data_3ND4 # _entry.id 3ND4 # _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 3ND4 pdb_00003nd4 10.2210/pdb3nd4/pdb NDB NA0576 ? ? RCSB RCSB059678 ? ? WWPDB D_1000059678 ? ? # 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 2011-09-21 2 'Structure model' 1 1 2011-11-30 3 'Structure model' 1 2 2024-02-21 # _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' pdbx_struct_conn_angle 5 3 'Structure model' struct_conn 6 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' '_pdbx_struct_conn_angle.ptnr1_auth_comp_id' 4 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 5 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_asym_id' 6 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_atom_id' 7 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_comp_id' 8 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_seq_id' 9 3 'Structure model' '_pdbx_struct_conn_angle.ptnr2_auth_comp_id' 10 3 'Structure model' '_pdbx_struct_conn_angle.ptnr2_auth_seq_id' 11 3 'Structure model' '_pdbx_struct_conn_angle.ptnr2_label_asym_id' 12 3 'Structure model' '_pdbx_struct_conn_angle.ptnr2_label_atom_id' 13 3 'Structure model' '_pdbx_struct_conn_angle.ptnr2_label_comp_id' 14 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_comp_id' 15 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 16 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id' 17 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_atom_id' 18 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_comp_id' 19 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_seq_id' 20 3 'Structure model' '_pdbx_struct_conn_angle.value' 21 3 'Structure model' '_struct_conn.pdbx_dist_value' 22 3 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 23 3 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 24 3 'Structure model' '_struct_conn.ptnr1_label_asym_id' 25 3 'Structure model' '_struct_conn.ptnr1_label_atom_id' 26 3 'Structure model' '_struct_conn.ptnr1_label_comp_id' 27 3 'Structure model' '_struct_conn.ptnr1_label_seq_id' 28 3 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 29 3 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 30 3 'Structure model' '_struct_conn.ptnr2_label_asym_id' 31 3 'Structure model' '_struct_conn.ptnr2_label_atom_id' 32 3 'Structure model' '_struct_conn.ptnr2_label_comp_id' 33 3 'Structure model' '_struct_site.pdbx_auth_asym_id' 34 3 'Structure model' '_struct_site.pdbx_auth_comp_id' 35 3 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.entry_id 3ND4 _pdbx_database_status.status_code REL _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2010-06-07 _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.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 3ND3 _pdbx_database_related.details . _pdbx_database_related.content_type unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Mooers, B.H.' 1 'Singh, A.' 2 # _citation.id primary _citation.title 'The crystal structure of an oligo(U):pre-mRNA duplex from a trypanosome RNA editing substrate.' _citation.journal_abbrev Rna _citation.journal_volume 17 _citation.page_first 1870 _citation.page_last 1883 _citation.year 2011 _citation.journal_id_ASTM RNARFU _citation.country UK _citation.journal_id_ISSN 1355-8382 _citation.journal_id_CSD 2122 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 21878548 _citation.pdbx_database_id_DOI 10.1261/rna.2880311 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Mooers, B.H.' 1 ? primary 'Singh, A.' 2 ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn "5'-R(*AP*GP*AP*GP*AP*AP*GP*AP*UP*CP*UP*UP*CP*UP*CP*U)-3'" 5083.063 1 ? ? ? 'control for U-helix RNA' 2 non-polymer syn 'MAGNESIUM ION' 24.305 1 ? ? ? ? 3 non-polymer syn 'POTASSIUM ION' 39.098 1 ? ? ? ? 4 non-polymer syn 'SODIUM ION' 22.990 1 ? ? ? ? 5 water nat water 18.015 95 ? ? ? ? # _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 AGAGAAGAUCUUCUCU _entity_poly.pdbx_seq_one_letter_code_can AGAGAAGAUCUUCUCU _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'MAGNESIUM ION' MG 3 'POTASSIUM ION' K 4 'SODIUM ION' NA 5 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 G n 1 3 A n 1 4 G n 1 5 A n 1 6 A n 1 7 G n 1 8 A n 1 9 U n 1 10 C n 1 11 U n 1 12 U n 1 13 C n 1 14 U n 1 15 C n 1 16 U n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num ? _pdbx_entity_src_syn.pdbx_end_seq_num ? _pdbx_entity_src_syn.organism_scientific ? _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id ? _pdbx_entity_src_syn.details 'chemically synthesized' # 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 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 K non-polymer . 'POTASSIUM ION' ? 'K 1' 39.098 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 NA non-polymer . 'SODIUM ION' ? 'Na 1' 22.990 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 A 1 1 1 A A A . n A 1 2 G 2 2 2 G G 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 A 6 6 6 A A A . n A 1 7 G 7 7 7 G G A . n A 1 8 A 8 8 8 A A A . n A 1 9 U 9 9 9 U U A . n A 1 10 C 10 10 10 C C A . n A 1 11 U 11 11 11 U U 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 C 15 15 15 C C A . n A 1 16 U 16 16 16 U U A . 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 B 2 MG 1 17 17 MG MG A . C 3 K 1 18 18 K K A . D 4 NA 1 19 19 NA NA A . E 5 HOH 1 20 20 HOH HOH A . E 5 HOH 2 21 21 HOH HOH A . E 5 HOH 3 22 22 HOH HOH A . E 5 HOH 4 23 23 HOH HOH A . E 5 HOH 5 24 24 HOH HOH A . E 5 HOH 6 25 25 HOH HOH A . E 5 HOH 7 26 26 HOH HOH A . E 5 HOH 8 27 27 HOH HOH A . E 5 HOH 9 28 28 HOH HOH A . E 5 HOH 10 29 29 HOH HOH A . E 5 HOH 11 30 30 HOH HOH A . E 5 HOH 12 31 31 HOH HOH A . E 5 HOH 13 32 32 HOH HOH A . E 5 HOH 14 33 33 HOH HOH A . E 5 HOH 15 34 34 HOH HOH A . E 5 HOH 16 35 35 HOH HOH A . E 5 HOH 17 36 36 HOH HOH A . E 5 HOH 18 37 37 HOH HOH A . E 5 HOH 19 38 38 HOH HOH A . E 5 HOH 20 39 39 HOH HOH A . E 5 HOH 21 40 40 HOH HOH A . E 5 HOH 22 41 41 HOH HOH A . E 5 HOH 23 42 42 HOH HOH A . E 5 HOH 24 43 43 HOH HOH A . E 5 HOH 25 44 44 HOH HOH A . E 5 HOH 26 45 45 HOH HOH A . E 5 HOH 27 46 46 HOH HOH A . E 5 HOH 28 47 47 HOH HOH A . E 5 HOH 29 48 48 HOH HOH A . E 5 HOH 30 49 49 HOH HOH A . E 5 HOH 31 51 51 HOH HOH A . E 5 HOH 32 52 52 HOH HOH A . E 5 HOH 33 53 53 HOH HOH A . E 5 HOH 34 54 54 HOH HOH A . E 5 HOH 35 55 55 HOH HOH A . E 5 HOH 36 56 56 HOH HOH A . E 5 HOH 37 57 57 HOH HOH A . E 5 HOH 38 58 58 HOH HOH A . E 5 HOH 39 59 59 HOH HOH A . E 5 HOH 40 60 60 HOH HOH A . E 5 HOH 41 61 61 HOH HOH A . E 5 HOH 42 62 62 HOH HOH A . E 5 HOH 43 63 63 HOH HOH A . E 5 HOH 44 64 64 HOH HOH A . E 5 HOH 45 65 65 HOH HOH A . E 5 HOH 46 66 66 HOH HOH A . E 5 HOH 47 67 67 HOH HOH A . E 5 HOH 48 68 68 HOH HOH A . E 5 HOH 49 69 69 HOH HOH A . E 5 HOH 50 70 70 HOH HOH A . E 5 HOH 51 71 71 HOH HOH A . E 5 HOH 52 72 72 HOH HOH A . E 5 HOH 53 73 73 HOH HOH A . E 5 HOH 54 74 74 HOH HOH A . E 5 HOH 55 75 75 HOH HOH A . E 5 HOH 56 76 76 HOH HOH A . E 5 HOH 57 77 77 HOH HOH A . E 5 HOH 58 78 78 HOH HOH A . E 5 HOH 59 79 79 HOH HOH A . E 5 HOH 60 80 80 HOH HOH A . E 5 HOH 61 81 81 HOH HOH A . E 5 HOH 62 82 82 HOH HOH A . E 5 HOH 63 83 83 HOH HOH A . E 5 HOH 64 84 84 HOH HOH A . E 5 HOH 65 85 85 HOH HOH A . E 5 HOH 66 86 86 HOH HOH A . E 5 HOH 67 87 87 HOH HOH A . E 5 HOH 68 88 88 HOH HOH A . E 5 HOH 69 89 89 HOH HOH A . E 5 HOH 70 90 90 HOH HOH A . E 5 HOH 71 91 91 HOH HOH A . E 5 HOH 72 92 92 HOH HOH A . E 5 HOH 73 93 93 HOH HOH A . E 5 HOH 74 94 94 HOH HOH A . E 5 HOH 75 95 95 HOH HOH A . E 5 HOH 76 96 96 HOH HOH A . E 5 HOH 77 97 97 HOH HOH A . E 5 HOH 78 98 98 HOH HOH A . E 5 HOH 79 99 99 HOH HOH A . E 5 HOH 80 100 100 HOH HOH A . E 5 HOH 81 101 101 HOH HOH A . E 5 HOH 82 102 102 HOH HOH A . E 5 HOH 83 103 103 HOH HOH A . E 5 HOH 84 104 104 HOH HOH A . E 5 HOH 85 105 105 HOH HOH A . E 5 HOH 86 106 106 HOH HOH A . E 5 HOH 87 107 107 HOH HOH A . E 5 HOH 88 108 108 HOH HOH A . E 5 HOH 89 109 109 HOH HOH A . E 5 HOH 90 117 117 HOH HOH A . E 5 HOH 91 119 119 HOH HOH A . E 5 HOH 92 219 219 HOH HOH A . E 5 HOH 93 319 319 HOH HOH A . E 5 HOH 94 419 419 HOH HOH A . E 5 HOH 95 519 519 HOH HOH A . # loop_ _software.pdbx_ordinal _software.name _software.version _software.date _software.type _software.contact_author _software.contact_author_email _software.classification _software.location _software.language _software.citation_id 1 SCALA 3.3.15 2009/03/31 other 'Phil R. Evans' pre@mrc-lmb.cam.ac.uk 'data scaling' http://www.ccp4.ac.uk/dist/html/scala.html Fortran_77 ? 2 MOLREP . ? program 'Alexei Vaguine' alexei@ysbl.york.ac.uk phasing http://www.ccp4.ac.uk/dist/html/molrep.html Fortran_77 ? 3 PHENIX 1.6.1_357 ? package 'Paul D. Adams' PAdams@lbl.gov refinement http://www.phenix-online.org/ C++ ? 4 PDB_EXTRACT 3.100 'May. 21, 2010' package PDB help@deposit.rcsb.org 'data extraction' http://sw-tools.pdb.org/apps/PDB_EXTRACT/ C++ ? 5 XSCALE . ? ? ? ? 'data scaling' ? ? ? # _cell.length_a 41.094 _cell.length_b 41.094 _cell.length_c 123.690 _cell.angle_alpha 90.000 _cell.angle_beta 90.000 _cell.angle_gamma 120.000 _cell.entry_id 3ND4 _cell.pdbx_unique_axis ? _cell.Z_PDB 18 _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.space_group_name_H-M 'H 3 2' _symmetry.entry_id 3ND4 _symmetry.Int_Tables_number 155 _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.space_group_name_Hall ? # _exptl.crystals_number 1 _exptl.entry_id 3ND4 _exptl.method 'X-RAY DIFFRACTION' # _exptl_crystal.id 1 _exptl_crystal.density_Matthews 1.98 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 37.79 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.pH 6.5 _exptl_crystal_grow.temp 298 _exptl_crystal_grow.pdbx_details '15 mM MgCl2, 10 mM Spermine, 2M lithium sulfate, pH 6.5, vapor diffusion, hanging drop, temperature 298K' _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'IMAGE PLATE' _diffrn_detector.type 'RIGAKU RAXIS IV' _diffrn_detector.pdbx_collection_date 2008-11-28 _diffrn_detector.details 'Varimax-HF confocal optical system' # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.monochromator 'Ni FILTER' _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _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 RUH3R' _diffrn_source.pdbx_wavelength_list 1.5418 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? # _reflns.entry_id 3ND4 _reflns.d_resolution_high 1.524 _reflns.d_resolution_low 18.390 _reflns.number_all 6419 _reflns.number_obs 6419 _reflns.pdbx_netI_over_sigmaI 26.000 _reflns.pdbx_Rsym_value 0.041 _reflns.pdbx_redundancy 7.300 _reflns.percent_possible_obs 99.500 _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.pdbx_Rmerge_I_obs ? _reflns.B_iso_Wilson_estimate ? _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 # loop_ _reflns_shell.d_res_high _reflns_shell.d_res_low _reflns_shell.number_measured_obs _reflns_shell.number_measured_all _reflns_shell.number_unique_obs _reflns_shell.Rmerge_I_obs _reflns_shell.meanI_over_sigI_obs _reflns_shell.pdbx_Rsym_value _reflns_shell.pdbx_chi_squared _reflns_shell.pdbx_redundancy _reflns_shell.percent_possible_obs _reflns_shell.number_unique_all _reflns_shell.percent_possible_all _reflns_shell.pdbx_ordinal _reflns_shell.pdbx_diffrn_id 1.52 1.61 ? 4063 ? 0.158 4.7 0.158 ? 4.60 ? 881 97.10 1 1 1.61 1.70 ? 6672 ? 0.104 7.0 0.104 ? 7.60 ? 882 100.00 2 1 1.70 1.82 ? 6337 ? 0.075 9.6 0.075 ? 7.70 ? 820 100.00 3 1 1.82 1.97 ? 5974 ? 0.069 10.0 0.069 ? 7.80 ? 767 100.00 4 1 1.97 2.16 ? 5780 ? 0.054 12.2 0.054 ? 7.90 ? 728 100.00 5 1 2.16 2.41 ? 5097 ? 0.046 13.4 0.046 ? 7.90 ? 646 100.00 6 1 2.41 2.78 ? 4486 ? 0.041 14.8 0.041 ? 7.80 ? 572 100.00 7 1 2.78 3.41 ? 3773 ? 0.035 13.6 0.035 ? 7.60 ? 496 100.00 8 1 3.41 4.82 ? 2952 ? 0.034 14.0 0.034 ? 7.50 ? 392 99.90 9 1 4.82 18.39 ? 1659 ? 0.033 14.3 0.033 ? 7.10 ? 235 98.50 10 1 # _refine.entry_id 3ND4 _refine.ls_d_res_high 1.524 _refine.ls_d_res_low 18.390 _refine.pdbx_ls_sigma_F 1.37 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_percent_reflns_obs 99.410 _refine.ls_number_reflns_obs 6412 _refine.ls_number_reflns_all ? _refine.pdbx_ls_cross_valid_method ? _refine.pdbx_R_Free_selection_details ? _refine.details ? _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.176 _refine.ls_R_factor_R_work 0.172 _refine.ls_wR_factor_R_work ? _refine.ls_R_factor_R_free 0.214 _refine.ls_wR_factor_R_free ? _refine.ls_percent_reflns_R_free 10.010 _refine.ls_number_reflns_R_free 642 _refine.ls_R_factor_R_free_error ? _refine.B_iso_mean 17.260 _refine.solvent_model_param_bsol 41.549 _refine.solvent_model_param_ksol 0.462 _refine.pdbx_isotropic_thermal_model ? _refine.aniso_B[1][1] 0.031 _refine.aniso_B[2][2] 0.031 _refine.aniso_B[3][3] -0.062 _refine.aniso_B[1][2] -0.000 _refine.aniso_B[1][3] -0.000 _refine.aniso_B[2][3] 0.000 _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML 0.180 _refine.overall_SU_B ? _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.pdbx_solvent_vdw_probe_radii 1.110 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.900 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_stereochemistry_target_values ML _refine.pdbx_stereochem_target_val_spec_case ? _refine.overall_FOM_work_R_set 0.859 _refine.B_iso_max 47.19 _refine.B_iso_min 6.77 _refine.occupancy_max 1.00 _refine.occupancy_min 0.50 _refine.pdbx_ls_sigma_I ? _refine.ls_redundancy_reflns_obs ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.overall_FOM_free_R_set ? _refine.pdbx_overall_phase_error ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_overall_ESU_R ? _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 336 _refine_hist.pdbx_number_atoms_ligand 3 _refine_hist.number_atoms_solvent 95 _refine_hist.number_atoms_total 434 _refine_hist.d_res_high 1.524 _refine_hist.d_res_low 18.390 # loop_ _refine_ls_restr.type _refine_ls_restr.number _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function f_bond_d 383 0.018 ? ? 'X-RAY DIFFRACTION' ? f_angle_d 591 1.614 ? ? 'X-RAY DIFFRACTION' ? f_chiral_restr 79 0.074 ? ? 'X-RAY DIFFRACTION' ? f_plane_restr 16 0.021 ? ? 'X-RAY DIFFRACTION' ? f_dihedral_angle_d 188 12.291 ? ? 'X-RAY DIFFRACTION' ? # loop_ _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.percent_reflns_obs _refine_ls_shell.number_reflns_R_work _refine_ls_shell.R_factor_all _refine_ls_shell.R_factor_R_work _refine_ls_shell.R_factor_R_free _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.number_reflns_R_free _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.number_reflns_all _refine_ls_shell.number_reflns_obs _refine_ls_shell.redundancy_reflns_obs _refine_ls_shell.pdbx_refine_id 1.524 1.642 5 98.000 1108 . 0.182 0.234 . 123 . 1231 . . 'X-RAY DIFFRACTION' 1.642 1.807 5 100.000 1125 . 0.173 0.228 . 126 . 1251 . . 'X-RAY DIFFRACTION' 1.807 2.068 5 100.000 1161 . 0.175 0.245 . 129 . 1290 . . 'X-RAY DIFFRACTION' 2.068 2.604 5 100.000 1154 . 0.176 0.237 . 127 . 1281 . . 'X-RAY DIFFRACTION' 2.604 18.391 5 100.000 1222 . 0.164 0.183 . 137 . 1359 . . 'X-RAY DIFFRACTION' # _struct.entry_id 3ND4 _struct.title 'Watson-Crick 16-mer dsRNA' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3ND4 _struct_keywords.text 'double-stranded RNA, RNA, 16 base pair RNA' _struct_keywords.pdbx_keywords 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 2 ? C N N 3 ? D N N 4 ? E N N 5 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 3ND4 _struct_ref.pdbx_db_accession 3ND4 _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin 1 _struct_ref.pdbx_seq_one_letter_code AGAGAAGAUCUUCUCU _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 3ND4 _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 16 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 3ND4 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 16 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 16 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 1680 ? 1 MORE -24 ? 1 'SSA (A^2)' 5890 ? # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E # 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' 4_555 y,x,-z -0.5000000000 0.8660254038 0.0000000000 0.0000000000 0.8660254038 0.5000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 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 metalc1 metalc ? ? A A 6 "O2'" ? ? ? 1_555 C K . K ? ? A A 6 A K 18 1_555 ? ? ? ? ? ? ? 2.831 ? ? metalc2 metalc ? ? A A 6 "O3'" ? ? ? 1_555 C K . K ? ? A A 6 A K 18 1_555 ? ? ? ? ? ? ? 3.038 ? ? metalc3 metalc ? ? A G 7 OP1 ? ? ? 1_555 B MG . MG ? ? A G 7 A MG 17 1_555 ? ? ? ? ? ? ? 2.168 ? ? metalc4 metalc ? ? A G 7 OP1 ? ? ? 1_555 C K . K ? ? A G 7 A K 18 1_555 ? ? ? ? ? ? ? 3.261 ? ? metalc5 metalc ? ? A G 7 "O5'" ? ? ? 1_555 C K . K ? ? A G 7 A K 18 1_555 ? ? ? ? ? ? ? 3.466 ? ? metalc6 metalc ? ? B MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 17 A HOH 117 1_555 ? ? ? ? ? ? ? 2.211 ? ? metalc7 metalc ? ? D NA . NA ? ? ? 1_555 E HOH . O ? ? A NA 19 A HOH 119 1_555 ? ? ? ? ? ? ? 2.556 ? ? metalc8 metalc ? ? D NA . NA ? ? ? 1_555 E HOH . O ? ? A NA 19 A HOH 219 1_555 ? ? ? ? ? ? ? 2.155 ? ? metalc9 metalc ? ? D NA . NA ? ? ? 1_555 E HOH . O ? ? A NA 19 A HOH 319 1_555 ? ? ? ? ? ? ? 2.386 ? ? metalc10 metalc ? ? D NA . NA ? ? ? 1_555 E HOH . O ? ? A NA 19 A HOH 419 1_555 ? ? ? ? ? ? ? 2.619 ? ? metalc11 metalc ? ? D NA . NA ? ? ? 1_555 E HOH . O ? ? A NA 19 A HOH 519 1_555 ? ? ? ? ? ? ? 2.238 ? ? hydrog1 hydrog ? ? A A 1 N1 ? ? ? 1_555 A U 16 N3 ? ? A A 1 A U 16 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A A 1 N6 ? ? ? 1_555 A U 16 O4 ? ? A A 1 A U 16 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 2 N1 ? ? ? 1_555 A C 15 N3 ? ? A G 2 A C 15 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 2 N2 ? ? ? 1_555 A C 15 O2 ? ? A G 2 A C 15 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A G 2 O6 ? ? ? 1_555 A C 15 N4 ? ? A G 2 A C 15 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A A 3 N1 ? ? ? 1_555 A U 14 N3 ? ? A A 3 A U 14 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A A 3 N6 ? ? ? 1_555 A U 14 O4 ? ? A A 3 A U 14 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A G 4 N1 ? ? ? 1_555 A C 13 N3 ? ? A G 4 A C 13 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G 4 N2 ? ? ? 1_555 A C 13 O2 ? ? A G 4 A C 13 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A G 4 O6 ? ? ? 1_555 A C 13 N4 ? ? A G 4 A C 13 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A A 5 N1 ? ? ? 1_555 A U 12 N3 ? ? A A 5 A U 12 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A A 5 N6 ? ? ? 1_555 A U 12 O4 ? ? A A 5 A U 12 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A A 6 N1 ? ? ? 1_555 A U 11 N3 ? ? A A 6 A U 11 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A A 6 N6 ? ? ? 1_555 A U 11 O4 ? ? A A 6 A U 11 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A G 7 N1 ? ? ? 1_555 A C 10 N3 ? ? A G 7 A C 10 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A G 7 N2 ? ? ? 1_555 A C 10 O2 ? ? A G 7 A C 10 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A G 7 O6 ? ? ? 1_555 A C 10 N4 ? ? A G 7 A C 10 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A A 8 N1 ? ? ? 1_555 A U 9 N3 ? ? A A 8 A U 9 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A A 8 N6 ? ? ? 1_555 A U 9 O4 ? ? A A 8 A U 9 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A U 9 N3 ? ? ? 1_555 A A 8 N1 ? ? A U 9 A A 8 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A U 9 O4 ? ? ? 1_555 A A 8 N6 ? ? A U 9 A A 8 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A C 10 N3 ? ? ? 1_555 A G 7 N1 ? ? A C 10 A G 7 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A C 10 N4 ? ? ? 1_555 A G 7 O6 ? ? A C 10 A G 7 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A C 10 O2 ? ? ? 1_555 A G 7 N2 ? ? A C 10 A G 7 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A U 11 N3 ? ? ? 1_555 A A 6 N1 ? ? A U 11 A A 6 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A U 11 O4 ? ? ? 1_555 A A 6 N6 ? ? A U 11 A A 6 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A U 12 N3 ? ? ? 1_555 A A 5 N1 ? ? A U 12 A A 5 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A U 12 O4 ? ? ? 1_555 A A 5 N6 ? ? A U 12 A A 5 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A C 13 N3 ? ? ? 1_555 A G 4 N1 ? ? A C 13 A G 4 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A C 13 N4 ? ? ? 1_555 A G 4 O6 ? ? A C 13 A G 4 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A C 13 O2 ? ? ? 1_555 A G 4 N2 ? ? A C 13 A G 4 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A U 14 N3 ? ? ? 1_555 A A 3 N1 ? ? A U 14 A A 3 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A U 14 O4 ? ? ? 1_555 A A 3 N6 ? ? A U 14 A A 3 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A C 15 N3 ? ? ? 1_555 A G 2 N1 ? ? A C 15 A G 2 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? A C 15 N4 ? ? ? 1_555 A G 2 O6 ? ? A C 15 A G 2 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? A C 15 O2 ? ? ? 1_555 A G 2 N2 ? ? A C 15 A G 2 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? A U 16 N3 ? ? ? 1_555 A A 1 N1 ? ? A U 16 A A 1 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? A U 16 O4 ? ? ? 1_555 A A 1 N6 ? ? A U 16 A A 1 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference 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 "O2'" ? A A 6 ? A A 6 ? 1_555 K ? C K . ? A K 18 ? 1_555 "O3'" ? A A 6 ? A A 6 ? 1_555 55.8 ? 2 "O2'" ? A A 6 ? A A 6 ? 1_555 K ? C K . ? A K 18 ? 1_555 OP1 ? A G 7 ? A G 7 ? 1_555 95.4 ? 3 "O3'" ? A A 6 ? A A 6 ? 1_555 K ? C K . ? A K 18 ? 1_555 OP1 ? A G 7 ? A G 7 ? 1_555 45.7 ? 4 "O2'" ? A A 6 ? A A 6 ? 1_555 K ? C K . ? A K 18 ? 1_555 "O5'" ? A G 7 ? A G 7 ? 1_555 60.6 ? 5 "O3'" ? A A 6 ? A A 6 ? 1_555 K ? C K . ? A K 18 ? 1_555 "O5'" ? A G 7 ? A G 7 ? 1_555 43.4 ? 6 OP1 ? A G 7 ? A G 7 ? 1_555 K ? C K . ? A K 18 ? 1_555 "O5'" ? A G 7 ? A G 7 ? 1_555 43.5 ? 7 OP1 ? A G 7 ? A G 7 ? 1_555 MG ? B MG . ? A MG 17 ? 1_555 O ? E HOH . ? A HOH 117 ? 1_555 82.6 ? 8 O ? E HOH . ? A HOH 119 ? 1_555 NA ? D NA . ? A NA 19 ? 1_555 O ? E HOH . ? A HOH 219 ? 1_555 174.6 ? 9 O ? E HOH . ? A HOH 119 ? 1_555 NA ? D NA . ? A NA 19 ? 1_555 O ? E HOH . ? A HOH 319 ? 1_555 79.7 ? 10 O ? E HOH . ? A HOH 219 ? 1_555 NA ? D NA . ? A NA 19 ? 1_555 O ? E HOH . ? A HOH 319 ? 1_555 96.8 ? 11 O ? E HOH . ? A HOH 119 ? 1_555 NA ? D NA . ? A NA 19 ? 1_555 O ? E HOH . ? A HOH 419 ? 1_555 86.1 ? 12 O ? E HOH . ? A HOH 219 ? 1_555 NA ? D NA . ? A NA 19 ? 1_555 O ? E HOH . ? A HOH 419 ? 1_555 96.6 ? 13 O ? E HOH . ? A HOH 319 ? 1_555 NA ? D NA . ? A NA 19 ? 1_555 O ? E HOH . ? A HOH 419 ? 1_555 162.3 ? 14 O ? E HOH . ? A HOH 119 ? 1_555 NA ? D NA . ? A NA 19 ? 1_555 O ? E HOH . ? A HOH 519 ? 1_555 81.1 ? 15 O ? E HOH . ? A HOH 219 ? 1_555 NA ? D NA . ? A NA 19 ? 1_555 O ? E HOH . ? A HOH 519 ? 1_555 94.4 ? 16 O ? E HOH . ? A HOH 319 ? 1_555 NA ? D NA . ? A NA 19 ? 1_555 O ? E HOH . ? A HOH 519 ? 1_555 83.0 ? 17 O ? E HOH . ? A HOH 419 ? 1_555 NA ? D NA . ? A NA 19 ? 1_555 O ? E HOH . ? A HOH 519 ? 1_555 84.5 ? # 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 MG 17 ? 9 'BINDING SITE FOR RESIDUE MG A 17' AC2 Software A K 18 ? 9 'BINDING SITE FOR RESIDUE K A 18' AC3 Software A NA 19 ? 6 'BINDING SITE FOR RESIDUE NA A 19' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 9 G A 7 ? G A 7 . ? 2_655 ? 2 AC1 9 G A 7 ? G A 7 . ? 1_555 ? 3 AC1 9 G A 7 ? G A 7 . ? 3_665 ? 4 AC1 9 K C . ? K A 18 . ? 3_665 ? 5 AC1 9 K C . ? K A 18 . ? 2_655 ? 6 AC1 9 K C . ? K A 18 . ? 1_555 ? 7 AC1 9 HOH E . ? HOH A 117 . ? 1_555 ? 8 AC1 9 HOH E . ? HOH A 117 . ? 3_665 ? 9 AC1 9 HOH E . ? HOH A 117 . ? 2_655 ? 10 AC2 9 A A 6 ? A A 6 . ? 2_655 ? 11 AC2 9 A A 6 ? A A 6 . ? 3_665 ? 12 AC2 9 A A 6 ? A A 6 . ? 1_555 ? 13 AC2 9 G A 7 ? G A 7 . ? 3_665 ? 14 AC2 9 G A 7 ? G A 7 . ? 1_555 ? 15 AC2 9 G A 7 ? G A 7 . ? 2_655 ? 16 AC2 9 MG B . ? MG A 17 . ? 3_665 ? 17 AC2 9 MG B . ? MG A 17 . ? 2_655 ? 18 AC2 9 MG B . ? MG A 17 . ? 1_555 ? 19 AC3 6 A A 3 ? A A 3 . ? 1_555 ? 20 AC3 6 HOH E . ? HOH A 119 . ? 1_555 ? 21 AC3 6 HOH E . ? HOH A 219 . ? 1_555 ? 22 AC3 6 HOH E . ? HOH A 319 . ? 1_555 ? 23 AC3 6 HOH E . ? HOH A 419 . ? 1_555 ? 24 AC3 6 HOH E . ? HOH A 519 . ? 1_555 ? # _pdbx_validate_symm_contact.id 1 _pdbx_validate_symm_contact.PDB_model_num 1 _pdbx_validate_symm_contact.auth_atom_id_1 "HO2'" _pdbx_validate_symm_contact.auth_asym_id_1 A _pdbx_validate_symm_contact.auth_comp_id_1 C _pdbx_validate_symm_contact.auth_seq_id_1 15 _pdbx_validate_symm_contact.PDB_ins_code_1 ? _pdbx_validate_symm_contact.label_alt_id_1 ? _pdbx_validate_symm_contact.site_symmetry_1 1_555 _pdbx_validate_symm_contact.auth_atom_id_2 "HO2'" _pdbx_validate_symm_contact.auth_asym_id_2 A _pdbx_validate_symm_contact.auth_comp_id_2 C _pdbx_validate_symm_contact.auth_seq_id_2 15 _pdbx_validate_symm_contact.PDB_ins_code_2 ? _pdbx_validate_symm_contact.label_alt_id_2 ? _pdbx_validate_symm_contact.site_symmetry_2 18_654 _pdbx_validate_symm_contact.dist 1.22 # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 N1 A A 1 ? ? C2 A A 1 ? ? N3 A A 1 ? ? 132.34 129.30 3.04 0.50 N 2 1 C2 A A 1 ? ? N3 A A 1 ? ? C4 A A 1 ? ? 106.87 110.60 -3.73 0.50 N 3 1 N1 A G 4 ? ? C6 A G 4 ? ? O6 A G 4 ? ? 123.56 119.90 3.66 0.60 N 4 1 N1 A U 11 ? ? C2 A U 11 ? ? O2 A U 11 ? ? 118.50 122.80 -4.30 0.70 N # 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 MG 17 ? B MG . 2 1 A K 18 ? C K . 3 1 A HOH 24 ? E HOH . 4 1 A HOH 25 ? E HOH . # _phasing.method MR # 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 C OP3 O N N 38 C P P N N 39 C OP1 O N N 40 C OP2 O N N 41 C "O5'" O N N 42 C "C5'" C N N 43 C "C4'" C N R 44 C "O4'" O N N 45 C "C3'" C N S 46 C "O3'" O N N 47 C "C2'" C N R 48 C "O2'" O N N 49 C "C1'" C N R 50 C N1 N N N 51 C C2 C N N 52 C O2 O N N 53 C N3 N N N 54 C C4 C N N 55 C N4 N N N 56 C C5 C N N 57 C C6 C N N 58 C HOP3 H N N 59 C HOP2 H N N 60 C "H5'" H N N 61 C "H5''" H N N 62 C "H4'" H N N 63 C "H3'" H N N 64 C "HO3'" H N N 65 C "H2'" H N N 66 C "HO2'" H N N 67 C "H1'" H N N 68 C H41 H N N 69 C H42 H N N 70 C H5 H N N 71 C H6 H N N 72 G OP3 O N N 73 G P P N N 74 G OP1 O N N 75 G OP2 O N N 76 G "O5'" O N N 77 G "C5'" C N N 78 G "C4'" C N R 79 G "O4'" O N N 80 G "C3'" C N S 81 G "O3'" O N N 82 G "C2'" C N R 83 G "O2'" O N N 84 G "C1'" C N R 85 G N9 N Y N 86 G C8 C Y N 87 G N7 N Y N 88 G C5 C Y N 89 G C6 C N N 90 G O6 O N N 91 G N1 N N N 92 G C2 C N N 93 G N2 N N N 94 G N3 N N N 95 G C4 C Y N 96 G HOP3 H N N 97 G HOP2 H N N 98 G "H5'" H N N 99 G "H5''" H N N 100 G "H4'" H N N 101 G "H3'" H N N 102 G "HO3'" H N N 103 G "H2'" H N N 104 G "HO2'" H N N 105 G "H1'" H N N 106 G H8 H N N 107 G H1 H N N 108 G H21 H N N 109 G H22 H N N 110 HOH O O N N 111 HOH H1 H N N 112 HOH H2 H N N 113 K K K N N 114 MG MG MG N N 115 NA NA NA N N 116 U OP3 O N N 117 U P P N N 118 U OP1 O N N 119 U OP2 O N N 120 U "O5'" O N N 121 U "C5'" C N N 122 U "C4'" C N R 123 U "O4'" O N N 124 U "C3'" C N S 125 U "O3'" O N N 126 U "C2'" C N R 127 U "O2'" O N N 128 U "C1'" C N R 129 U N1 N N N 130 U C2 C N N 131 U O2 O N N 132 U N3 N N N 133 U C4 C N N 134 U O4 O N N 135 U C5 C N N 136 U C6 C N N 137 U HOP3 H N N 138 U HOP2 H N N 139 U "H5'" H N N 140 U "H5''" H N N 141 U "H4'" H N N 142 U "H3'" H N N 143 U "HO3'" H N N 144 U "H2'" H N N 145 U "HO2'" H N N 146 U "H1'" H N N 147 U H3 H N N 148 U H5 H N N 149 U H6 H N N 150 # 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 C OP3 P sing N N 40 C OP3 HOP3 sing N N 41 C P OP1 doub N N 42 C P OP2 sing N N 43 C P "O5'" sing N N 44 C OP2 HOP2 sing N N 45 C "O5'" "C5'" sing N N 46 C "C5'" "C4'" sing N N 47 C "C5'" "H5'" sing N N 48 C "C5'" "H5''" sing N N 49 C "C4'" "O4'" sing N N 50 C "C4'" "C3'" sing N N 51 C "C4'" "H4'" sing N N 52 C "O4'" "C1'" sing N N 53 C "C3'" "O3'" sing N N 54 C "C3'" "C2'" sing N N 55 C "C3'" "H3'" sing N N 56 C "O3'" "HO3'" sing N N 57 C "C2'" "O2'" sing N N 58 C "C2'" "C1'" sing N N 59 C "C2'" "H2'" sing N N 60 C "O2'" "HO2'" sing N N 61 C "C1'" N1 sing N N 62 C "C1'" "H1'" sing N N 63 C N1 C2 sing N N 64 C N1 C6 sing N N 65 C C2 O2 doub N N 66 C C2 N3 sing N N 67 C N3 C4 doub N N 68 C C4 N4 sing N N 69 C C4 C5 sing N N 70 C N4 H41 sing N N 71 C N4 H42 sing N N 72 C C5 C6 doub N N 73 C C5 H5 sing N N 74 C C6 H6 sing N N 75 G OP3 P sing N N 76 G OP3 HOP3 sing N N 77 G P OP1 doub N N 78 G P OP2 sing N N 79 G P "O5'" sing N N 80 G OP2 HOP2 sing N N 81 G "O5'" "C5'" sing N N 82 G "C5'" "C4'" sing N N 83 G "C5'" "H5'" sing N N 84 G "C5'" "H5''" sing N N 85 G "C4'" "O4'" sing N N 86 G "C4'" "C3'" sing N N 87 G "C4'" "H4'" sing N N 88 G "O4'" "C1'" sing N N 89 G "C3'" "O3'" sing N N 90 G "C3'" "C2'" sing N N 91 G "C3'" "H3'" sing N N 92 G "O3'" "HO3'" sing N N 93 G "C2'" "O2'" sing N N 94 G "C2'" "C1'" sing N N 95 G "C2'" "H2'" sing N N 96 G "O2'" "HO2'" sing N N 97 G "C1'" N9 sing N N 98 G "C1'" "H1'" sing N N 99 G N9 C8 sing Y N 100 G N9 C4 sing Y N 101 G C8 N7 doub Y N 102 G C8 H8 sing N N 103 G N7 C5 sing Y N 104 G C5 C6 sing N N 105 G C5 C4 doub Y N 106 G C6 O6 doub N N 107 G C6 N1 sing N N 108 G N1 C2 sing N N 109 G N1 H1 sing N N 110 G C2 N2 sing N N 111 G C2 N3 doub N N 112 G N2 H21 sing N N 113 G N2 H22 sing N N 114 G N3 C4 sing N N 115 HOH O H1 sing N N 116 HOH O H2 sing N N 117 U OP3 P sing N N 118 U OP3 HOP3 sing N N 119 U P OP1 doub N N 120 U P OP2 sing N N 121 U P "O5'" sing N N 122 U OP2 HOP2 sing N N 123 U "O5'" "C5'" sing N N 124 U "C5'" "C4'" sing N N 125 U "C5'" "H5'" sing N N 126 U "C5'" "H5''" sing N N 127 U "C4'" "O4'" sing N N 128 U "C4'" "C3'" sing N N 129 U "C4'" "H4'" sing N N 130 U "O4'" "C1'" sing N N 131 U "C3'" "O3'" sing N N 132 U "C3'" "C2'" sing N N 133 U "C3'" "H3'" sing N N 134 U "O3'" "HO3'" sing N N 135 U "C2'" "O2'" sing N N 136 U "C2'" "C1'" sing N N 137 U "C2'" "H2'" sing N N 138 U "O2'" "HO2'" sing N N 139 U "C1'" N1 sing N N 140 U "C1'" "H1'" sing N N 141 U N1 C2 sing N N 142 U N1 C6 sing N N 143 U C2 O2 doub N N 144 U C2 N3 sing N N 145 U N3 C4 sing N N 146 U N3 H3 sing N N 147 U C4 O4 doub N N 148 U C4 C5 sing N N 149 U C5 C6 doub N N 150 U C5 H5 sing N N 151 U C6 H6 sing N N 152 # _ndb_struct_conf_na.entry_id 3ND4 _ndb_struct_conf_na.feature 'a-form double helix' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A A 1 1_555 A U 16 4_555 -0.057 -0.122 0.032 -0.673 -10.597 1.157 1 A_A1:U16_A A 1 ? A 16 ? 20 1 1 A G 2 1_555 A C 15 4_555 -0.231 -0.171 -0.084 -5.128 -15.819 -0.968 2 A_G2:C15_A A 2 ? A 15 ? 19 1 1 A A 3 1_555 A U 14 4_555 0.076 -0.121 0.069 -3.467 -12.757 0.822 3 A_A3:U14_A A 3 ? A 14 ? 20 1 1 A G 4 1_555 A C 13 4_555 -0.404 -0.178 -0.113 -1.905 -10.231 -1.027 4 A_G4:C13_A A 4 ? A 13 ? 19 1 1 A A 5 1_555 A U 12 4_555 0.078 -0.239 -0.065 -5.348 -9.193 2.563 5 A_A5:U12_A A 5 ? A 12 ? 20 1 1 A A 6 1_555 A U 11 4_555 -0.029 -0.018 0.058 -7.592 -16.918 2.960 6 A_A6:U11_A A 6 ? A 11 ? 20 1 1 A G 7 1_555 A C 10 4_555 -0.247 -0.170 0.114 -3.081 -9.164 -0.303 7 A_G7:C10_A A 7 ? A 10 ? 19 1 1 A A 8 1_555 A U 9 4_555 -0.046 -0.132 -0.063 -0.360 -14.500 0.036 8 A_A8:U9_A A 8 ? A 9 ? 20 1 1 A U 9 1_555 A A 8 4_555 0.046 -0.132 -0.063 0.360 -14.500 0.036 9 A_U9:A8_A A 9 ? A 8 ? 20 1 1 A C 10 1_555 A G 7 4_555 0.247 -0.170 0.114 3.081 -9.164 -0.303 10 A_C10:G7_A A 10 ? A 7 ? 19 1 1 A U 11 1_555 A A 6 4_555 0.029 -0.018 0.058 7.592 -16.918 2.960 11 A_U11:A6_A A 11 ? A 6 ? 20 1 1 A U 12 1_555 A A 5 4_555 -0.078 -0.239 -0.065 5.348 -9.193 2.563 12 A_U12:A5_A A 12 ? A 5 ? 20 1 1 A C 13 1_555 A G 4 4_555 0.404 -0.178 -0.113 1.905 -10.231 -1.027 13 A_C13:G4_A A 13 ? A 4 ? 19 1 1 A U 14 1_555 A A 3 4_555 -0.076 -0.121 0.069 3.467 -12.757 0.822 14 A_U14:A3_A A 14 ? A 3 ? 20 1 1 A C 15 1_555 A G 2 4_555 0.231 -0.171 -0.084 5.128 -15.819 -0.968 15 A_C15:G2_A A 15 ? A 2 ? 19 1 1 A U 16 1_555 A A 1 4_555 0.057 -0.122 0.032 0.673 -10.597 1.157 16 A_U16:A1_A A 16 ? A 1 ? 20 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A A 1 1_555 A U 16 4_555 A G 2 1_555 A C 15 4_555 -0.646 -1.140 3.259 -1.360 8.329 34.408 -3.053 0.871 2.934 13.823 2.257 35.397 1 AA_A1G2:C15U16_AA A 1 ? A 16 ? A 2 ? A 15 ? 1 A G 2 1_555 A C 15 4_555 A A 3 1_555 A U 14 4_555 0.543 -1.167 3.168 0.270 4.148 33.786 -2.621 -0.887 3.012 7.103 -0.463 34.033 2 AA_G2A3:U14C15_AA A 2 ? A 15 ? A 3 ? A 14 ? 1 A A 3 1_555 A U 14 4_555 A G 4 1_555 A C 13 4_555 -0.300 -1.395 3.179 -0.502 10.036 31.498 -4.001 0.450 2.627 17.925 0.896 33.024 3 AA_A3G4:C13U14_AA A 3 ? A 14 ? A 4 ? A 13 ? 1 A G 4 1_555 A C 13 4_555 A A 5 1_555 A U 12 4_555 0.512 -1.577 3.346 -0.129 12.186 30.730 -4.710 -0.922 2.551 21.943 0.233 33.004 4 AA_G4A5:U12C13_AA A 4 ? A 13 ? A 5 ? A 12 ? 1 A A 5 1_555 A U 12 4_555 A A 6 1_555 A U 11 4_555 0.922 -1.513 3.260 4.052 14.374 32.863 -4.334 -0.960 2.497 23.928 -6.746 36.012 5 AA_A5A6:U11U12_AA A 5 ? A 12 ? A 6 ? A 11 ? 1 A A 6 1_555 A U 11 4_555 A G 7 1_555 A C 10 4_555 -0.458 -2.352 3.041 -0.622 9.754 22.962 -7.750 0.913 1.908 23.198 1.478 24.930 6 AA_A6G7:C10U11_AA A 6 ? A 11 ? A 7 ? A 10 ? 1 A G 7 1_555 A C 10 4_555 A A 8 1_555 A U 9 4_555 -0.585 -1.431 3.170 -0.013 5.004 33.928 -3.165 0.990 2.935 8.517 0.022 34.285 7 AA_G7A8:U9C10_AA A 7 ? A 10 ? A 8 ? A 9 ? 1 A A 8 1_555 A U 9 4_555 A U 9 1_555 A A 8 4_555 0.000 -1.070 3.177 0.000 9.373 32.170 -3.292 0.000 2.765 16.483 0.000 33.473 8 AA_A8U9:A8U9_AA A 8 ? A 9 ? A 9 ? A 8 ? 1 A U 9 1_555 A A 8 4_555 A C 10 1_555 A G 7 4_555 0.585 -1.431 3.170 0.013 5.004 33.928 -3.165 -0.990 2.935 8.517 -0.022 34.285 9 AA_U9C10:G7A8_AA A 9 ? A 8 ? A 10 ? A 7 ? 1 A C 10 1_555 A G 7 4_555 A U 11 1_555 A A 6 4_555 0.458 -2.352 3.041 0.622 9.754 22.962 -7.750 -0.913 1.908 23.199 -1.478 24.930 10 AA_C10U11:A6G7_AA A 10 ? A 7 ? A 11 ? A 6 ? 1 A U 11 1_555 A A 6 4_555 A U 12 1_555 A A 5 4_555 -0.922 -1.513 3.260 -4.052 14.374 32.863 -4.334 0.960 2.497 23.928 6.746 36.012 11 AA_U11U12:A5A6_AA A 11 ? A 6 ? A 12 ? A 5 ? 1 A U 12 1_555 A A 5 4_555 A C 13 1_555 A G 4 4_555 -0.512 -1.577 3.346 0.129 12.186 30.730 -4.710 0.922 2.551 21.943 -0.233 33.004 12 AA_U12C13:G4A5_AA A 12 ? A 5 ? A 13 ? A 4 ? 1 A C 13 1_555 A G 4 4_555 A U 14 1_555 A A 3 4_555 0.300 -1.395 3.179 0.502 10.036 31.498 -4.001 -0.450 2.627 17.924 -0.896 33.024 13 AA_C13U14:A3G4_AA A 13 ? A 4 ? A 14 ? A 3 ? 1 A U 14 1_555 A A 3 4_555 A C 15 1_555 A G 2 4_555 -0.543 -1.167 3.168 -0.270 4.148 33.786 -2.621 0.887 3.012 7.103 0.463 34.033 14 AA_U14C15:G2A3_AA A 14 ? A 3 ? A 15 ? A 2 ? 1 A C 15 1_555 A G 2 4_555 A U 16 1_555 A A 1 4_555 0.646 -1.140 3.259 1.360 8.329 34.408 -3.053 -0.871 2.934 13.823 -2.257 35.397 15 AA_C15U16:A1G2_AA A 15 ? A 2 ? A 16 ? A 1 ? # _atom_sites.entry_id 3ND4 _atom_sites.fract_transf_matrix[1][1] 0.024334 _atom_sites.fract_transf_matrix[1][2] 0.014050 _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] 0.028099 _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] 0.008085 _atom_sites.fract_transf_vector[1] 0.000000 _atom_sites.fract_transf_vector[2] 0.000000 _atom_sites.fract_transf_vector[3] 0.000000 # loop_ _atom_type.symbol C H K MG N NA O P # loop_