data_1YRM # _entry.id 1YRM # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.389 _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 1YRM pdb_00001yrm 10.2210/pdb1yrm/pdb NDB AR0057 ? ? RCSB RCSB031851 ? ? WWPDB D_1000031851 ? ? # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2005-10-18 2 'Structure model' 1 1 2008-04-30 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2011-11-16 5 'Structure model' 1 4 2024-02-14 6 'Structure model' 1 5 2024-04-03 # _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' 'Atomic model' 4 5 'Structure model' 'Data collection' 5 5 'Structure model' 'Database references' 6 5 'Structure model' 'Derived calculations' 7 6 'Structure model' 'Refinement description' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 5 'Structure model' chem_comp_atom 2 5 'Structure model' chem_comp_bond 3 5 'Structure model' database_2 4 5 'Structure model' pdbx_struct_conn_angle 5 5 'Structure model' struct_conn 6 5 'Structure model' struct_site 7 6 'Structure model' pdbx_initial_refinement_model # 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 5 'Structure model' '_database_2.pdbx_DOI' 2 5 'Structure model' '_database_2.pdbx_database_accession' 3 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 4 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_symmetry' 5 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 6 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_symmetry' 7 5 'Structure model' '_pdbx_struct_conn_angle.value' 8 5 'Structure model' '_struct_conn.conn_type_id' 9 5 'Structure model' '_struct_conn.id' 10 5 'Structure model' '_struct_conn.pdbx_dist_value' 11 5 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 12 5 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 13 5 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 14 5 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 15 5 'Structure model' '_struct_conn.ptnr1_label_asym_id' 16 5 'Structure model' '_struct_conn.ptnr1_label_atom_id' 17 5 'Structure model' '_struct_conn.ptnr1_label_comp_id' 18 5 'Structure model' '_struct_conn.ptnr1_label_seq_id' 19 5 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 20 5 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 21 5 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 22 5 'Structure model' '_struct_conn.ptnr2_label_asym_id' 23 5 'Structure model' '_struct_conn.ptnr2_label_atom_id' 24 5 'Structure model' '_struct_conn.ptnr2_label_comp_id' 25 5 'Structure model' '_struct_conn.ptnr2_label_seq_id' 26 5 'Structure model' '_struct_conn.ptnr2_symmetry' 27 5 'Structure model' '_struct_site.pdbx_auth_asym_id' 28 5 'Structure model' '_struct_site.pdbx_auth_comp_id' 29 5 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1YRM _pdbx_database_status.recvd_initial_deposition_date 2005-02-04 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # _pdbx_database_related.db_name NDB _pdbx_database_related.db_id AR0002 _pdbx_database_related.details ;The same sequence without the 2'-amine substitution, molecular replacement model ; _pdbx_database_related.content_type unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Gherghe, C.M.' 1 'Krahn, J.M.' 2 'Weeks, K.M.' 3 # _citation.id primary _citation.title ;Crystal structures, reactivity and inferred acylation transition States for 2'-amine substituted RNA. ; _citation.journal_abbrev J.Am.Chem.Soc. _citation.journal_volume 127 _citation.page_first 13622 _citation.page_last 13628 _citation.year 2005 _citation.journal_id_ASTM JACSAT _citation.country US _citation.journal_id_ISSN 0002-7863 _citation.journal_id_CSD 0004 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 16190727 _citation.pdbx_database_id_DOI 10.1021/ja053647y # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Gherghe, C.M.' 1 ? primary 'Krahn, J.M.' 2 ? primary 'Weeks, K.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 ;DNA/RNA (5'-R(*GP*CP*AP*GP*A)-D(P*(A5M))-R(P*UP*UP*AP*AP*AP*UP*CP*UP*GP*C)-3') ; 5081.094 3 ? ? ? ? 2 non-polymer syn 'STRONTIUM ION' 87.620 2 ? ? ? ? 3 water nat water 18.015 50 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type 'polydeoxyribonucleotide/polyribonucleotide hybrid' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code 'GCAGA(A5M)UUAAAUCUGC' _entity_poly.pdbx_seq_one_letter_code_can GCAGACUUAAAUCUGC _entity_poly.pdbx_strand_id A,B,C _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'STRONTIUM ION' SR 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 A n 1 4 G n 1 5 A n 1 6 A5M n 1 7 U n 1 8 U n 1 9 A n 1 10 A n 1 11 A n 1 12 U n 1 13 C n 1 14 U n 1 15 G n 1 16 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 A 'RNA linking' y "ADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 A5M 'RNA linking' n "2'-AMINE-CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H15 N4 O7 P' 322.212 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 SR non-polymer . 'STRONTIUM ION' ? 'Sr 2' 87.620 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 A 3 3 3 A A A . n A 1 4 G 4 4 4 G G A . n A 1 5 A 5 5 5 A A A . n A 1 6 A5M 6 6 6 A5M C A . n A 1 7 U 7 7 7 U U A . n A 1 8 U 8 8 8 U U A . n A 1 9 A 9 9 9 A A A . n A 1 10 A 10 10 10 A A A . n A 1 11 A 11 11 11 A A A . n A 1 12 U 12 12 12 U U A . n A 1 13 C 13 13 13 C C A . n A 1 14 U 14 14 14 U U A . n A 1 15 G 15 15 15 G G A . n A 1 16 C 16 16 16 C C A . n B 1 1 G 1 1 1 G G B . n B 1 2 C 2 2 2 C C B . n B 1 3 A 3 3 3 A A B . n B 1 4 G 4 4 4 G G B . n B 1 5 A 5 5 5 A A B . n B 1 6 A5M 6 6 6 A5M C B . n B 1 7 U 7 7 7 U U B . n B 1 8 U 8 8 8 U U B . n B 1 9 A 9 9 9 A A B . n B 1 10 A 10 10 10 A A B . n B 1 11 A 11 11 11 A A B . n B 1 12 U 12 12 12 U U B . n B 1 13 C 13 13 13 C C B . n B 1 14 U 14 14 14 U U B . n B 1 15 G 15 15 15 G G B . n B 1 16 C 16 16 16 C C B . n C 1 1 G 1 1 1 G G C . n C 1 2 C 2 2 2 C C C . n C 1 3 A 3 3 3 A A C . n C 1 4 G 4 4 4 G G C . n C 1 5 A 5 5 5 A A C . n C 1 6 A5M 6 6 6 A5M C C . n C 1 7 U 7 7 7 U U C . n C 1 8 U 8 8 8 U U C . n C 1 9 A 9 9 9 A A C . n C 1 10 A 10 10 10 A A C . n C 1 11 A 11 11 11 A A C . n C 1 12 U 12 12 12 U U C . n C 1 13 C 13 13 13 C C C . n C 1 14 U 14 14 14 U U C . n C 1 15 G 15 15 15 G G C . n C 1 16 C 16 16 16 C C C . 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 D 2 SR 1 17 1 SR SR A . E 2 SR 1 17 3 SR SR C . F 3 HOH 1 22 22 HOH HOH A . F 3 HOH 2 26 26 HOH HOH A . F 3 HOH 3 34 34 HOH HOH A . F 3 HOH 4 36 36 HOH HOH A . F 3 HOH 5 37 37 HOH HOH A . F 3 HOH 6 38 38 HOH HOH A . F 3 HOH 7 40 40 HOH HOH A . F 3 HOH 8 45 45 HOH HOH A . F 3 HOH 9 51 51 HOH HOH A . F 3 HOH 10 52 52 HOH HOH A . G 3 HOH 1 17 16 HOH HOH B . G 3 HOH 2 18 21 HOH HOH B . G 3 HOH 3 19 24 HOH HOH B . G 3 HOH 4 20 25 HOH HOH B . G 3 HOH 5 21 27 HOH HOH B . G 3 HOH 6 22 28 HOH HOH B . G 3 HOH 7 23 29 HOH HOH B . G 3 HOH 8 24 33 HOH HOH B . G 3 HOH 9 25 35 HOH HOH B . G 3 HOH 10 26 41 HOH HOH B . G 3 HOH 11 27 43 HOH HOH B . G 3 HOH 12 28 44 HOH HOH B . G 3 HOH 13 29 48 HOH HOH B . G 3 HOH 14 30 49 HOH HOH B . H 3 HOH 1 18 2 HOH HOH C . H 3 HOH 2 19 4 HOH HOH C . H 3 HOH 3 20 5 HOH HOH C . H 3 HOH 4 21 6 HOH HOH C . H 3 HOH 5 22 7 HOH HOH C . H 3 HOH 6 23 8 HOH HOH C . H 3 HOH 7 24 9 HOH HOH C . H 3 HOH 8 25 10 HOH HOH C . H 3 HOH 9 26 11 HOH HOH C . H 3 HOH 10 27 12 HOH HOH C . H 3 HOH 11 28 13 HOH HOH C . H 3 HOH 12 29 14 HOH HOH C . H 3 HOH 13 30 15 HOH HOH C . H 3 HOH 14 31 17 HOH HOH C . H 3 HOH 15 32 18 HOH HOH C . H 3 HOH 16 33 19 HOH HOH C . H 3 HOH 17 34 20 HOH HOH C . H 3 HOH 18 35 23 HOH HOH C . H 3 HOH 19 36 30 HOH HOH C . H 3 HOH 20 37 31 HOH HOH C . H 3 HOH 21 38 32 HOH HOH C . H 3 HOH 22 39 39 HOH HOH C . H 3 HOH 23 40 42 HOH HOH C . H 3 HOH 24 41 46 HOH HOH C . H 3 HOH 25 42 47 HOH HOH C . H 3 HOH 26 43 50 HOH HOH C . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal CNS refinement 1.1 ? 1 SCALEPACK 'data scaling' . ? 2 AMoRE phasing . ? 3 # _cell.entry_id 1YRM _cell.length_a 43.000 _cell.length_b 43.000 _cell.length_c 122.500 _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 1YRM _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 ? # _exptl.entry_id 1YRM _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.14 _exptl_crystal.density_percent_sol 42.65 _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 273 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 8.0 _exptl_crystal_grow.pdbx_details 'MPD, cacodylate, spermidine, strontium chloride, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 273K' _exptl_crystal_grow.pdbx_pH_range . # loop_ _exptl_crystal_grow_comp.crystal_id _exptl_crystal_grow_comp.id _exptl_crystal_grow_comp.sol_id _exptl_crystal_grow_comp.name _exptl_crystal_grow_comp.volume _exptl_crystal_grow_comp.conc _exptl_crystal_grow_comp.details 1 1 1 MPD ? ? ? 1 2 1 spermidine ? ? ? 1 3 1 'strontium chloride' ? ? ? 1 4 1 cacodylate ? ? ? 1 5 2 'strontium chloride' ? ? ? 1 6 2 MPD ? ? ? 1 7 2 cacodylate ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'IMAGE PLATE' _diffrn_detector.type 'RIGAKU RAXIS IV' _diffrn_detector.pdbx_collection_date 2003-03-15 _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 1YRM _reflns.observed_criterion_sigma_I 1 _reflns.observed_criterion_sigma_F 0 _reflns.d_resolution_low 21.50 _reflns.d_resolution_high 2.40 _reflns.number_obs 5305 _reflns.number_all 5573 _reflns.percent_possible_obs 95.2 _reflns.pdbx_Rmerge_I_obs 0.044 _reflns.pdbx_Rsym_value 0.041 _reflns.pdbx_netI_over_sigmaI 17.19 _reflns.B_iso_Wilson_estimate 39.0 _reflns.pdbx_redundancy 13.09 _reflns.R_free_details ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 2.40 _reflns_shell.d_res_low 2.49 _reflns_shell.percent_possible_all 75.2 _reflns_shell.Rmerge_I_obs 0.255 _reflns_shell.pdbx_Rsym_value 0.187 _reflns_shell.meanI_over_sigI_obs 3.77 _reflns_shell.pdbx_redundancy ? _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 395 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 1YRM _refine.ls_number_reflns_obs 4649 _refine.ls_number_reflns_all 4649 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.0 _refine.pdbx_data_cutoff_high_absF 696091.00 _refine.pdbx_data_cutoff_low_absF 0.000000 _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 7.98 _refine.ls_d_res_high 2.50 _refine.ls_percent_reflns_obs 97.9 _refine.ls_R_factor_obs 0.234 _refine.ls_R_factor_all 0.234 _refine.ls_R_factor_R_work 0.234 _refine.ls_R_factor_R_free 0.278 _refine.ls_R_factor_R_free_error 0.018 _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 5.4 _refine.ls_number_reflns_R_free 253 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean 42.3 _refine.aniso_B[1][1] 6.26 _refine.aniso_B[2][2] 6.26 _refine.aniso_B[3][3] -12.52 _refine.aniso_B[1][2] 5.47 _refine.aniso_B[1][3] 0.00 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details 'FLAT MODEL' _refine.solvent_model_param_ksol 0.228829 _refine.solvent_model_param_bsol 36.6756 _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details ? _refine.pdbx_starting_model 'NDB ENTRY AR0002' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model RESTRAINED _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.ls_redundancy_reflns_obs ? _refine.overall_SU_R_Cruickshank_DPI ? _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_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_phase_error ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_analyze.entry_id 1YRM _refine_analyze.Luzzati_coordinate_error_obs 0.36 _refine_analyze.Luzzati_sigma_a_obs 0.44 _refine_analyze.Luzzati_d_res_low_obs 5.00 _refine_analyze.Luzzati_coordinate_error_free 0.44 _refine_analyze.Luzzati_sigma_a_free 0.43 _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues ? _refine_analyze.occupancy_sum_hydrogen ? _refine_analyze.occupancy_sum_non_hydrogen ? _refine_analyze.pdbx_refine_id 'X-RAY DIFFRACTION' # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 1008 _refine_hist.pdbx_number_atoms_ligand 2 _refine_hist.number_atoms_solvent 50 _refine_hist.number_atoms_total 1060 _refine_hist.d_res_high 2.50 _refine_hist.d_res_low 7.98 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function c_bond_d 0.005 ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg 0.9 ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d 7.3 ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d 1.35 ? ? ? 'X-RAY DIFFRACTION' ? c_mcbond_it 0.00 1.50 ? ? 'X-RAY DIFFRACTION' ? c_mcangle_it 0.00 2.00 ? ? 'X-RAY DIFFRACTION' ? c_scbond_it 0.36 2.00 ? ? 'X-RAY DIFFRACTION' ? c_scangle_it 0.62 2.50 ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 6 _refine_ls_shell.d_res_high 2.50 _refine_ls_shell.d_res_low 2.65 _refine_ls_shell.number_reflns_R_work 648 _refine_ls_shell.R_factor_R_work 0.335 _refine_ls_shell.percent_reflns_obs 90.2 _refine_ls_shell.R_factor_R_free 0.379 _refine_ls_shell.R_factor_R_free_error 0.058 _refine_ls_shell.percent_reflns_R_free 6.2 _refine_ls_shell.number_reflns_R_free 43 _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? # loop_ _pdbx_xplor_file.serial_no _pdbx_xplor_file.param_file _pdbx_xplor_file.topol_file _pdbx_xplor_file.pdbx_refine_id 1 C2N.PARAM C2N.TOP 'X-RAY DIFFRACTION' 2 DNA-RNA.PARAM DNA-RNA.TOP 'X-RAY DIFFRACTION' 3 WATER.PARAM WATER.TOP 'X-RAY DIFFRACTION' 4 ION.PARAM ION.TOP 'X-RAY DIFFRACTION' # _database_PDB_matrix.entry_id 1YRM _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 1YRM _struct.title ;Crystal Structure of an RNA duplex containing site specific 2'-amine substitutions at a C-A mismatch ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1YRM _struct_keywords.pdbx_keywords RNA _struct_keywords.text ;2'-AMINE, RNA, DUPLEX, MISMATCH ; # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 1 ? C N N 1 ? D N N 2 ? E N N 2 ? F N N 3 ? 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 1YRM _struct_ref.pdbx_db_accession 1YRM _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 1YRM A 1 ? 16 ? 1YRM 1 ? 16 ? 1 16 2 1 1YRM B 1 ? 16 ? 1YRM 1 ? 16 ? 1 16 3 1 1YRM C 1 ? 16 ? 1YRM 1 ? 16 ? 1 16 # loop_ _pdbx_struct_assembly.id _pdbx_struct_assembly.details _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count 1 author_defined_assembly ? dimeric 2 2 author_defined_assembly ? dimeric 2 # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 1 A,B,D,F,G 2 1,2 C,E,H # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 2 'crystal symmetry operation' 6_765 -x+2,-x+y+1,-z+1/3 -0.5000000000 -0.8660254038 0.0000000000 64.5000000000 -0.8660254038 0.5000000000 0.0000000000 37.2390923627 0.0000000000 0.0000000000 -1.0000000000 40.8333333333 # loop_ _struct_biol.id _struct_biol.pdbx_parent_biol_id _struct_biol.details 1 ? ? 2 ? ? # 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 A 5 "O3'" ? ? ? 1_555 A A5M 6 P ? ? A A 5 A A5M 6 1_555 ? ? ? ? ? ? ? 1.618 ? ? covale2 covale both ? A A5M 6 "O3'" ? ? ? 1_555 A U 7 P ? ? A A5M 6 A U 7 1_555 ? ? ? ? ? ? ? 1.604 ? ? covale3 covale both ? B A 5 "O3'" ? ? ? 1_555 B A5M 6 P ? ? B A 5 B A5M 6 1_555 ? ? ? ? ? ? ? 1.609 ? ? covale4 covale both ? B A5M 6 "O3'" ? ? ? 1_555 B U 7 P ? ? B A5M 6 B U 7 1_555 ? ? ? ? ? ? ? 1.603 ? ? covale5 covale both ? C A 5 "O3'" ? ? ? 1_555 C A5M 6 P ? ? C A 5 C A5M 6 1_555 ? ? ? ? ? ? ? 1.608 ? ? covale6 covale both ? C A5M 6 "O3'" ? ? ? 1_555 C U 7 P ? ? C A5M 6 C U 7 1_555 ? ? ? ? ? ? ? 1.609 ? ? metalc1 metalc ? ? A C 16 "O3'" ? ? ? 1_555 D SR . SR ? ? A C 16 A SR 17 1_555 ? ? ? ? ? ? ? 2.952 ? ? metalc2 metalc ? ? A C 16 "O2'" ? ? ? 1_555 D SR . SR ? ? A C 16 A SR 17 1_555 ? ? ? ? ? ? ? 2.567 ? ? metalc3 metalc ? ? D SR . SR ? ? ? 1_555 H HOH . O ? ? A SR 17 C HOH 18 2_665 ? ? ? ? ? ? ? 3.043 ? ? metalc4 metalc ? ? E SR . SR ? ? ? 1_555 H HOH . O ? ? C SR 17 C HOH 19 1_555 ? ? ? ? ? ? ? 3.307 ? ? metalc5 metalc ? ? E SR . SR ? ? ? 1_555 H HOH . O ? ? C SR 17 C HOH 19 6_765 ? ? ? ? ? ? ? 3.238 ? ? metalc6 metalc ? ? E SR . SR ? ? ? 1_555 H HOH . O ? ? C SR 17 C HOH 20 1_555 ? ? ? ? ? ? ? 2.812 ? ? metalc7 metalc ? ? E SR . SR ? ? ? 1_555 H HOH . O ? ? C SR 17 C HOH 20 6_765 ? ? ? ? ? ? ? 2.779 ? ? hydrog1 hydrog ? ? A G 1 N1 ? ? ? 1_555 B C 16 N3 ? ? A G 1 B C 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 B C 16 O2 ? ? A G 1 B C 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 B C 16 N4 ? ? A G 1 B C 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A C 2 N3 ? ? ? 1_555 B G 15 N1 ? ? A C 2 B G 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A C 2 N4 ? ? ? 1_555 B G 15 O6 ? ? A C 2 B G 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A C 2 O2 ? ? ? 1_555 B G 15 N2 ? ? A C 2 B G 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A A 3 N1 ? ? ? 1_555 B U 14 N3 ? ? A A 3 B U 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A A 3 N6 ? ? ? 1_555 B U 14 O4 ? ? A A 3 B U 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G 4 N1 ? ? ? 1_555 B C 13 N3 ? ? A G 4 B C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A G 4 N2 ? ? ? 1_555 B C 13 O2 ? ? A G 4 B C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A G 4 O6 ? ? ? 1_555 B C 13 N4 ? ? A G 4 B C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A A 5 N1 ? ? ? 1_555 B U 12 N3 ? ? A A 5 B U 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A A 5 N6 ? ? ? 1_555 B U 12 O4 ? ? A A 5 B U 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A A5M 6 N3 ? ? ? 1_555 B A 11 N6 ? ? A A5M 6 B A 11 1_555 ? ? ? ? ? ? 'A5M-A MISPAIR' ? ? ? hydrog15 hydrog ? ? A U 7 N3 ? ? ? 1_555 B A 10 N1 ? ? A U 7 B A 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A U 7 O4 ? ? ? 1_555 B A 10 N6 ? ? A U 7 B A 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A U 8 N3 ? ? ? 1_555 B A 9 N1 ? ? A U 8 B A 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A U 8 O4 ? ? ? 1_555 B A 9 N6 ? ? A U 8 B A 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A A 9 N1 ? ? ? 1_555 B U 8 N3 ? ? A A 9 B U 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A A 9 N6 ? ? ? 1_555 B U 8 O4 ? ? A A 9 B U 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A A 10 N1 ? ? ? 1_555 B U 7 N3 ? ? A A 10 B U 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A A 10 N6 ? ? ? 1_555 B U 7 O4 ? ? A A 10 B U 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A A 11 N6 ? ? ? 1_555 B A5M 6 N3 ? ? A A 11 B A5M 6 1_555 ? ? ? ? ? ? 'A-A5M MISPAIR' ? ? ? hydrog24 hydrog ? ? A U 12 N3 ? ? ? 1_555 B A 5 N1 ? ? A U 12 B A 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A U 12 O4 ? ? ? 1_555 B A 5 N6 ? ? A U 12 B A 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A C 13 N3 ? ? ? 1_555 B G 4 N1 ? ? A C 13 B G 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A C 13 N4 ? ? ? 1_555 B G 4 O6 ? ? A C 13 B G 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A C 13 O2 ? ? ? 1_555 B G 4 N2 ? ? A C 13 B G 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A U 14 N3 ? ? ? 1_555 B A 3 N1 ? ? A U 14 B A 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A U 14 O4 ? ? ? 1_555 B A 3 N6 ? ? A U 14 B A 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A G 15 N1 ? ? ? 1_555 B C 2 N3 ? ? A G 15 B C 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A G 15 N2 ? ? ? 1_555 B C 2 O2 ? ? A G 15 B C 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A G 15 O6 ? ? ? 1_555 B C 2 N4 ? ? A G 15 B C 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A C 16 N3 ? ? ? 1_555 B G 1 N1 ? ? A C 16 B G 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? A C 16 N4 ? ? ? 1_555 B G 1 O6 ? ? A C 16 B G 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? A C 16 O2 ? ? ? 1_555 B G 1 N2 ? ? A C 16 B G 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? C G 1 N1 ? ? ? 1_555 C C 16 N3 ? ? C G 1 C C 16 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? C G 1 N2 ? ? ? 1_555 C C 16 O2 ? ? C G 1 C C 16 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? C G 1 O6 ? ? ? 1_555 C C 16 N4 ? ? C G 1 C C 16 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? C C 2 N3 ? ? ? 1_555 C G 15 N1 ? ? C C 2 C G 15 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? C C 2 N4 ? ? ? 1_555 C G 15 O6 ? ? C C 2 C G 15 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? C C 2 O2 ? ? ? 1_555 C G 15 N2 ? ? C C 2 C G 15 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? C A 3 N1 ? ? ? 1_555 C U 14 N3 ? ? C A 3 C U 14 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? C A 3 N6 ? ? ? 1_555 C U 14 O4 ? ? C A 3 C U 14 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? C G 4 N1 ? ? ? 1_555 C C 13 N3 ? ? C G 4 C C 13 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? C G 4 N2 ? ? ? 1_555 C C 13 O2 ? ? C G 4 C C 13 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog47 hydrog ? ? C G 4 O6 ? ? ? 1_555 C C 13 N4 ? ? C G 4 C C 13 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog48 hydrog ? ? C A 5 N1 ? ? ? 1_555 C U 12 N3 ? ? C A 5 C U 12 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog49 hydrog ? ? C A 5 N6 ? ? ? 1_555 C U 12 O4 ? ? C A 5 C U 12 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog50 hydrog ? ? C A5M 6 O2 ? ? ? 1_555 C A 11 N6 ? ? C A5M 6 C A 11 6_765 ? ? ? ? ? ? 'A5M-A MISPAIR' ? ? ? hydrog51 hydrog ? ? C U 7 N3 ? ? ? 1_555 C A 10 N1 ? ? C U 7 C A 10 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog52 hydrog ? ? C U 7 O4 ? ? ? 1_555 C A 10 N6 ? ? C U 7 C A 10 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog53 hydrog ? ? C U 8 N3 ? ? ? 1_555 C A 9 N1 ? ? C U 8 C A 9 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog54 hydrog ? ? C U 8 O4 ? ? ? 1_555 C A 9 N6 ? ? C U 8 C A 9 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog55 hydrog ? ? C A 9 N1 ? ? ? 1_555 C U 8 N3 ? ? C A 9 C U 8 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog56 hydrog ? ? C A 9 N6 ? ? ? 1_555 C U 8 O4 ? ? C A 9 C U 8 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog57 hydrog ? ? C A 10 N1 ? ? ? 1_555 C U 7 N3 ? ? C A 10 C U 7 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog58 hydrog ? ? C A 10 N6 ? ? ? 1_555 C U 7 O4 ? ? C A 10 C U 7 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog59 hydrog ? ? C A 11 N6 ? ? ? 1_555 C A5M 6 O2 ? ? C A 11 C A5M 6 6_765 ? ? ? ? ? ? 'A-A5M MISPAIR' ? ? ? hydrog60 hydrog ? ? C U 12 N3 ? ? ? 1_555 C A 5 N1 ? ? C U 12 C A 5 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog61 hydrog ? ? C U 12 O4 ? ? ? 1_555 C A 5 N6 ? ? C U 12 C A 5 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog62 hydrog ? ? C C 13 N3 ? ? ? 1_555 C G 4 N1 ? ? C C 13 C G 4 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog63 hydrog ? ? C C 13 N4 ? ? ? 1_555 C G 4 O6 ? ? C C 13 C G 4 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog64 hydrog ? ? C C 13 O2 ? ? ? 1_555 C G 4 N2 ? ? C C 13 C G 4 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog65 hydrog ? ? C U 14 N3 ? ? ? 1_555 C A 3 N1 ? ? C U 14 C A 3 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog66 hydrog ? ? C U 14 O4 ? ? ? 1_555 C A 3 N6 ? ? C U 14 C A 3 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog67 hydrog ? ? C G 15 N1 ? ? ? 1_555 C C 2 N3 ? ? C G 15 C C 2 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog68 hydrog ? ? C G 15 N2 ? ? ? 1_555 C C 2 O2 ? ? C G 15 C C 2 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog69 hydrog ? ? C G 15 O6 ? ? ? 1_555 C C 2 N4 ? ? C G 15 C C 2 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog70 hydrog ? ? C C 16 N3 ? ? ? 1_555 C G 1 N1 ? ? C C 16 C G 1 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog71 hydrog ? ? C C 16 N4 ? ? ? 1_555 C G 1 O6 ? ? C C 16 C G 1 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog72 hydrog ? ? C C 16 O2 ? ? ? 1_555 C G 1 N2 ? ? C C 16 C G 1 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? metalc ? ? hydrog ? ? # loop_ _pdbx_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 "O3'" ? A C 16 ? A C 16 ? 1_555 SR ? D SR . ? A SR 17 ? 1_555 "O2'" ? A C 16 ? A C 16 ? 1_555 62.0 ? 2 "O3'" ? A C 16 ? A C 16 ? 1_555 SR ? D SR . ? A SR 17 ? 1_555 O ? H HOH . ? C HOH 18 ? 2_665 75.6 ? 3 "O2'" ? A C 16 ? A C 16 ? 1_555 SR ? D SR . ? A SR 17 ? 1_555 O ? H HOH . ? C HOH 18 ? 2_665 112.1 ? 4 O ? H HOH . ? C HOH 19 ? 1_555 SR ? E SR . ? C SR 17 ? 1_555 O ? H HOH . ? C HOH 19 ? 6_765 125.7 ? 5 O ? H HOH . ? C HOH 19 ? 1_555 SR ? E SR . ? C SR 17 ? 1_555 O ? H HOH . ? C HOH 20 ? 1_555 71.1 ? 6 O ? H HOH . ? C HOH 19 ? 6_765 SR ? E SR . ? C SR 17 ? 1_555 O ? H HOH . ? C HOH 20 ? 1_555 140.1 ? 7 O ? H HOH . ? C HOH 19 ? 1_555 SR ? E SR . ? C SR 17 ? 1_555 O ? H HOH . ? C HOH 20 ? 6_765 138.2 ? 8 O ? H HOH . ? C HOH 19 ? 6_765 SR ? E SR . ? C SR 17 ? 1_555 O ? H HOH . ? C HOH 20 ? 6_765 72.6 ? 9 O ? H HOH . ? C HOH 20 ? 1_555 SR ? E SR . ? C SR 17 ? 1_555 O ? H HOH . ? C HOH 20 ? 6_765 121.6 ? # 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 SR 17 ? 2 'BINDING SITE FOR RESIDUE SR A 17' AC2 Software C SR 17 ? 2 'BINDING SITE FOR RESIDUE SR C 17' # 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 2 C A 16 ? C A 16 . ? 1_555 ? 2 AC1 2 HOH H . ? HOH C 18 . ? 2_665 ? 3 AC2 2 HOH H . ? HOH C 20 . ? 6_765 ? 4 AC2 2 HOH H . ? HOH C 20 . ? 1_555 ? # 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 A5M 6 A A5M 6 ? C "2'-AMINE-CYTIDINE-5'-MONOPHOSPHATE" 2 B A5M 6 B A5M 6 ? C "2'-AMINE-CYTIDINE-5'-MONOPHOSPHATE" 3 C A5M 6 C A5M 6 ? C "2'-AMINE-CYTIDINE-5'-MONOPHOSPHATE" # 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 C SR 17 ? E SR . 2 1 A HOH 51 ? F 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 A OP3 O N N 1 A P P N N 2 A OP1 O N N 3 A OP2 O N N 4 A "O5'" O N N 5 A "C5'" C N N 6 A "C4'" C N R 7 A "O4'" O N N 8 A "C3'" C N S 9 A "O3'" O N N 10 A "C2'" C N R 11 A "O2'" O N N 12 A "C1'" C N R 13 A N9 N Y N 14 A C8 C Y N 15 A N7 N Y N 16 A C5 C Y N 17 A C6 C Y N 18 A N6 N N N 19 A N1 N Y N 20 A C2 C Y N 21 A N3 N Y N 22 A C4 C Y N 23 A HOP3 H N N 24 A HOP2 H N N 25 A "H5'" H N N 26 A "H5''" H N N 27 A "H4'" H N N 28 A "H3'" H N N 29 A "HO3'" H N N 30 A "H2'" H N N 31 A "HO2'" H N N 32 A "H1'" H N N 33 A H8 H N N 34 A H61 H N N 35 A H62 H N N 36 A H2 H N N 37 A5M P P N N 38 A5M OP1 O N N 39 A5M OP2 O N N 40 A5M "O5'" O N N 41 A5M "C5'" C N N 42 A5M "C4'" C N R 43 A5M "O4'" O N N 44 A5M "C1'" C N R 45 A5M N1 N N N 46 A5M C6 C N N 47 A5M C2 C N N 48 A5M O2 O N N 49 A5M N3 N N N 50 A5M C4 C N N 51 A5M N4 N N N 52 A5M C5 C N N 53 A5M "C2'" C N R 54 A5M "N2'" N N N 55 A5M "C3'" C N S 56 A5M "O3'" O N N 57 A5M OP3 O N N 58 A5M HOP2 H N N 59 A5M "H5'" H N N 60 A5M "H5''" H N N 61 A5M "H4'" H N N 62 A5M "H1'" H N N 63 A5M H6 H N N 64 A5M H41 H N N 65 A5M H42 H N N 66 A5M H5 H N N 67 A5M "H2'" H N N 68 A5M "H'1N" H N N 69 A5M "H'2N" H N N 70 A5M "H3'" H N N 71 A5M "HO3'" H N N 72 A5M HOP3 H N N 73 C OP3 O N N 74 C P P N N 75 C OP1 O N N 76 C OP2 O N N 77 C "O5'" O N N 78 C "C5'" C N N 79 C "C4'" C N R 80 C "O4'" O N N 81 C "C3'" C N S 82 C "O3'" O N N 83 C "C2'" C N R 84 C "O2'" O N N 85 C "C1'" C N R 86 C N1 N N N 87 C C2 C N N 88 C O2 O N N 89 C N3 N N N 90 C C4 C N N 91 C N4 N N N 92 C C5 C N N 93 C C6 C N N 94 C HOP3 H N N 95 C HOP2 H N N 96 C "H5'" H N N 97 C "H5''" H N N 98 C "H4'" H N N 99 C "H3'" H N N 100 C "HO3'" H N N 101 C "H2'" H N N 102 C "HO2'" H N N 103 C "H1'" H N N 104 C H41 H N N 105 C H42 H N N 106 C H5 H N N 107 C H6 H N N 108 G OP3 O N N 109 G P P N N 110 G OP1 O N N 111 G OP2 O N N 112 G "O5'" O N N 113 G "C5'" C N N 114 G "C4'" C N R 115 G "O4'" O N N 116 G "C3'" C N S 117 G "O3'" O N N 118 G "C2'" C N R 119 G "O2'" O N N 120 G "C1'" C N R 121 G N9 N Y N 122 G C8 C Y N 123 G N7 N Y N 124 G C5 C Y N 125 G C6 C N N 126 G O6 O N N 127 G N1 N N N 128 G C2 C N N 129 G N2 N N N 130 G N3 N N N 131 G C4 C Y N 132 G HOP3 H N N 133 G HOP2 H N N 134 G "H5'" H N N 135 G "H5''" H N N 136 G "H4'" H N N 137 G "H3'" H N N 138 G "HO3'" H N N 139 G "H2'" H N N 140 G "HO2'" H N N 141 G "H1'" H N N 142 G H8 H N N 143 G H1 H N N 144 G H21 H N N 145 G H22 H N N 146 HOH O O N N 147 HOH H1 H N N 148 HOH H2 H N N 149 SR SR SR N N 150 U OP3 O N N 151 U P P N N 152 U OP1 O N N 153 U OP2 O N N 154 U "O5'" O N N 155 U "C5'" C N N 156 U "C4'" C N R 157 U "O4'" O N N 158 U "C3'" C N S 159 U "O3'" O N N 160 U "C2'" C N R 161 U "O2'" O N N 162 U "C1'" C N R 163 U N1 N N N 164 U C2 C N N 165 U O2 O N N 166 U N3 N N N 167 U C4 C N N 168 U O4 O N N 169 U C5 C N N 170 U C6 C N N 171 U HOP3 H N N 172 U HOP2 H N N 173 U "H5'" H N N 174 U "H5''" H N N 175 U "H4'" H N N 176 U "H3'" H N N 177 U "HO3'" H N N 178 U "H2'" H N N 179 U "HO2'" H N N 180 U "H1'" H N N 181 U H3 H N N 182 U H5 H N N 183 U H6 H N N 184 # 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 A OP3 P sing N N 1 A OP3 HOP3 sing N N 2 A P OP1 doub N N 3 A P OP2 sing N N 4 A P "O5'" sing N N 5 A OP2 HOP2 sing N N 6 A "O5'" "C5'" sing N N 7 A "C5'" "C4'" sing N N 8 A "C5'" "H5'" sing N N 9 A "C5'" "H5''" sing N N 10 A "C4'" "O4'" sing N N 11 A "C4'" "C3'" sing N N 12 A "C4'" "H4'" sing N N 13 A "O4'" "C1'" sing N N 14 A "C3'" "O3'" sing N N 15 A "C3'" "C2'" sing N N 16 A "C3'" "H3'" sing N N 17 A "O3'" "HO3'" sing N N 18 A "C2'" "O2'" sing N N 19 A "C2'" "C1'" sing N N 20 A "C2'" "H2'" sing N N 21 A "O2'" "HO2'" sing N N 22 A "C1'" N9 sing N N 23 A "C1'" "H1'" sing N N 24 A N9 C8 sing Y N 25 A N9 C4 sing Y N 26 A C8 N7 doub Y N 27 A C8 H8 sing N N 28 A N7 C5 sing Y N 29 A C5 C6 sing Y N 30 A C5 C4 doub Y N 31 A C6 N6 sing N N 32 A C6 N1 doub Y N 33 A N6 H61 sing N N 34 A N6 H62 sing N N 35 A N1 C2 sing Y N 36 A C2 N3 doub Y N 37 A C2 H2 sing N N 38 A N3 C4 sing Y N 39 A5M P OP1 doub N N 40 A5M P OP2 sing N N 41 A5M P "O5'" sing N N 42 A5M P OP3 sing N N 43 A5M OP2 HOP2 sing N N 44 A5M "O5'" "C5'" sing N N 45 A5M "C5'" "C4'" sing N N 46 A5M "C5'" "H5'" sing N N 47 A5M "C5'" "H5''" sing N N 48 A5M "C4'" "O4'" sing N N 49 A5M "C4'" "C3'" sing N N 50 A5M "C4'" "H4'" sing N N 51 A5M "O4'" "C1'" sing N N 52 A5M "C1'" N1 sing N N 53 A5M "C1'" "C2'" sing N N 54 A5M "C1'" "H1'" sing N N 55 A5M N1 C6 sing N N 56 A5M N1 C2 sing N N 57 A5M C6 C5 doub N N 58 A5M C6 H6 sing N N 59 A5M C2 O2 doub N N 60 A5M C2 N3 sing N N 61 A5M N3 C4 doub N N 62 A5M C4 N4 sing N N 63 A5M C4 C5 sing N N 64 A5M N4 H41 sing N N 65 A5M N4 H42 sing N N 66 A5M C5 H5 sing N N 67 A5M "C2'" "N2'" sing N N 68 A5M "C2'" "C3'" sing N N 69 A5M "C2'" "H2'" sing N N 70 A5M "N2'" "H'1N" sing N N 71 A5M "N2'" "H'2N" sing N N 72 A5M "C3'" "O3'" sing N N 73 A5M "C3'" "H3'" sing N N 74 A5M "O3'" "HO3'" sing N N 75 A5M OP3 HOP3 sing N N 76 C OP3 P sing N N 77 C OP3 HOP3 sing N N 78 C P OP1 doub N N 79 C P OP2 sing N N 80 C P "O5'" sing N N 81 C OP2 HOP2 sing N N 82 C "O5'" "C5'" sing N N 83 C "C5'" "C4'" sing N N 84 C "C5'" "H5'" sing N N 85 C "C5'" "H5''" sing N N 86 C "C4'" "O4'" sing N N 87 C "C4'" "C3'" sing N N 88 C "C4'" "H4'" sing N N 89 C "O4'" "C1'" sing N N 90 C "C3'" "O3'" sing N N 91 C "C3'" "C2'" sing N N 92 C "C3'" "H3'" sing N N 93 C "O3'" "HO3'" sing N N 94 C "C2'" "O2'" sing N N 95 C "C2'" "C1'" sing N N 96 C "C2'" "H2'" sing N N 97 C "O2'" "HO2'" sing N N 98 C "C1'" N1 sing N N 99 C "C1'" "H1'" sing N N 100 C N1 C2 sing N N 101 C N1 C6 sing N N 102 C C2 O2 doub N N 103 C C2 N3 sing N N 104 C N3 C4 doub N N 105 C C4 N4 sing N N 106 C C4 C5 sing N N 107 C N4 H41 sing N N 108 C N4 H42 sing N N 109 C C5 C6 doub N N 110 C C5 H5 sing N N 111 C C6 H6 sing N N 112 G OP3 P sing N N 113 G OP3 HOP3 sing N N 114 G P OP1 doub N N 115 G P OP2 sing N N 116 G P "O5'" sing N N 117 G OP2 HOP2 sing N N 118 G "O5'" "C5'" sing N N 119 G "C5'" "C4'" sing N N 120 G "C5'" "H5'" sing N N 121 G "C5'" "H5''" sing N N 122 G "C4'" "O4'" sing N N 123 G "C4'" "C3'" sing N N 124 G "C4'" "H4'" sing N N 125 G "O4'" "C1'" sing N N 126 G "C3'" "O3'" sing N N 127 G "C3'" "C2'" sing N N 128 G "C3'" "H3'" sing N N 129 G "O3'" "HO3'" sing N N 130 G "C2'" "O2'" sing N N 131 G "C2'" "C1'" sing N N 132 G "C2'" "H2'" sing N N 133 G "O2'" "HO2'" sing N N 134 G "C1'" N9 sing N N 135 G "C1'" "H1'" sing N N 136 G N9 C8 sing Y N 137 G N9 C4 sing Y N 138 G C8 N7 doub Y N 139 G C8 H8 sing N N 140 G N7 C5 sing Y N 141 G C5 C6 sing N N 142 G C5 C4 doub Y N 143 G C6 O6 doub N N 144 G C6 N1 sing N N 145 G N1 C2 sing N N 146 G N1 H1 sing N N 147 G C2 N2 sing N N 148 G C2 N3 doub N N 149 G N2 H21 sing N N 150 G N2 H22 sing N N 151 G N3 C4 sing N N 152 HOH O H1 sing N N 153 HOH O H2 sing N N 154 U OP3 P sing N N 155 U OP3 HOP3 sing N N 156 U P OP1 doub N N 157 U P OP2 sing N N 158 U P "O5'" sing N N 159 U OP2 HOP2 sing N N 160 U "O5'" "C5'" sing N N 161 U "C5'" "C4'" sing N N 162 U "C5'" "H5'" sing N N 163 U "C5'" "H5''" sing N N 164 U "C4'" "O4'" sing N N 165 U "C4'" "C3'" sing N N 166 U "C4'" "H4'" sing N N 167 U "O4'" "C1'" sing N N 168 U "C3'" "O3'" sing N N 169 U "C3'" "C2'" sing N N 170 U "C3'" "H3'" sing N N 171 U "O3'" "HO3'" sing N N 172 U "C2'" "O2'" sing N N 173 U "C2'" "C1'" sing N N 174 U "C2'" "H2'" sing N N 175 U "O2'" "HO2'" sing N N 176 U "C1'" N1 sing N N 177 U "C1'" "H1'" sing N N 178 U N1 C2 sing N N 179 U N1 C6 sing N N 180 U C2 O2 doub N N 181 U C2 N3 sing N N 182 U N3 C4 sing N N 183 U N3 H3 sing N N 184 U C4 O4 doub N N 185 U C4 C5 sing N N 186 U C5 C6 doub N N 187 U C5 H5 sing N N 188 U C6 H6 sing N N 189 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1YRM 'a-form double helix' 1YRM '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 16 1_555 -0.580 -0.054 -0.175 -1.639 -18.527 -0.707 1 A_G1:C16_B A 1 ? B 16 ? 19 1 1 A C 2 1_555 B G 15 1_555 -0.005 -0.118 0.019 4.828 -15.341 0.932 2 A_C2:G15_B A 2 ? B 15 ? 19 1 1 A A 3 1_555 B U 14 1_555 0.601 -0.283 0.570 10.329 -16.233 2.707 3 A_A3:U14_B A 3 ? B 14 ? 20 1 1 A G 4 1_555 B C 13 1_555 -0.572 -0.157 0.205 -0.021 -19.853 5.887 4 A_G4:C13_B A 4 ? B 13 ? 19 1 1 A A 5 1_555 B U 12 1_555 -0.493 -0.206 0.174 -3.430 -13.999 7.812 5 A_A5:U12_B A 5 ? B 12 ? 20 1 1 A A5M 6 1_555 B A 11 1_555 2.451 -0.316 0.318 1.913 -18.805 12.007 6 A_A5M6:A11_B A 6 ? B 11 ? ? 1 1 A U 7 1_555 B A 10 1_555 0.114 -0.267 -0.043 1.918 -12.122 0.581 7 A_U7:A10_B A 7 ? B 10 ? 20 1 1 A U 8 1_555 B A 9 1_555 -0.314 -0.130 0.075 4.970 -16.218 6.620 8 A_U8:A9_B A 8 ? B 9 ? 20 1 1 A A 9 1_555 B U 8 1_555 -0.352 -0.068 -0.014 -4.773 -10.307 2.361 9 A_A9:U8_B A 9 ? B 8 ? 20 1 1 A A 10 1_555 B U 7 1_555 -0.136 -0.299 -0.059 -4.052 -11.458 3.707 10 A_A10:U7_B A 10 ? B 7 ? 20 1 1 A A 11 1_555 B A5M 6 1_555 -2.541 -0.262 0.444 4.736 -16.481 13.915 11 A_A11:A5M6_B A 11 ? B 6 ? ? 1 1 A U 12 1_555 B A 5 1_555 0.024 -0.259 0.295 6.518 -9.850 -0.687 12 A_U12:A5_B A 12 ? B 5 ? 20 1 1 A C 13 1_555 B G 4 1_555 0.111 -0.064 0.180 8.173 -20.316 2.068 13 A_C13:G4_B A 13 ? B 4 ? 19 1 1 A U 14 1_555 B A 3 1_555 -0.214 -0.109 0.015 6.638 -15.369 4.173 14 A_U14:A3_B A 14 ? B 3 ? 20 1 1 A G 15 1_555 B C 2 1_555 -0.421 -0.035 0.306 5.660 -16.301 4.315 15 A_G15:C2_B A 15 ? B 2 ? 19 1 1 A C 16 1_555 B G 1 1_555 0.350 -0.211 0.048 4.065 -4.658 -0.879 16 A_C16:G1_B A 16 ? B 1 ? 19 1 1 C G 1 1_555 C C 16 6_765 -0.614 -0.020 0.116 -2.777 -8.214 3.758 17 C_G1:C16_C C 1 ? C 16 ? 19 1 1 C C 2 1_555 C G 15 6_765 0.112 -0.014 -0.446 5.843 -13.475 1.095 18 C_C2:G15_C C 2 ? C 15 ? 19 1 1 C A 3 1_555 C U 14 6_765 -0.043 -0.151 0.034 -0.954 -4.332 2.939 19 C_A3:U14_C C 3 ? C 14 ? 20 1 1 C G 4 1_555 C C 13 6_765 -0.345 -0.184 -0.113 -0.213 -11.144 -3.181 20 C_G4:C13_C C 4 ? C 13 ? 19 1 1 C A 5 1_555 C U 12 6_765 -0.125 -0.260 0.243 -2.824 -12.885 0.762 21 C_A5:U12_C C 5 ? C 12 ? 20 1 1 C A5M 6 1_555 C A 11 6_765 2.797 -0.506 0.057 -4.668 -12.605 3.580 22 C_A5M6:A11_C C 6 ? C 11 ? ? 1 1 C U 7 1_555 C A 10 6_765 0.356 -0.125 -0.098 -0.934 -14.480 0.726 23 C_U7:A10_C C 7 ? C 10 ? 20 1 1 C U 8 1_555 C A 9 6_765 0.342 -0.126 0.024 2.707 -18.048 6.007 24 C_U8:A9_C C 8 ? C 9 ? 20 1 1 C A 9 1_555 C U 8 6_765 -0.342 -0.126 0.024 -2.707 -18.048 6.007 25 C_A9:U8_C C 9 ? C 8 ? 20 1 1 C A 10 1_555 C U 7 6_765 -0.356 -0.125 -0.098 0.934 -14.480 0.726 26 C_A10:U7_C C 10 ? C 7 ? 20 1 1 C A 11 1_555 C A5M 6 6_765 -2.797 -0.506 0.057 4.668 -12.605 3.580 27 C_A11:A5M6_C C 11 ? C 6 ? ? 1 1 C U 12 1_555 C A 5 6_765 0.125 -0.260 0.243 2.824 -12.885 0.762 28 C_U12:A5_C C 12 ? C 5 ? 20 1 1 C C 13 1_555 C G 4 6_765 0.345 -0.184 -0.113 0.213 -11.144 -3.181 29 C_C13:G4_C C 13 ? C 4 ? 19 1 1 C U 14 1_555 C A 3 6_765 0.043 -0.151 0.034 0.954 -4.332 2.939 30 C_U14:A3_C C 14 ? C 3 ? 20 1 1 C G 15 1_555 C C 2 6_765 -0.112 -0.014 -0.446 -5.843 -13.475 1.095 31 C_G15:C2_C C 15 ? C 2 ? 19 1 1 C C 16 1_555 C G 1 6_765 0.614 -0.020 0.116 2.777 -8.214 3.758 32 C_C16:G1_C C 16 ? C 1 ? 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 16 1_555 A C 2 1_555 B G 15 1_555 -0.422 -1.395 3.098 -4.042 -0.516 34.499 -2.261 0.115 3.146 -0.866 6.786 34.731 1 AA_G1C2:G15C16_BB A 1 ? B 16 ? A 2 ? B 15 ? 1 A C 2 1_555 B G 15 1_555 A A 3 1_555 B U 14 1_555 -0.236 -1.424 2.986 -2.993 7.014 34.102 -3.301 -0.003 2.660 11.778 5.025 34.919 2 AA_C2A3:U14G15_BB A 2 ? B 15 ? A 3 ? B 14 ? 1 A A 3 1_555 B U 14 1_555 A G 4 1_555 B C 13 1_555 0.914 -1.074 3.428 4.726 12.018 26.582 -4.685 -0.782 2.810 24.392 -9.593 29.501 3 AA_A3G4:C13U14_BB A 3 ? B 14 ? A 4 ? B 13 ? 1 A G 4 1_555 B C 13 1_555 A A 5 1_555 B U 12 1_555 0.422 -1.741 3.184 -0.726 7.725 30.856 -4.463 -0.892 2.670 14.237 1.339 31.793 4 AA_G4A5:U12C13_BB A 4 ? B 13 ? A 5 ? B 12 ? 1 A A 5 1_555 B U 12 1_555 A A5M 6 1_555 B A 11 1_555 0.190 -0.965 3.123 0.813 6.184 42.123 -1.913 -0.185 2.962 8.547 -1.123 42.562 5 AA_A5A5M6:A11U12_BB A 5 ? B 12 ? A 6 ? B 11 ? 1 A A5M 6 1_555 B A 11 1_555 A U 7 1_555 B A 10 1_555 -2.083 -1.784 3.217 -1.093 12.476 16.762 -9.317 5.358 1.636 36.833 3.227 20.897 6 AA_A5M6U7:A10A11_BB A 6 ? B 11 ? A 7 ? B 10 ? 1 A U 7 1_555 B A 10 1_555 A U 8 1_555 B A 9 1_555 0.970 -1.289 3.108 -0.739 10.248 30.864 -3.895 -1.848 2.538 18.619 1.342 32.490 7 AA_U7U8:A9A10_BB A 7 ? B 10 ? A 8 ? B 9 ? 1 A U 8 1_555 B A 9 1_555 A A 9 1_555 B U 8 1_555 -0.170 -1.446 3.120 -0.110 19.323 32.260 -4.384 0.252 1.973 31.500 0.179 37.472 8 AA_U8A9:U8A9_BB A 8 ? B 9 ? A 9 ? B 8 ? 1 A A 9 1_555 B U 8 1_555 A A 10 1_555 B U 7 1_555 0.075 -1.480 3.384 1.221 2.623 34.182 -2.928 0.068 3.265 4.453 -2.072 34.301 9 AA_A9A10:U7U8_BB A 9 ? B 8 ? A 10 ? B 7 ? 1 A A 10 1_555 B U 7 1_555 A A 11 1_555 B A5M 6 1_555 0.577 -1.908 2.768 -2.881 7.032 16.493 -8.900 -2.997 1.692 22.991 9.418 18.148 10 AA_A10A11:A5M6U7_BB A 10 ? B 7 ? A 11 ? B 6 ? 1 A A 11 1_555 B A5M 6 1_555 A U 12 1_555 B A 5 1_555 -0.512 -1.058 3.288 -2.897 4.776 41.582 -1.971 0.416 3.179 6.691 4.059 41.939 11 AA_A11U12:A5A5M6_BB A 11 ? B 6 ? A 12 ? B 5 ? 1 A U 12 1_555 B A 5 1_555 A C 13 1_555 B G 4 1_555 -0.404 -1.713 3.113 -1.526 9.007 32.557 -4.240 0.476 2.577 15.684 2.657 33.781 12 AA_U12C13:G4A5_BB A 12 ? B 5 ? A 13 ? B 4 ? 1 A C 13 1_555 B G 4 1_555 A U 14 1_555 B A 3 1_555 -0.207 -1.442 3.174 -0.167 13.779 28.418 -4.901 0.354 2.253 26.208 0.317 31.520 13 AA_C13U14:A3G4_BB A 13 ? B 4 ? A 14 ? B 3 ? 1 A U 14 1_555 B A 3 1_555 A G 15 1_555 B C 2 1_555 0.066 -1.266 3.177 -1.836 12.207 32.804 -3.773 -0.360 2.551 20.723 3.116 34.990 14 AA_U14G15:C2A3_BB A 14 ? B 3 ? A 15 ? B 2 ? 1 A G 15 1_555 B C 2 1_555 A C 16 1_555 B G 1 1_555 0.213 -1.183 3.190 2.815 7.130 39.430 -2.492 -0.006 2.949 10.447 -4.124 40.139 15 AA_G15C16:G1C2_BB A 15 ? B 2 ? A 16 ? B 1 ? 1 C G 1 1_555 C C 16 6_765 C C 2 1_555 C G 15 6_765 -0.477 -1.442 3.092 3.892 3.292 34.892 -2.830 1.317 2.880 5.454 -6.448 35.251 16 CC_G1C2:G15C16_CC C 1 ? C 16 ? C 2 ? C 15 ? 1 C C 2 1_555 C G 15 6_765 C A 3 1_555 C U 14 6_765 0.366 -1.525 3.406 -3.233 11.053 31.932 -4.326 -1.128 2.696 19.322 5.651 33.894 17 CC_C2A3:U14G15_CC C 2 ? C 15 ? C 3 ? C 14 ? 1 C A 3 1_555 C U 14 6_765 C G 4 1_555 C C 13 6_765 -0.286 -1.442 3.204 0.290 9.226 29.425 -4.361 0.589 2.639 17.624 -0.555 30.809 18 CC_A3G4:C13U14_CC C 3 ? C 14 ? C 4 ? C 13 ? 1 C G 4 1_555 C C 13 6_765 C A 5 1_555 C U 12 6_765 0.046 -1.849 3.252 -2.635 11.044 33.476 -4.534 -0.430 2.524 18.524 4.419 35.297 19 CC_G4A5:U12C13_CC C 4 ? C 13 ? C 5 ? C 12 ? 1 C A 5 1_555 C U 12 6_765 C A5M 6 1_555 C A 11 6_765 0.297 -1.210 3.340 4.590 11.818 43.053 -2.643 0.020 2.941 15.701 -6.098 44.796 20 CC_A5A5M6:A11U12_CC C 5 ? C 12 ? C 6 ? C 11 ? 1 C A5M 6 1_555 C A 11 6_765 C U 7 1_555 C A 10 6_765 -0.321 -1.685 2.884 3.105 11.074 21.172 -6.721 1.522 1.734 27.663 -7.758 24.063 21 CC_A5M6U7:A10A11_CC C 6 ? C 11 ? C 7 ? C 10 ? 1 C U 7 1_555 C A 10 6_765 C U 8 1_555 C A 9 6_765 0.294 -1.297 3.190 -0.265 7.412 30.856 -3.641 -0.584 2.808 13.683 0.489 31.713 22 CC_U7U8:A9A10_CC C 7 ? C 10 ? C 8 ? C 9 ? 1 C U 8 1_555 C A 9 6_765 C A 9 1_555 C U 8 6_765 0.000 -1.265 3.181 0.000 16.109 31.424 -4.215 0.000 2.284 27.590 0.000 35.220 23 CC_U8A9:U8A9_CC C 8 ? C 9 ? C 9 ? C 8 ? 1 C A 9 1_555 C U 8 6_765 C A 10 1_555 C U 7 6_765 -0.294 -1.297 3.190 0.265 7.412 30.856 -3.641 0.584 2.808 13.683 -0.489 31.713 24 CC_A9A10:U7U8_CC C 9 ? C 8 ? C 10 ? C 7 ? 1 C A 10 1_555 C U 7 6_765 C A 11 1_555 C A5M 6 6_765 0.321 -1.685 2.884 -3.105 11.074 21.172 -6.721 -1.522 1.734 27.663 7.758 24.063 25 CC_A10A11:A5M6U7_CC C 10 ? C 7 ? C 11 ? C 6 ? 1 C A 11 1_555 C A5M 6 6_765 C U 12 1_555 C A 5 6_765 -0.297 -1.210 3.340 -4.590 11.818 43.053 -2.643 -0.020 2.941 15.701 6.098 44.796 26 CC_A11U12:A5A5M6_CC C 11 ? C 6 ? C 12 ? C 5 ? 1 C U 12 1_555 C A 5 6_765 C C 13 1_555 C G 4 6_765 -0.046 -1.849 3.252 2.635 11.044 33.476 -4.534 0.430 2.524 18.524 -4.419 35.297 27 CC_U12C13:G4A5_CC C 12 ? C 5 ? C 13 ? C 4 ? 1 C C 13 1_555 C G 4 6_765 C U 14 1_555 C A 3 6_765 0.286 -1.442 3.204 -0.290 9.226 29.425 -4.361 -0.589 2.639 17.624 0.555 30.809 28 CC_C13U14:A3G4_CC C 13 ? C 4 ? C 14 ? C 3 ? 1 C U 14 1_555 C A 3 6_765 C G 15 1_555 C C 2 6_765 -0.366 -1.525 3.406 3.233 11.053 31.932 -4.326 1.128 2.696 19.322 -5.651 33.894 29 CC_U14G15:C2A3_CC C 14 ? C 3 ? C 15 ? C 2 ? 1 C G 15 1_555 C C 2 6_765 C C 16 1_555 C G 1 6_765 0.477 -1.442 3.092 -3.892 3.292 34.892 -2.830 -1.317 2.880 5.454 6.448 35.251 30 CC_G15C16:G1C2_CC C 15 ? C 2 ? C 16 ? C 1 ? # _pdbx_initial_refinement_model.accession_code 405D _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.details 'NDB ENTRY AR0002' # _atom_sites.entry_id 1YRM _atom_sites.fract_transf_matrix[1][1] 0.023256 _atom_sites.fract_transf_matrix[1][2] 0.013427 _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] 0.026854 _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] 0.008163 _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 SR # loop_