data_4JRD # _entry.id 4JRD # _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 4JRD pdb_00004jrd 10.2210/pdb4jrd/pdb NDB NA2300 ? ? RCSB RCSB078407 ? ? WWPDB D_1000078407 ? ? # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2013-06-05 2 'Structure model' 1 1 2015-08-12 3 'Structure model' 1 2 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' 'Database references' 2 3 'Structure model' 'Data collection' 3 3 'Structure model' 'Database references' 4 3 '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 3 'Structure model' chem_comp_atom 2 3 'Structure model' chem_comp_bond 3 3 'Structure model' database_2 4 3 '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 3 'Structure model' '_database_2.pdbx_DOI' 2 3 'Structure model' '_database_2.pdbx_database_accession' 3 3 'Structure model' '_struct_site.pdbx_auth_asym_id' 4 3 'Structure model' '_struct_site.pdbx_auth_comp_id' 5 3 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 4JRD _pdbx_database_status.recvd_initial_deposition_date 2013-03-21 _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.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Safaee, N.' 1 'Noronha, A.M.' 2 'Kozlov, G.' 3 'Rodionov, D.' 4 'Wilds, C.J.' 5 'Sheldrick, G.M.' 6 'Gehring, K.' 7 # _citation.id primary _citation.title 'Structure of the parallel duplex of poly(A) RNA: evaluation of a 50 year-old prediction.' _citation.journal_abbrev Angew.Chem.Int.Ed.Engl. _citation.journal_volume 52 _citation.page_first 10370 _citation.page_last 10373 _citation.year 2013 _citation.journal_id_ASTM ? _citation.country GE _citation.journal_id_ISSN 1433-7851 _citation.journal_id_CSD 9999 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 23813654 _citation.pdbx_database_id_DOI 10.1002/anie.201303461 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Safaee, N.' 1 ? primary 'Noronha, A.M.' 2 ? primary 'Rodionov, D.' 3 ? primary 'Kozlov, G.' 4 ? primary 'Wilds, C.J.' 5 ? primary 'Sheldrick, G.M.' 6 ? primary 'Gehring, K.' 7 ? # 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(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3') ; 3576.306 2 ? ? ? ? 2 non-polymer syn 'AMMONIUM ION' 18.038 18 ? ? ? ? 3 water nat water 18.015 76 ? ? ? ? # _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 AAAAAAAAAAA _entity_poly.pdbx_seq_one_letter_code_can AAAAAAAAAAA _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 'AMMONIUM ION' NH4 3 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 A n 1 2 A n 1 3 A n 1 4 A n 1 5 A n 1 6 A n 1 7 A n 1 8 A n 1 9 A n 1 10 A n 1 11 A 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 HOH non-polymer . WATER ? 'H2 O' 18.015 NH4 non-polymer . 'AMMONIUM ION' ? 'H4 N 1' 18.038 # 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 A 1 1 1 A A A . n A 1 2 A 2 2 2 A A A . n A 1 3 A 3 3 3 A A A . n A 1 4 A 4 4 4 A A A . n A 1 5 A 5 5 5 A A A . n A 1 6 A 6 6 6 A A A . n A 1 7 A 7 7 7 A A A . n A 1 8 A 8 8 8 A A 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 B 1 1 A 1 1 1 A A B . n B 1 2 A 2 2 2 A A B . n B 1 3 A 3 3 3 A A B . n B 1 4 A 4 4 4 A A B . n B 1 5 A 5 5 5 A A B . n B 1 6 A 6 6 6 A A B . n B 1 7 A 7 7 7 A A B . n B 1 8 A 8 8 8 A A 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 # 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 NH4 1 101 101 NH4 NH4 A . D 2 NH4 1 102 102 NH4 NH4 A . E 2 NH4 1 103 103 NH4 NH4 A . F 2 NH4 1 104 104 NH4 NH4 A . G 2 NH4 1 105 105 NH4 NH4 A . H 2 NH4 1 106 106 NH4 NH4 A . I 2 NH4 1 107 107 NH4 NH4 A . J 2 NH4 1 108 108 NH4 NH4 A . K 2 NH4 1 109 109 NH4 NH4 A . L 2 NH4 1 110 110 NH4 NH4 A . M 2 NH4 1 111 111 NH4 NH4 A . N 2 NH4 1 101 101 NH4 NH4 B . O 2 NH4 1 102 102 NH4 NH4 B . P 2 NH4 1 103 103 NH4 NH4 B . Q 2 NH4 1 104 104 NH4 NH4 B . R 2 NH4 1 105 105 NH4 NH4 B . S 2 NH4 1 106 106 NH4 NH4 B . T 2 NH4 1 107 107 NH4 NH4 B . U 3 HOH 1 201 201 HOH HOH A . U 3 HOH 2 202 202 HOH HOH A . U 3 HOH 3 203 203 HOH HOH A . U 3 HOH 4 204 204 HOH HOH A . U 3 HOH 5 205 205 HOH HOH A . U 3 HOH 6 206 206 HOH HOH A . U 3 HOH 7 207 207 HOH HOH A . U 3 HOH 8 208 208 HOH HOH A . U 3 HOH 9 209 209 HOH HOH A . U 3 HOH 10 210 210 HOH HOH A . U 3 HOH 11 211 211 HOH HOH A . U 3 HOH 12 212 212 HOH HOH A . U 3 HOH 13 213 213 HOH HOH A . U 3 HOH 14 214 214 HOH HOH A . U 3 HOH 15 215 215 HOH HOH A . U 3 HOH 16 216 216 HOH HOH A . U 3 HOH 17 217 217 HOH HOH A . U 3 HOH 18 218 218 HOH HOH A . U 3 HOH 19 219 219 HOH HOH A . U 3 HOH 20 220 220 HOH HOH A . U 3 HOH 21 221 221 HOH HOH A . U 3 HOH 22 222 222 HOH HOH A . U 3 HOH 23 223 223 HOH HOH A . U 3 HOH 24 224 224 HOH HOH A . U 3 HOH 25 225 225 HOH HOH A . U 3 HOH 26 226 226 HOH HOH A . U 3 HOH 27 227 227 HOH HOH A . U 3 HOH 28 228 228 HOH HOH A . U 3 HOH 29 229 229 HOH HOH A . U 3 HOH 30 230 230 HOH HOH A . U 3 HOH 31 231 231 HOH HOH A . U 3 HOH 32 232 232 HOH HOH A . U 3 HOH 33 233 233 HOH HOH A . U 3 HOH 34 234 234 HOH HOH A . V 3 HOH 1 201 201 HOH HOH B . V 3 HOH 2 202 202 HOH HOH B . V 3 HOH 3 203 203 HOH HOH B . V 3 HOH 4 204 204 HOH HOH B . V 3 HOH 5 205 205 HOH HOH B . V 3 HOH 6 206 206 HOH HOH B . V 3 HOH 7 207 207 HOH HOH B . V 3 HOH 8 208 208 HOH HOH B . V 3 HOH 9 209 209 HOH HOH B . V 3 HOH 10 210 210 HOH HOH B . V 3 HOH 11 211 211 HOH HOH B . V 3 HOH 12 212 212 HOH HOH B . V 3 HOH 13 213 213 HOH HOH B . V 3 HOH 14 214 214 HOH HOH B . V 3 HOH 15 215 215 HOH HOH B . V 3 HOH 16 216 216 HOH HOH B . V 3 HOH 17 217 217 HOH HOH B . V 3 HOH 18 218 218 HOH HOH B . V 3 HOH 19 219 219 HOH HOH B . V 3 HOH 20 220 220 HOH HOH B . V 3 HOH 21 221 221 HOH HOH B . V 3 HOH 22 222 222 HOH HOH B . V 3 HOH 23 223 223 HOH HOH B . V 3 HOH 24 224 224 HOH HOH B . V 3 HOH 25 225 225 HOH HOH B . V 3 HOH 26 226 226 HOH HOH B . V 3 HOH 27 227 227 HOH HOH B . V 3 HOH 28 228 228 HOH HOH B . V 3 HOH 29 229 229 HOH HOH B . V 3 HOH 30 230 230 HOH HOH B . V 3 HOH 31 231 231 HOH HOH B . V 3 HOH 32 232 232 HOH HOH B . V 3 HOH 33 233 233 HOH HOH B . V 3 HOH 34 234 234 HOH HOH B . V 3 HOH 35 235 235 HOH HOH B . V 3 HOH 36 236 236 HOH HOH B . V 3 HOH 37 237 237 HOH HOH B . V 3 HOH 38 238 238 HOH HOH B . V 3 HOH 39 239 239 HOH HOH B . V 3 HOH 40 240 240 HOH HOH B . V 3 HOH 41 241 241 HOH HOH B . V 3 HOH 42 242 242 HOH HOH B . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal MxDC 'data collection' . ? 1 SHELXD phasing . ? 2 SHELXL refinement . ? 3 HKL-2000 'data reduction' . ? 4 HKL-2000 'data scaling' . ? 5 # _cell.entry_id 4JRD _cell.length_a 22.800 _cell.length_b 22.800 _cell.length_c 163.700 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.entry_id 4JRD _symmetry.space_group_name_H-M 'P 41 21 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? # _exptl.entry_id 4JRD _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 5 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 1.49 _exptl_crystal.density_percent_sol 17.29 _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 294 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH ? _exptl_crystal_grow.pdbx_details ;RNA WATER SOLUTION PLUS BUFFER (10 MM HEPES, 50 MM NACL, 0.5 MM TCEP, PH 7.0) MIXED 1:1 V/V WITH 2 M (NH4)2SO4 + 0.2 M NH4NO3 AND EQUILIBRATED AGAINST 2 M (NH4)2SO4 + 0.2 M NH4NO3, VAPOR DIFFUSION, SITTING DROP, temperature 294K ; _exptl_crystal_grow.pdbx_pH_range ? # loop_ _diffrn.id _diffrn.ambient_temp _diffrn.ambient_temp_details _diffrn.crystal_id 1 100 ? 1 2 100 ? 1 3 100 ? 1 4 100 ? 1 # loop_ _diffrn_detector.diffrn_id _diffrn_detector.detector _diffrn_detector.type _diffrn_detector.pdbx_collection_date _diffrn_detector.details 1 CCD 'MARMOSAIC 300 mm CCD' 2010-05-29 'FOCUSING MIRRORS' 2 CCD 'ADSC QUANTUM 210' 2010-10-21 'FOCUSING MIRRORS' 3 CCD 'ADSC QUANTUM 210' 2010-10-21 'FOCUSING MIRRORS' 4 CCD 'ADSC QUANTUM 210' 2010-10-21 'FOCUSING MIRRORS' # 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 'SI 111 DOUBLE' 'SINGLE WAVELENGTH' x-ray 2 1 M 'Horizontal focusing 5.05 asymmetric cut Si(111)' 'SINGLE WAVELENGTH' x-ray 3 1 M 'Horizontal focusing 5.05 asymmetric cut Si(111)' 'SINGLE WAVELENGTH' x-ray 4 1 M 'Horizontal focusing 5.05 asymmetric cut Si(111)' 'SINGLE WAVELENGTH' x-ray # loop_ _diffrn_radiation_wavelength.id _diffrn_radiation_wavelength.wavelength _diffrn_radiation_wavelength.wt 1 0.977 1.0 2 0.987 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 'CLSI BEAMLINE 08ID-1' CLSI 08ID-1 0.977 ? 2 SYNCHROTRON 'CHESS BEAMLINE A1' CHESS A1 0.987 ? 3 SYNCHROTRON 'CHESS BEAMLINE A1' CHESS A1 0.987 ? 4 SYNCHROTRON 'CHESS BEAMLINE A1' CHESS A1 0.987 ? # _reflns.entry_id 4JRD _reflns.observed_criterion_sigma_I -3.000 _reflns.observed_criterion_sigma_F 4 _reflns.d_resolution_low 41.000 _reflns.d_resolution_high 1.000 _reflns.number_obs 22972 _reflns.number_all 23042 _reflns.percent_possible_obs 92.6 _reflns.pdbx_Rmerge_I_obs 0.09440 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 34.3500 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 2.730 _reflns.R_free_details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1,2,3,4 # _reflns_shell.d_res_high 1.00 _reflns_shell.d_res_low 1.10 _reflns_shell.percent_possible_all 73.1 _reflns_shell.Rmerge_I_obs 0.14190 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 4.720 _reflns_shell.pdbx_redundancy 1.20 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all ? _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1,2,3,4 # _refine.entry_id 4JRD _refine.ls_number_reflns_obs 22972 _refine.ls_number_reflns_all 23042 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 1.000 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 41.00 _refine.ls_d_res_high 1.00 _refine.ls_percent_reflns_obs 92.6 _refine.ls_R_factor_obs 0.126 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.118 _refine.ls_R_factor_R_free 0.158 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 5.010 _refine.ls_number_reflns_R_free 1152 _refine.ls_number_parameters 5165 _refine.ls_number_restraints 6773 _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _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 BABINET _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_ls_cross_valid_method 'FREE R' _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct 'AB INITIO PHASING' _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.pdbx_overall_phase_error ? _refine.overall_SU_B ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _refine.overall_SU_R_free ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_diffrn_id 1,2,3,4 _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_analyze.entry_id 4JRD _refine_analyze.Luzzati_coordinate_error_obs ? _refine_analyze.Luzzati_sigma_a_obs ? _refine_analyze.Luzzati_d_res_low_obs ? _refine_analyze.Luzzati_coordinate_error_free ? _refine_analyze.Luzzati_sigma_a_free ? _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues 0 _refine_analyze.occupancy_sum_hydrogen 242.00 _refine_analyze.occupancy_sum_non_hydrogen 571.00 _refine_analyze.pdbx_Luzzati_d_res_high_obs ? _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 478 _refine_hist.pdbx_number_atoms_ligand 18 _refine_hist.number_atoms_solvent 76 _refine_hist.number_atoms_total 572 _refine_hist.d_res_high 1.00 _refine_hist.d_res_low 41.00 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_restraint_function _refine_ls_restr.pdbx_refine_id s_bond_d 0.007 ? ? ? ? 'X-RAY DIFFRACTION' s_angle_d 0.021 ? ? ? ? 'X-RAY DIFFRACTION' s_from_restr_planes 0.038 ? ? ? ? 'X-RAY DIFFRACTION' s_anti_bump_dis_restr 0.021 ? ? ? ? 'X-RAY DIFFRACTION' s_rigid_bond_adp_cmpnt 0.005 ? ? ? ? 'X-RAY DIFFRACTION' s_similar_adp_cmpnt 0.015 ? ? ? ? 'X-RAY DIFFRACTION' s_approx_iso_adps 0.100 ? ? ? ? 'X-RAY DIFFRACTION' # _pdbx_refine.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine.entry_id 4JRD _pdbx_refine.R_factor_all_no_cutoff 0.128 _pdbx_refine.R_factor_obs_no_cutoff 0.126 _pdbx_refine.free_R_factor_no_cutoff 0.158 _pdbx_refine.free_R_error_no_cutoff ? _pdbx_refine.free_R_val_test_set_size_perc_no_cutoff 5.010 _pdbx_refine.free_R_val_test_set_ct_no_cutoff 1152 _pdbx_refine.R_factor_all_4sig_cutoff 0.120 _pdbx_refine.R_factor_obs_4sig_cutoff 0.118 _pdbx_refine.free_R_factor_4sig_cutoff 0.151 _pdbx_refine.free_R_val_test_set_size_perc_4sig_cutoff 5.260 _pdbx_refine.free_R_val_test_set_ct_4sig_cutoff 986 _pdbx_refine.number_reflns_obs_4sig_cutoff 18730 # _database_PDB_matrix.entry_id 4JRD _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 4JRD _struct.title 'Crystal structure of the parallel double-stranded helix of poly(A) RNA' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 4JRD _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'PARALLEL DOUBLE HELIX, POLY(A), MRNA, PABP, Poly(A) motif, 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 ? E N N 2 ? F N N 2 ? G N N 2 ? H N N 2 ? I N N 2 ? J N N 2 ? K N N 2 ? L N N 2 ? M N N 2 ? N N N 2 ? O N N 2 ? P N N 2 ? Q N N 2 ? R N N 2 ? S N N 2 ? T N N 2 ? U N N 3 ? V N N 3 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 4JRD _struct_ref.pdbx_db_accession 4JRD _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_db_isoform ? # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 4JRD A 1 ? 11 ? 4JRD 1 ? 11 ? 1 11 2 1 4JRD B 1 ? 11 ? 4JRD 1 ? 11 ? 1 11 # _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,I,J,K,L,M,N,O,P,Q,R,S,T,U,V # _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 _struct_biol.details ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role hydrog1 hydrog ? ? A A 2 N6 ? ? ? 1_555 B A 1 N7 ? ? A A 2 B A 1 1_555 ? ? ? ? ? ? TYPE_2_PAIR ? ? ? hydrog2 hydrog ? ? A A 2 N7 ? ? ? 1_555 B A 1 N6 ? ? A A 2 B A 1 1_555 ? ? ? ? ? ? TYPE_2_PAIR ? ? ? hydrog3 hydrog ? ? A A 3 N6 ? ? ? 1_555 B A 2 N7 ? ? A A 3 B A 2 1_555 ? ? ? ? ? ? TYPE_2_PAIR ? ? ? hydrog4 hydrog ? ? A A 3 N7 ? ? ? 1_555 B A 2 N6 ? ? A A 3 B A 2 1_555 ? ? ? ? ? ? TYPE_2_PAIR ? ? ? hydrog5 hydrog ? ? A A 4 N6 ? ? ? 1_555 B A 3 N7 ? ? A A 4 B A 3 1_555 ? ? ? ? ? ? TYPE_2_PAIR ? ? ? hydrog6 hydrog ? ? A A 4 N7 ? ? ? 1_555 B A 3 N6 ? ? A A 4 B A 3 1_555 ? ? ? ? ? ? TYPE_2_PAIR ? ? ? hydrog7 hydrog ? ? A A 5 N6 ? ? ? 1_555 B A 4 N7 ? ? A A 5 B A 4 1_555 ? ? ? ? ? ? TYPE_2_PAIR ? ? ? hydrog8 hydrog ? ? A A 5 N7 ? ? ? 1_555 B A 4 N6 ? ? A A 5 B A 4 1_555 ? ? ? ? ? ? TYPE_2_PAIR ? ? ? hydrog9 hydrog ? ? A A 6 N6 ? ? ? 1_555 B A 5 N7 ? ? A A 6 B A 5 1_555 ? ? ? ? ? ? TYPE_2_PAIR ? ? ? hydrog10 hydrog ? ? A A 6 N7 ? ? ? 1_555 B A 5 N6 ? ? A A 6 B A 5 1_555 ? ? ? ? ? ? TYPE_2_PAIR ? ? ? hydrog11 hydrog ? ? A A 7 N6 ? ? ? 1_555 B A 6 N7 ? ? A A 7 B A 6 1_555 ? ? ? ? ? ? TYPE_2_PAIR ? ? ? hydrog12 hydrog ? ? A A 7 N7 ? ? ? 1_555 B A 6 N6 ? ? A A 7 B A 6 1_555 ? ? ? ? ? ? TYPE_2_PAIR ? ? ? hydrog13 hydrog ? ? A A 8 N6 ? ? ? 1_555 B A 7 N7 ? ? A A 8 B A 7 1_555 ? ? ? ? ? ? TYPE_2_PAIR ? ? ? hydrog14 hydrog ? ? A A 8 N7 ? ? ? 1_555 B A 7 N6 ? ? A A 8 B A 7 1_555 ? ? ? ? ? ? TYPE_2_PAIR ? ? ? hydrog15 hydrog ? ? A A 9 N6 ? ? ? 1_555 B A 8 N7 ? ? A A 9 B A 8 1_555 ? ? ? ? ? ? TYPE_2_PAIR ? ? ? hydrog16 hydrog ? ? A A 9 N7 ? ? ? 1_555 B A 8 N6 ? ? A A 9 B A 8 1_555 ? ? ? ? ? ? TYPE_2_PAIR ? ? ? hydrog17 hydrog ? ? A A 10 N6 ? ? ? 1_555 B A 9 N7 ? ? A A 10 B A 9 1_555 ? ? ? ? ? ? TYPE_2_PAIR ? ? ? hydrog18 hydrog ? ? A A 10 N7 ? ? ? 1_555 B A 9 N6 ? ? A A 10 B A 9 1_555 ? ? ? ? ? ? TYPE_2_PAIR ? ? ? hydrog19 hydrog ? ? A A 11 N6 ? ? ? 1_555 B A 10 N7 ? ? A A 11 B A 10 1_555 ? ? ? ? ? ? TYPE_2_PAIR ? ? ? hydrog20 hydrog ? ? A A 11 N7 ? ? ? 1_555 B A 10 N6 ? ? A A 11 B A 10 1_555 ? ? ? ? ? ? TYPE_2_PAIR ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software A NH4 101 ? 3 'BINDING SITE FOR RESIDUE NH4 A 101' AC2 Software A NH4 102 ? 4 'BINDING SITE FOR RESIDUE NH4 A 102' AC3 Software A NH4 103 ? 4 'BINDING SITE FOR RESIDUE NH4 A 103' AC4 Software A NH4 104 ? 6 'BINDING SITE FOR RESIDUE NH4 A 104' AC5 Software A NH4 105 ? 4 'BINDING SITE FOR RESIDUE NH4 A 105' AC6 Software A NH4 106 ? 1 'BINDING SITE FOR RESIDUE NH4 A 106' AC7 Software A NH4 107 ? 5 'BINDING SITE FOR RESIDUE NH4 A 107' AC8 Software A NH4 108 ? 5 'BINDING SITE FOR RESIDUE NH4 A 108' AC9 Software A NH4 109 ? 5 'BINDING SITE FOR RESIDUE NH4 A 109' BC1 Software A NH4 110 ? 5 'BINDING SITE FOR RESIDUE NH4 A 110' BC2 Software A NH4 111 ? 4 'BINDING SITE FOR RESIDUE NH4 A 111' BC3 Software B NH4 101 ? 4 'BINDING SITE FOR RESIDUE NH4 B 101' BC4 Software B NH4 102 ? 5 'BINDING SITE FOR RESIDUE NH4 B 102' BC5 Software B NH4 103 ? 6 'BINDING SITE FOR RESIDUE NH4 B 103' BC6 Software B NH4 104 ? 6 'BINDING SITE FOR RESIDUE NH4 B 104' BC7 Software B NH4 105 ? 5 'BINDING SITE FOR RESIDUE NH4 B 105' BC8 Software B NH4 106 ? 5 'BINDING SITE FOR RESIDUE NH4 B 106' BC9 Software B NH4 107 ? 5 'BINDING SITE FOR RESIDUE NH4 B 107' # 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 3 A A 2 ? A A 2 . ? 1_555 ? 2 AC1 3 A A 3 ? A A 3 . ? 1_555 ? 3 AC1 3 A B 2 ? A B 2 . ? 1_555 ? 4 AC2 4 A A 3 ? A A 3 . ? 1_555 ? 5 AC2 4 A A 4 ? A A 4 . ? 1_555 ? 6 AC2 4 A A 11 ? A A 11 . ? 7_645 ? 7 AC2 4 A B 3 ? A B 3 . ? 1_555 ? 8 AC3 4 A A 6 ? A A 6 . ? 1_555 ? 9 AC3 4 A A 7 ? A A 7 . ? 1_555 ? 10 AC3 4 HOH U . ? HOH A 216 . ? 7_655 ? 11 AC3 4 A B 6 ? A B 6 . ? 1_555 ? 12 AC4 6 A A 5 ? A A 5 . ? 7_545 ? 13 AC4 6 A A 9 ? A A 9 . ? 1_555 ? 14 AC4 6 A A 10 ? A A 10 . ? 1_555 ? 15 AC4 6 A B 9 ? A B 9 . ? 1_555 ? 16 AC4 6 A B 10 ? A B 10 . ? 1_555 ? 17 AC4 6 NH4 P . ? NH4 B 103 . ? 7_545 ? 18 AC5 4 A A 4 ? A A 4 . ? 7_545 ? 19 AC5 4 A A 10 ? A A 10 . ? 1_555 ? 20 AC5 4 A A 11 ? A A 11 . ? 1_555 ? 21 AC5 4 A B 10 ? A B 10 . ? 1_555 ? 22 AC6 1 A A 11 ? A A 11 . ? 1_555 ? 23 AC7 5 A A 7 ? A A 7 . ? 1_555 ? 24 AC7 5 A A 8 ? A A 8 . ? 1_555 ? 25 AC7 5 HOH U . ? HOH A 213 . ? 7_555 ? 26 AC7 5 A B 7 ? A B 7 . ? 1_555 ? 27 AC7 5 A B 8 ? A B 8 . ? 1_555 ? 28 AC8 5 A A 8 ? A A 8 . ? 1_555 ? 29 AC8 5 A A 9 ? A A 9 . ? 1_555 ? 30 AC8 5 HOH U . ? HOH A 233 . ? 1_555 ? 31 AC8 5 A B 8 ? A B 8 . ? 1_555 ? 32 AC8 5 A B 9 ? A B 9 . ? 1_555 ? 33 AC9 5 A A 4 ? A A 4 . ? 1_555 ? 34 AC9 5 A A 5 ? A A 5 . ? 1_555 ? 35 AC9 5 HOH U . ? HOH A 234 . ? 1_555 ? 36 AC9 5 A B 4 ? A B 4 . ? 1_555 ? 37 AC9 5 A B 5 ? A B 5 . ? 1_555 ? 38 BC1 5 A A 7 ? A A 7 . ? 1_555 ? 39 BC1 5 A A 8 ? A A 8 . ? 1_555 ? 40 BC1 5 HOH U . ? HOH A 227 . ? 1_555 ? 41 BC1 5 A B 5 ? A B 5 . ? 1_555 ? 42 BC1 5 A B 6 ? A B 6 . ? 1_555 ? 43 BC2 4 A A 10 ? A A 10 . ? 1_555 ? 44 BC2 4 A A 11 ? A A 11 . ? 1_555 ? 45 BC2 4 A B 8 ? A B 8 . ? 1_555 ? 46 BC2 4 A B 9 ? A B 9 . ? 1_555 ? 47 BC3 4 A A 1 ? A A 1 . ? 3_645 ? 48 BC3 4 A A 11 ? A A 11 . ? 1_555 ? 49 BC3 4 A B 9 ? A B 9 . ? 1_555 ? 50 BC3 4 A B 10 ? A B 10 . ? 1_555 ? 51 BC4 5 A A 3 ? A A 3 . ? 1_555 ? 52 BC4 5 A A 4 ? A A 4 . ? 1_555 ? 53 BC4 5 A B 1 ? A B 1 . ? 1_555 ? 54 BC4 5 A B 2 ? A B 2 . ? 1_555 ? 55 BC4 5 HOH V . ? HOH B 201 . ? 1_555 ? 56 BC5 6 A A 5 ? A A 5 . ? 1_555 ? 57 BC5 6 A A 6 ? A A 6 . ? 1_555 ? 58 BC5 6 A A 9 ? A A 9 . ? 7_655 ? 59 BC5 6 NH4 F . ? NH4 A 104 . ? 7_655 ? 60 BC5 6 A B 5 ? A B 5 . ? 1_555 ? 61 BC5 6 A B 6 ? A B 6 . ? 1_555 ? 62 BC6 6 A A 9 ? A A 9 . ? 1_555 ? 63 BC6 6 A A 10 ? A A 10 . ? 1_555 ? 64 BC6 6 A B 5 ? A B 5 . ? 7_645 ? 65 BC6 6 A B 7 ? A B 7 . ? 1_555 ? 66 BC6 6 A B 8 ? A B 8 . ? 1_555 ? 67 BC6 6 HOH V . ? HOH B 213 . ? 7_645 ? 68 BC7 5 A A 4 ? A A 4 . ? 1_555 ? 69 BC7 5 A A 5 ? A A 5 . ? 1_555 ? 70 BC7 5 A B 2 ? A B 2 . ? 1_555 ? 71 BC7 5 A B 3 ? A B 3 . ? 1_555 ? 72 BC7 5 HOH V . ? HOH B 204 . ? 7_555 ? 73 BC8 5 A A 6 ? A A 6 . ? 1_555 ? 74 BC8 5 A A 7 ? A A 7 . ? 1_555 ? 75 BC8 5 A B 4 ? A B 4 . ? 1_555 ? 76 BC8 5 A B 5 ? A B 5 . ? 1_555 ? 77 BC8 5 HOH V . ? HOH B 210 . ? 7_545 ? 78 BC9 5 A A 5 ? A A 5 . ? 1_555 ? 79 BC9 5 A A 6 ? A A 6 . ? 1_555 ? 80 BC9 5 A B 3 ? A B 3 . ? 1_555 ? 81 BC9 5 A B 4 ? A B 4 . ? 1_555 ? 82 BC9 5 HOH V . ? HOH B 214 . ? 1_555 ? # _pdbx_validate_rmsd_angle.id 1 _pdbx_validate_rmsd_angle.PDB_model_num 1 _pdbx_validate_rmsd_angle.auth_atom_id_1 N1 _pdbx_validate_rmsd_angle.auth_asym_id_1 A _pdbx_validate_rmsd_angle.auth_comp_id_1 A _pdbx_validate_rmsd_angle.auth_seq_id_1 3 _pdbx_validate_rmsd_angle.PDB_ins_code_1 ? _pdbx_validate_rmsd_angle.label_alt_id_1 ? _pdbx_validate_rmsd_angle.auth_atom_id_2 C2 _pdbx_validate_rmsd_angle.auth_asym_id_2 A _pdbx_validate_rmsd_angle.auth_comp_id_2 A _pdbx_validate_rmsd_angle.auth_seq_id_2 3 _pdbx_validate_rmsd_angle.PDB_ins_code_2 ? _pdbx_validate_rmsd_angle.label_alt_id_2 ? _pdbx_validate_rmsd_angle.auth_atom_id_3 N3 _pdbx_validate_rmsd_angle.auth_asym_id_3 A _pdbx_validate_rmsd_angle.auth_comp_id_3 A _pdbx_validate_rmsd_angle.auth_seq_id_3 3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 ? _pdbx_validate_rmsd_angle.label_alt_id_3 ? _pdbx_validate_rmsd_angle.angle_value 134.20 _pdbx_validate_rmsd_angle.angle_target_value 129.30 _pdbx_validate_rmsd_angle.angle_deviation 4.90 _pdbx_validate_rmsd_angle.angle_standard_deviation 0.50 _pdbx_validate_rmsd_angle.linker_flag N # 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 A A 1 ? ? 0.079 'SIDE CHAIN' 2 1 A A 3 ? ? 0.067 'SIDE CHAIN' 3 1 A A 4 ? ? 0.055 'SIDE CHAIN' 4 1 A A 7 ? ? 0.053 'SIDE CHAIN' 5 1 A A 9 ? ? 0.055 'SIDE CHAIN' 6 1 A B 4 ? ? 0.084 'SIDE CHAIN' 7 1 A B 11 ? ? 0.056 '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 225 ? U HOH . 2 1 B HOH 217 ? V 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 HOH O O N N 38 HOH H1 H N N 39 HOH H2 H N N 40 NH4 N N N N 41 NH4 HN1 H N N 42 NH4 HN2 H N N 43 NH4 HN3 H N N 44 NH4 HN4 H N N 45 # 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 HOH O H1 sing N N 40 HOH O H2 sing N N 41 NH4 N HN1 sing N N 42 NH4 N HN2 sing N N 43 NH4 N HN3 sing N N 44 NH4 N HN4 sing N N 45 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 4JRD 'double helix' 4JRD 'parallel strands' 4JRD '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 A 2 1_555 B A 1 1_555 -6.182 5.025 -0.025 -13.408 4.781 -179.467 1 A_A2:A1_B A 2 ? B 1 ? 2 8 1 A A 3 1_555 B A 2 1_555 -6.071 5.012 -0.335 -10.282 3.293 -179.334 2 A_A3:A2_B A 3 ? B 2 ? 2 8 1 A A 4 1_555 B A 3 1_555 6.228 -4.982 0.020 5.218 -10.155 179.914 3 A_A4:A3_B A 4 ? B 3 ? 2 8 1 A A 5 1_555 B A 4 1_555 6.173 -5.037 0.102 2.843 -11.912 179.150 4 A_A5:A4_B A 5 ? B 4 ? 2 8 1 A A 6 1_555 B A 5 1_555 -6.191 5.006 0.080 -0.083 12.517 -179.982 5 A_A6:A5_B A 6 ? B 5 ? 2 8 1 A A 7 1_555 B A 6 1_555 -6.156 5.094 0.057 3.242 13.478 -176.770 6 A_A7:A6_B A 7 ? B 6 ? 2 8 1 A A 8 1_555 B A 7 1_555 -6.001 5.151 -0.025 0.631 14.220 -179.556 7 A_A8:A7_B A 8 ? B 7 ? 2 8 1 A A 9 1_555 B A 8 1_555 6.110 -5.056 -0.051 -2.264 -15.216 179.228 8 A_A9:A8_B A 9 ? B 8 ? 2 8 1 A A 10 1_555 B A 9 1_555 -6.191 4.996 -0.033 4.937 13.390 -179.243 9 A_A10:A9_B A 10 ? B 9 ? 2 8 1 A A 11 1_555 B A 10 1_555 -6.148 5.017 0.102 0.116 5.294 -178.911 10 A_A11:A10_B A 11 ? B 10 ? 2 8 # 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 A 2 1_555 B A 1 1_555 A A 3 1_555 B A 2 1_555 -0.079 -1.754 3.491 4.899 4.432 33.016 -3.776 0.961 3.191 7.702 -8.514 33.652 1 AA_A2A3:A2A1_BB A 2 ? B 1 ? A 3 ? B 2 ? 1 A A 3 1_555 B A 2 1_555 A A 4 1_555 B A 3 1_555 0.025 -0.462 3.817 0.081 -3.624 -138.966 0.271 0.014 3.812 1.934 0.043 -138.988 2 AA_A3A4:A3A2_BB A 3 ? B 2 ? A 4 ? B 3 ? 1 A A 4 1_555 B A 3 1_555 A A 5 1_555 B A 4 1_555 0.165 -0.403 3.750 0.341 1.511 41.576 -0.751 -0.191 3.735 2.128 -0.480 41.604 3 AA_A4A5:A4A3_BB A 4 ? B 3 ? A 5 ? B 4 ? 1 A A 5 1_555 B A 4 1_555 A A 6 1_555 B A 5 1_555 0.287 -0.515 3.780 -1.113 1.330 -136.301 0.268 0.146 3.783 -0.716 -0.599 -136.306 4 AA_A5A6:A5A4_BB A 5 ? B 4 ? A 6 ? B 5 ? 1 A A 6 1_555 B A 5 1_555 A A 7 1_555 B A 6 1_555 0.238 -0.441 3.764 -0.199 0.191 41.128 -0.651 -0.364 3.761 0.271 0.283 41.129 5 AA_A6A7:A6A5_BB A 6 ? B 5 ? A 7 ? B 6 ? 1 A A 7 1_555 B A 6 1_555 A A 8 1_555 B A 7 1_555 -0.151 0.078 3.811 1.084 0.742 45.108 0.025 0.310 3.807 0.967 -1.413 45.127 6 AA_A7A8:A7A6_BB A 7 ? B 6 ? A 8 ? B 7 ? 1 A A 8 1_555 B A 7 1_555 A A 9 1_555 B A 8 1_555 -0.224 -0.024 3.827 0.426 -0.264 -139.076 0.014 -0.117 3.828 0.141 0.227 -139.077 7 AA_A8A9:A8A7_BB A 8 ? B 7 ? A 9 ? B 8 ? 1 A A 9 1_555 B A 8 1_555 A A 10 1_555 B A 9 1_555 -0.362 0.231 3.778 0.234 0.693 -138.296 -0.128 -0.192 3.778 -0.371 0.125 -138.297 8 AA_A9A10:A9A8_BB A 9 ? B 8 ? A 10 ? B 9 ? 1 A A 10 1_555 B A 9 1_555 A A 11 1_555 B A 10 1_555 -0.134 -0.036 3.563 -0.878 -1.142 40.050 0.089 0.086 3.565 -1.667 1.282 40.074 9 AA_A10A11:A10A9_BB A 10 ? B 9 ? A 11 ? B 10 ? # _atom_sites.entry_id 4JRD _atom_sites.fract_transf_matrix[1][1] 0.043860 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.043860 _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] 0.006109 _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_