data_438D # _entry.id 438D # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.387 _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 438D pdb_0000438d 10.2210/pdb438d/pdb RCSB AR0011 ? ? WWPDB D_1000179232 ? ? # 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 1999-05-12 2 'Structure model' 1 1 2008-05-22 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2024-02-28 # _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' # 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 # 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' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 438D _pdbx_database_status.recvd_initial_deposition_date 1998-12-28 _pdbx_database_status.deposit_site NDB _pdbx_database_status.process_site NDB _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 'Shi, K.' 1 'Wahl, M.C.' 2 'Sundaralingam, M.' 3 # _citation.id primary _citation.title 'Crystal structure of an RNA duplex r(G GCGC CC)2 with non-adjacent G*U base pairs.' _citation.journal_abbrev 'Nucleic Acids Res.' _citation.journal_volume 27 _citation.page_first 2196 _citation.page_last 2201 _citation.year 1999 _citation.journal_id_ASTM NARHAD _citation.country UK _citation.journal_id_ISSN 0305-1048 _citation.journal_id_CSD 0389 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 10219093 _citation.pdbx_database_id_DOI 10.1093/nar/27.10.2196 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Shi, K.' 1 ? primary 'Wahl, M.' 2 ? primary 'Sundaralingam, M.' 3 ? # 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 ;RNA (5'-R(*GP*GP*GP*CP*GP*CP*UP*CP*C)-3') ; 2862.759 2 ? ? ? ? 2 water nat water 18.015 34 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code GGGCGCUCC _entity_poly.pdbx_seq_one_letter_code_can GGGCGCUCC _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id 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 G n 1 3 G n 1 4 C n 1 5 G n 1 6 C n 1 7 U n 1 8 C n 1 9 C 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 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 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 G 2 2 2 G G A . n A 1 3 G 3 3 3 G G A . n A 1 4 C 4 4 4 C C A . n A 1 5 G 5 5 5 G G A . n A 1 6 C 6 6 6 C C A . n A 1 7 U 7 7 7 U U A . n A 1 8 C 8 8 8 C C A . n A 1 9 C 9 9 9 C C A . n B 1 1 G 1 10 10 G G B . n B 1 2 G 2 11 11 G G B . n B 1 3 G 3 12 12 G G B . n B 1 4 C 4 13 13 C C B . n B 1 5 G 5 14 14 G G B . n B 1 6 C 6 15 15 C C B . n B 1 7 U 7 16 16 U U B . n B 1 8 C 8 17 17 C C B . n B 1 9 C 9 18 18 C 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 HOH 1 101 101 HOH HOH A . C 2 HOH 2 102 102 HOH HOH A . C 2 HOH 3 103 103 HOH HOH A . C 2 HOH 4 104 104 HOH HOH A . C 2 HOH 5 110 110 HOH HOH A . C 2 HOH 6 112 112 HOH HOH A . C 2 HOH 7 113 113 HOH HOH A . C 2 HOH 8 114 114 HOH HOH A . C 2 HOH 9 115 115 HOH HOH A . C 2 HOH 10 119 119 HOH HOH A . C 2 HOH 11 121 121 HOH HOH A . C 2 HOH 12 122 122 HOH HOH A . C 2 HOH 13 124 124 HOH HOH A . C 2 HOH 14 125 125 HOH HOH A . C 2 HOH 15 126 126 HOH HOH A . C 2 HOH 16 127 127 HOH HOH A . C 2 HOH 17 201 201 HOH HOH A . C 2 HOH 18 203 203 HOH HOH A . C 2 HOH 19 205 205 HOH HOH A . D 2 HOH 1 105 105 HOH HOH B . D 2 HOH 2 106 106 HOH HOH B . D 2 HOH 3 107 107 HOH HOH B . D 2 HOH 4 108 108 HOH HOH B . D 2 HOH 5 109 109 HOH HOH B . D 2 HOH 6 111 111 HOH HOH B . D 2 HOH 7 116 116 HOH HOH B . D 2 HOH 8 117 117 HOH HOH B . D 2 HOH 9 118 118 HOH HOH B . D 2 HOH 10 120 120 HOH HOH B . D 2 HOH 11 123 123 HOH HOH B . D 2 HOH 12 128 128 HOH HOH B . D 2 HOH 13 129 129 HOH HOH B . D 2 HOH 14 130 130 HOH HOH B . D 2 HOH 15 202 202 HOH HOH B . # loop_ _pdbx_unobs_or_zero_occ_atoms.id _pdbx_unobs_or_zero_occ_atoms.PDB_model_num _pdbx_unobs_or_zero_occ_atoms.polymer_flag _pdbx_unobs_or_zero_occ_atoms.occupancy_flag _pdbx_unobs_or_zero_occ_atoms.auth_asym_id _pdbx_unobs_or_zero_occ_atoms.auth_comp_id _pdbx_unobs_or_zero_occ_atoms.auth_seq_id _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code _pdbx_unobs_or_zero_occ_atoms.auth_atom_id _pdbx_unobs_or_zero_occ_atoms.label_alt_id _pdbx_unobs_or_zero_occ_atoms.label_asym_id _pdbx_unobs_or_zero_occ_atoms.label_comp_id _pdbx_unobs_or_zero_occ_atoms.label_seq_id _pdbx_unobs_or_zero_occ_atoms.label_atom_id 1 1 Y 1 A C 9 ? "C5'" ? A C 9 "C5'" 2 1 Y 1 A C 9 ? "C4'" ? A C 9 "C4'" 3 1 Y 1 A C 9 ? "O4'" ? A C 9 "O4'" 4 1 Y 1 A C 9 ? "C3'" ? A C 9 "C3'" 5 1 Y 1 A C 9 ? "O3'" ? A C 9 "O3'" 6 1 Y 1 A C 9 ? "C2'" ? A C 9 "C2'" 7 1 Y 1 A C 9 ? "O2'" ? A C 9 "O2'" 8 1 Y 1 A C 9 ? "C1'" ? A C 9 "C1'" 9 1 Y 1 A C 9 ? N1 ? A C 9 N1 10 1 Y 1 A C 9 ? C2 ? A C 9 C2 11 1 Y 1 A C 9 ? O2 ? A C 9 O2 12 1 Y 1 A C 9 ? N3 ? A C 9 N3 13 1 Y 1 A C 9 ? C4 ? A C 9 C4 14 1 Y 1 A C 9 ? N4 ? A C 9 N4 15 1 Y 1 A C 9 ? C5 ? A C 9 C5 16 1 Y 1 A C 9 ? C6 ? A C 9 C6 17 1 Y 0 A C 9 ? OP1 ? A C 9 OP1 18 1 Y 0 A C 9 ? OP2 ? A C 9 OP2 19 1 Y 0 A C 9 ? "O5'" ? A C 9 "O5'" 20 1 Y 1 B C 18 ? "C5'" ? B C 9 "C5'" 21 1 Y 1 B C 18 ? "C4'" ? B C 9 "C4'" 22 1 Y 1 B C 18 ? "O4'" ? B C 9 "O4'" 23 1 Y 1 B C 18 ? "C3'" ? B C 9 "C3'" 24 1 Y 1 B C 18 ? "O3'" ? B C 9 "O3'" 25 1 Y 1 B C 18 ? "C2'" ? B C 9 "C2'" 26 1 Y 1 B C 18 ? "O2'" ? B C 9 "O2'" 27 1 Y 1 B C 18 ? "C1'" ? B C 9 "C1'" 28 1 Y 1 B C 18 ? N1 ? B C 9 N1 29 1 Y 1 B C 18 ? C2 ? B C 9 C2 30 1 Y 1 B C 18 ? O2 ? B C 9 O2 31 1 Y 1 B C 18 ? N3 ? B C 9 N3 32 1 Y 1 B C 18 ? C4 ? B C 9 C4 33 1 Y 1 B C 18 ? N4 ? B C 9 N4 34 1 Y 1 B C 18 ? C5 ? B C 9 C5 35 1 Y 1 B C 18 ? C6 ? B C 9 C6 36 1 Y 0 B C 18 ? OP1 ? B C 9 OP1 37 1 Y 0 B C 18 ? OP2 ? B C 9 OP2 38 1 Y 0 B C 18 ? "O5'" ? B C 9 "O5'" # _software.name X-PLOR _software.classification refinement _software.version 3.1 _software.citation_id ? _software.pdbx_ordinal 1 # _cell.entry_id 438D _cell.length_a 45.68 _cell.length_b 45.68 _cell.length_c 59.95 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 438D _symmetry.space_group_name_H-M 'H 3' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting hexagonal _symmetry.Int_Tables_number 146 # _exptl.entry_id 438D _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.10 _exptl_crystal.density_percent_sol 41.50 _exptl_crystal.description ? # _diffrn.id 1 _diffrn.crystal_id 1 _diffrn.ambient_temp ? _diffrn.ambient_temp_details ? # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'IMAGE PLATE' _diffrn_detector.type 'RIGAKU RAXIS IIC' _diffrn_detector.pdbx_collection_date ? _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 ? _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 _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength 1.5418 _diffrn_source.pdbx_wavelength_list ? # _reflns.entry_id 438D _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F 2.0 _reflns.d_resolution_low 10.0 _reflns.d_resolution_high 2.50 _reflns.number_obs 1403 _reflns.number_all 1521 _reflns.percent_possible_obs 83.8 _reflns.pdbx_Rmerge_I_obs 0.0430000 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 37 _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _refine.entry_id 438D _refine.ls_number_reflns_obs 1403 _refine.ls_number_reflns_all 1521 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 2.0 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 10.0 _refine.ls_d_res_high 2.50 _refine.ls_percent_reflns_obs 83.8 _refine.ls_R_factor_obs 0.1860000 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.1860000 _refine.ls_R_factor_R_free 0.2400000 _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 THROUGHOUT _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 RANDOM _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 346 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 34 _refine_hist.number_atoms_total 380 _refine_hist.d_res_high 2.50 _refine_hist.d_res_low 10.0 # _database_PDB_matrix.entry_id 438D _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 438D _struct.title 'STRUCTURE OF AN RNA DUPLEX R(GGGCGCUCC)2 WITH NON-ADJACENT G.U BASE PAIRS' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 438D _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'A-RNA, DOUBLE HELIX, MISMATCHED, RNA' # 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 ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 438D _struct_ref.pdbx_db_accession 438D _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 438D A 1 ? 9 ? 438D 1 ? 9 ? 1 9 2 1 438D B 1 ? 9 ? 438D 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 # _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 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 G 2 N1 ? ? ? 1_555 B U 7 O2 ? ? A G 2 B U 16 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog5 hydrog ? ? A G 2 O6 ? ? ? 1_555 B U 7 N3 ? ? A G 2 B U 16 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog6 hydrog ? ? A G 3 N1 ? ? ? 1_555 B C 6 N3 ? ? A G 3 B C 15 1_555 ? ? ? ? ? ? 'G-C PAIR' ? ? ? hydrog7 hydrog ? ? A C 4 N3 ? ? ? 1_555 B G 5 N1 ? ? A C 4 B G 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A C 4 N4 ? ? ? 1_555 B G 5 O6 ? ? A C 4 B G 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A C 4 O2 ? ? ? 1_555 B G 5 N2 ? ? A C 4 B G 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A G 5 N1 ? ? ? 1_555 B C 4 N3 ? ? A G 5 B C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A G 5 N2 ? ? ? 1_555 B C 4 O2 ? ? A G 5 B C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A G 5 O6 ? ? ? 1_555 B C 4 N4 ? ? A G 5 B C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A C 6 N3 ? ? ? 1_555 B G 3 N1 ? ? A C 6 B G 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A C 6 N4 ? ? ? 1_555 B G 3 O6 ? ? A C 6 B G 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A C 6 O2 ? ? ? 1_555 B G 3 N2 ? ? A C 6 B G 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A U 7 N3 ? ? ? 1_555 B G 2 O6 ? ? A U 7 B G 11 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog17 hydrog ? ? A U 7 O2 ? ? ? 1_555 B G 2 N1 ? ? A U 7 B G 11 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog18 hydrog ? ? A C 8 N3 ? ? ? 1_555 B G 1 N1 ? ? A C 8 B G 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A C 8 N4 ? ? ? 1_555 B G 1 O6 ? ? A C 8 B G 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A C 8 O2 ? ? ? 1_555 B G 1 N2 ? ? A C 8 B G 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _pdbx_validate_rmsd_bond.id 1 _pdbx_validate_rmsd_bond.PDB_model_num 1 _pdbx_validate_rmsd_bond.auth_atom_id_1 C5 _pdbx_validate_rmsd_bond.auth_asym_id_1 A _pdbx_validate_rmsd_bond.auth_comp_id_1 G _pdbx_validate_rmsd_bond.auth_seq_id_1 3 _pdbx_validate_rmsd_bond.PDB_ins_code_1 ? _pdbx_validate_rmsd_bond.label_alt_id_1 ? _pdbx_validate_rmsd_bond.auth_atom_id_2 C6 _pdbx_validate_rmsd_bond.auth_asym_id_2 A _pdbx_validate_rmsd_bond.auth_comp_id_2 G _pdbx_validate_rmsd_bond.auth_seq_id_2 3 _pdbx_validate_rmsd_bond.PDB_ins_code_2 ? _pdbx_validate_rmsd_bond.label_alt_id_2 ? _pdbx_validate_rmsd_bond.bond_value 1.357 _pdbx_validate_rmsd_bond.bond_target_value 1.419 _pdbx_validate_rmsd_bond.bond_deviation -0.062 _pdbx_validate_rmsd_bond.bond_standard_deviation 0.010 _pdbx_validate_rmsd_bond.linker_flag N # _pdbx_validate_planes.id 1 _pdbx_validate_planes.PDB_model_num 1 _pdbx_validate_planes.auth_comp_id C _pdbx_validate_planes.auth_asym_id B _pdbx_validate_planes.auth_seq_id 15 _pdbx_validate_planes.PDB_ins_code ? _pdbx_validate_planes.label_alt_id ? _pdbx_validate_planes.rmsd 0.061 _pdbx_validate_planes.type 'SIDE CHAIN' # loop_ _pdbx_struct_special_symmetry.id _pdbx_struct_special_symmetry.PDB_model_num _pdbx_struct_special_symmetry.auth_asym_id _pdbx_struct_special_symmetry.auth_comp_id _pdbx_struct_special_symmetry.auth_seq_id _pdbx_struct_special_symmetry.PDB_ins_code _pdbx_struct_special_symmetry.label_asym_id _pdbx_struct_special_symmetry.label_comp_id _pdbx_struct_special_symmetry.label_seq_id 1 1 A HOH 201 ? C HOH . 2 1 A HOH 203 ? C HOH . 3 1 A HOH 205 ? C HOH . 4 1 B HOH 202 ? D HOH . # 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 C OP3 O N N 1 C P P N N 2 C OP1 O N N 3 C OP2 O N N 4 C "O5'" O N N 5 C "C5'" C N N 6 C "C4'" C N R 7 C "O4'" O N N 8 C "C3'" C N S 9 C "O3'" O N N 10 C "C2'" C N R 11 C "O2'" O N N 12 C "C1'" C N R 13 C N1 N N N 14 C C2 C N N 15 C O2 O N N 16 C N3 N N N 17 C C4 C N N 18 C N4 N N N 19 C C5 C N N 20 C C6 C N N 21 C HOP3 H N N 22 C HOP2 H N N 23 C "H5'" H N N 24 C "H5''" H N N 25 C "H4'" H N N 26 C "H3'" H N N 27 C "HO3'" H N N 28 C "H2'" H N N 29 C "HO2'" H N N 30 C "H1'" H N N 31 C H41 H N N 32 C H42 H N N 33 C H5 H N N 34 C H6 H N N 35 G OP3 O N N 36 G P P N N 37 G OP1 O N N 38 G OP2 O N N 39 G "O5'" O N N 40 G "C5'" C N N 41 G "C4'" C N R 42 G "O4'" O N N 43 G "C3'" C N S 44 G "O3'" O N N 45 G "C2'" C N R 46 G "O2'" O N N 47 G "C1'" C N R 48 G N9 N Y N 49 G C8 C Y N 50 G N7 N Y N 51 G C5 C Y N 52 G C6 C N N 53 G O6 O N N 54 G N1 N N N 55 G C2 C N N 56 G N2 N N N 57 G N3 N N N 58 G C4 C Y N 59 G HOP3 H N N 60 G HOP2 H N N 61 G "H5'" H N N 62 G "H5''" H N N 63 G "H4'" H N N 64 G "H3'" H N N 65 G "HO3'" H N N 66 G "H2'" H N N 67 G "HO2'" H N N 68 G "H1'" H N N 69 G H8 H N N 70 G H1 H N N 71 G H21 H N N 72 G H22 H N N 73 HOH O O N N 74 HOH H1 H N N 75 HOH H2 H N N 76 U OP3 O N N 77 U P P N N 78 U OP1 O N N 79 U OP2 O N N 80 U "O5'" O N N 81 U "C5'" C N N 82 U "C4'" C N R 83 U "O4'" O N N 84 U "C3'" C N S 85 U "O3'" O N N 86 U "C2'" C N R 87 U "O2'" O N N 88 U "C1'" C N R 89 U N1 N N N 90 U C2 C N N 91 U O2 O N N 92 U N3 N N N 93 U C4 C N N 94 U O4 O N N 95 U C5 C N N 96 U C6 C N N 97 U HOP3 H N N 98 U HOP2 H N N 99 U "H5'" H N N 100 U "H5''" H N N 101 U "H4'" H N N 102 U "H3'" H N N 103 U "HO3'" H N N 104 U "H2'" H N N 105 U "HO2'" H N N 106 U "H1'" H N N 107 U H3 H N N 108 U H5 H N N 109 U H6 H N N 110 # 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 C OP3 P sing N N 1 C OP3 HOP3 sing N N 2 C P OP1 doub N N 3 C P OP2 sing N N 4 C P "O5'" sing N N 5 C OP2 HOP2 sing N N 6 C "O5'" "C5'" sing N N 7 C "C5'" "C4'" sing N N 8 C "C5'" "H5'" sing N N 9 C "C5'" "H5''" sing N N 10 C "C4'" "O4'" sing N N 11 C "C4'" "C3'" sing N N 12 C "C4'" "H4'" sing N N 13 C "O4'" "C1'" sing N N 14 C "C3'" "O3'" sing N N 15 C "C3'" "C2'" sing N N 16 C "C3'" "H3'" sing N N 17 C "O3'" "HO3'" sing N N 18 C "C2'" "O2'" sing N N 19 C "C2'" "C1'" sing N N 20 C "C2'" "H2'" sing N N 21 C "O2'" "HO2'" sing N N 22 C "C1'" N1 sing N N 23 C "C1'" "H1'" sing N N 24 C N1 C2 sing N N 25 C N1 C6 sing N N 26 C C2 O2 doub N N 27 C C2 N3 sing N N 28 C N3 C4 doub N N 29 C C4 N4 sing N N 30 C C4 C5 sing N N 31 C N4 H41 sing N N 32 C N4 H42 sing N N 33 C C5 C6 doub N N 34 C C5 H5 sing N N 35 C C6 H6 sing N N 36 G OP3 P sing N N 37 G OP3 HOP3 sing N N 38 G P OP1 doub N N 39 G P OP2 sing N N 40 G P "O5'" sing N N 41 G OP2 HOP2 sing N N 42 G "O5'" "C5'" sing N N 43 G "C5'" "C4'" sing N N 44 G "C5'" "H5'" sing N N 45 G "C5'" "H5''" sing N N 46 G "C4'" "O4'" sing N N 47 G "C4'" "C3'" sing N N 48 G "C4'" "H4'" sing N N 49 G "O4'" "C1'" sing N N 50 G "C3'" "O3'" sing N N 51 G "C3'" "C2'" sing N N 52 G "C3'" "H3'" sing N N 53 G "O3'" "HO3'" sing N N 54 G "C2'" "O2'" sing N N 55 G "C2'" "C1'" sing N N 56 G "C2'" "H2'" sing N N 57 G "O2'" "HO2'" sing N N 58 G "C1'" N9 sing N N 59 G "C1'" "H1'" sing N N 60 G N9 C8 sing Y N 61 G N9 C4 sing Y N 62 G C8 N7 doub Y N 63 G C8 H8 sing N N 64 G N7 C5 sing Y N 65 G C5 C6 sing N N 66 G C5 C4 doub Y N 67 G C6 O6 doub N N 68 G C6 N1 sing N N 69 G N1 C2 sing N N 70 G N1 H1 sing N N 71 G C2 N2 sing N N 72 G C2 N3 doub N N 73 G N2 H21 sing N N 74 G N2 H22 sing N N 75 G N3 C4 sing N N 76 HOH O H1 sing N N 77 HOH O H2 sing N N 78 U OP3 P sing N N 79 U OP3 HOP3 sing N N 80 U P OP1 doub N N 81 U P OP2 sing N N 82 U P "O5'" sing N N 83 U OP2 HOP2 sing N N 84 U "O5'" "C5'" sing N N 85 U "C5'" "C4'" sing N N 86 U "C5'" "H5'" sing N N 87 U "C5'" "H5''" sing N N 88 U "C4'" "O4'" sing N N 89 U "C4'" "C3'" sing N N 90 U "C4'" "H4'" sing N N 91 U "O4'" "C1'" sing N N 92 U "C3'" "O3'" sing N N 93 U "C3'" "C2'" sing N N 94 U "C3'" "H3'" sing N N 95 U "O3'" "HO3'" sing N N 96 U "C2'" "O2'" sing N N 97 U "C2'" "C1'" sing N N 98 U "C2'" "H2'" sing N N 99 U "O2'" "HO2'" sing N N 100 U "C1'" N1 sing N N 101 U "C1'" "H1'" sing N N 102 U N1 C2 sing N N 103 U N1 C6 sing N N 104 U C2 O2 doub N N 105 U C2 N3 sing N N 106 U N3 C4 sing N N 107 U N3 H3 sing N N 108 U C4 O4 doub N N 109 U C4 C5 sing N N 110 U C5 C6 doub N N 111 U C5 H5 sing N N 112 U C6 H6 sing N N 113 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 438D 'a-form double helix' 438D '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 -0.309 -0.397 0.360 2.237 -10.793 0.549 1 A_G1:C17_B A 1 ? B 17 ? 19 1 1 A G 2 1_555 B U 7 1_555 -2.237 -0.576 0.432 5.547 -17.948 -1.165 2 A_G2:U16_B A 2 ? B 16 ? 28 ? 1 A G 3 1_555 B C 6 1_555 -0.011 0.045 0.910 7.931 -16.257 5.587 3 A_G3:C15_B A 3 ? B 15 ? ? 1 1 A C 4 1_555 B G 5 1_555 -0.014 -0.218 -0.118 5.101 -17.511 0.005 4 A_C4:G14_B A 4 ? B 14 ? 19 1 1 A G 5 1_555 B C 4 1_555 -0.164 -0.242 0.120 -7.503 -15.725 1.236 5 A_G5:C13_B A 5 ? B 13 ? 19 1 1 A C 6 1_555 B G 3 1_555 0.608 -0.538 0.209 -8.876 -13.067 -1.099 6 A_C6:G12_B A 6 ? B 12 ? 19 1 1 A U 7 1_555 B G 2 1_555 2.617 -0.866 0.333 -3.665 -19.935 -0.517 7 A_U7:G11_B A 7 ? B 11 ? 28 ? 1 A C 8 1_555 B G 1 1_555 0.548 -0.151 0.001 9.074 -13.056 0.575 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 G 2 1_555 B U 7 1_555 0.119 -1.986 3.025 -3.137 8.556 26.578 -5.770 -0.860 2.260 17.953 6.581 28.070 1 AA_G1G2:U16C17_BB A 1 ? B 17 ? A 2 ? B 16 ? 1 A G 2 1_555 B U 7 1_555 A G 3 1_555 B C 6 1_555 0.051 -1.441 3.085 -5.462 8.655 42.349 -2.698 -0.545 2.727 11.776 7.431 43.513 2 AA_G2G3:C15U16_BB A 2 ? B 16 ? A 3 ? B 15 ? 1 A G 3 1_555 B C 6 1_555 A C 4 1_555 B G 5 1_555 -0.261 -1.474 3.328 9.164 12.999 31.416 -4.243 1.703 2.388 22.306 -15.726 35.122 3 AA_G3C4:G14C15_BB A 3 ? B 15 ? A 4 ? B 14 ? 1 A C 4 1_555 B G 5 1_555 A G 5 1_555 B C 4 1_555 0.571 -1.767 3.529 -1.124 15.797 31.383 -5.200 -1.109 2.375 27.147 1.932 35.063 4 AA_C4G5:C13G14_BB A 4 ? B 14 ? A 5 ? B 13 ? 1 A G 5 1_555 B C 4 1_555 A C 6 1_555 B G 3 1_555 -0.411 -1.553 3.402 -2.347 3.497 35.114 -3.085 0.323 3.257 5.771 3.872 35.357 5 AA_G5C6:G12C13_BB A 5 ? B 13 ? A 6 ? B 12 ? 1 A C 6 1_555 B G 3 1_555 A U 7 1_555 B G 2 1_555 -0.117 -1.292 3.166 1.209 5.655 39.635 -2.497 0.301 2.957 8.286 -1.771 40.038 6 AA_C6U7:G11G12_BB A 6 ? B 12 ? A 7 ? B 11 ? 1 A U 7 1_555 B G 2 1_555 A C 8 1_555 B G 1 1_555 0.106 -1.433 2.886 6.430 2.412 27.554 -3.406 1.069 2.708 4.967 -13.241 28.381 7 AA_U7C8:G10G11_BB A 7 ? B 11 ? A 8 ? B 10 ? # _atom_sites.entry_id 438D _atom_sites.fract_transf_matrix[1][1] 0.021891 _atom_sites.fract_transf_matrix[1][2] 0.012639 _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] 0.025278 _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] 0.016681 _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_