
_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]   0.021211 
_atom_sites.fract_transf_vector[1]      0.00000 
_atom_sites.fract_transf_vector[2]      0.00000 
_atom_sites.fract_transf_vector[3]      0.00000 
# 
_atom_sites_footnote.id     1 
_atom_sites_footnote.text   
;THE DEOXY-BROMO-URACIL +U IS WELL ORDERED ON STRAND A BUT NOT ON STRAND B (RESIDUE +U 18) WHERE TWO (50:50) DISORDERED POSITIONS WERE GIVEN. FOUR RHODIUM HEXAMINE IONS RH(NH3)6 ++ WERE LOCATED (NAMED RHD), TWO WITH FULL OCCUPANCY FACTORS (RESIDUES 19 AND 20) AND TWO WITH PARTIAL OCCUPANCIES (RESIDUES 21 AND 22).
;
# 
loop_
_atom_type.symbol 
BR 
C  
N  
O  
P  
RH 
# 
loop_