data_3JXQ # _entry.id 3JXQ # _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 3JXQ pdb_00003jxq 10.2210/pdb3jxq/pdb NDB NA0193 ? ? RCSB RCSB055291 ? ? WWPDB D_1000055291 ? ? # 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 2010-02-09 2 'Structure model' 1 1 2011-07-13 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' 'Version format compliance' 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' diffrn_source 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' '_diffrn_source.pdbx_synchrotron_site' 4 3 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 5 3 'Structure model' '_struct_site.pdbx_auth_asym_id' 6 3 'Structure model' '_struct_site.pdbx_auth_comp_id' 7 3 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3JXQ _pdbx_database_status.recvd_initial_deposition_date 2009-09-21 _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.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 PDB _pdbx_database_related.db_id 3JXR _pdbx_database_related.details . _pdbx_database_related.content_type unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Adamiak, D.A.' 1 'Milecki, J.' 2 'Adamiak, R.W.' 3 'Rypniewski, W.' 4 # _citation.id primary _citation.title 'The hydration and unusual hydrogen bonding in the crystal structure of an RNA duplex containing alternating CG base pairs' _citation.journal_abbrev 'New J.Chem.' _citation.journal_volume 34 _citation.page_first 903 _citation.page_last 909 _citation.year 2010 _citation.journal_id_ASTM ? _citation.country FR _citation.journal_id_ISSN 1144-0546 _citation.journal_id_CSD ? _citation.book_publisher ? _citation.pdbx_database_id_PubMed ? _citation.pdbx_database_id_DOI 10.1039/b9nj00601j # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Adamiak, D.A.' 1 ? primary 'Milecki, J.' 2 ? primary 'Adamiak, R.W.' 3 ? primary 'Rypniewski, W.' 4 ? # 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 'r[CGCG(5-fluoro)CG]2' 1924.195 4 ? ? ? ? 2 non-polymer syn 'MAGNESIUM ION' 24.305 4 ? ? ? ? 3 water nat water 18.015 132 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code 'CGCG(5CF)G' _entity_poly.pdbx_seq_one_letter_code_can CGCGXG _entity_poly.pdbx_strand_id A,B,K,L _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 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 C n 1 2 G n 1 3 C n 1 4 G n 1 5 5CF n 1 6 G 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 'This is a modification of a naturally occuring sequence' # 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 5CF 'RNA linking' . ;5-fluorocytidine 5'-(dihydrogen phosphate) ; ? 'C9 H13 F N3 O8 P' 341.187 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 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 # 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 C 1 1 1 C C A . n A 1 2 G 2 2 2 G G A . n A 1 3 C 3 3 3 C C A . n A 1 4 G 4 4 4 G G A . n A 1 5 5CF 5 5 5 5CF 5CF A . n A 1 6 G 6 6 6 G G A . n B 1 1 C 1 1 1 C C B . n B 1 2 G 2 2 2 G G B . n B 1 3 C 3 3 3 C C B . n B 1 4 G 4 4 4 G G B . n B 1 5 5CF 5 5 5 5CF 5CF B . n B 1 6 G 6 6 6 G G B . n C 1 1 C 1 1 1 C C K . n C 1 2 G 2 2 2 G G K . n C 1 3 C 3 3 3 C C K . n C 1 4 G 4 4 4 G G K . n C 1 5 5CF 5 5 5 5CF 5CF K . n C 1 6 G 6 6 6 G G K . n D 1 1 C 1 1 1 C C L . n D 1 2 G 2 2 2 G G L . n D 1 3 C 3 3 3 C C L . n D 1 4 G 4 4 4 G G L . n D 1 5 5CF 5 5 5 5CF 5CF L . n D 1 6 G 6 6 6 G G L . 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 E 2 MG 1 7 4 MG MG A . F 2 MG 1 7 1 MG MG B . G 2 MG 1 7 2 MG MG K . H 2 MG 1 7 3 MG MG L . I 3 HOH 1 8 4 HOH HOH A . I 3 HOH 2 9 8 HOH HOH A . I 3 HOH 3 10 10 HOH HOH A . I 3 HOH 4 11 11 HOH HOH A . I 3 HOH 5 13 13 HOH HOH A . I 3 HOH 6 15 15 HOH HOH A . I 3 HOH 7 18 18 HOH HOH A . I 3 HOH 8 19 19 HOH HOH A . I 3 HOH 9 21 21 HOH HOH A . I 3 HOH 10 22 22 HOH HOH A . I 3 HOH 11 23 23 HOH HOH A . I 3 HOH 12 24 24 HOH HOH A . I 3 HOH 13 31 31 HOH HOH A . I 3 HOH 14 32 32 HOH HOH A . I 3 HOH 15 49 49 HOH HOH A . I 3 HOH 16 51 51 HOH HOH A . I 3 HOH 17 60 60 HOH HOH A . I 3 HOH 18 62 62 HOH HOH A . I 3 HOH 19 65 65 HOH HOH A . I 3 HOH 20 78 78 HOH HOH A . I 3 HOH 21 79 79 HOH HOH A . I 3 HOH 22 81 81 HOH HOH A . I 3 HOH 23 83 83 HOH HOH A . I 3 HOH 24 87 87 HOH HOH A . I 3 HOH 25 89 89 HOH HOH A . I 3 HOH 26 90 90 HOH HOH A . I 3 HOH 27 97 97 HOH HOH A . I 3 HOH 28 100 100 HOH HOH A . I 3 HOH 29 109 109 HOH HOH A . I 3 HOH 30 118 118 HOH HOH A . I 3 HOH 31 119 119 HOH HOH A . I 3 HOH 32 125 125 HOH HOH A . I 3 HOH 33 127 127 HOH HOH A . I 3 HOH 34 129 129 HOH HOH A . I 3 HOH 35 130 130 HOH HOH A . J 3 HOH 1 8 3 HOH HOH B . J 3 HOH 2 9 9 HOH HOH B . J 3 HOH 3 10 5 HOH HOH B . J 3 HOH 4 11 6 HOH HOH B . J 3 HOH 5 12 12 HOH HOH B . J 3 HOH 6 14 14 HOH HOH B . J 3 HOH 7 17 17 HOH HOH B . J 3 HOH 8 25 25 HOH HOH B . J 3 HOH 9 28 28 HOH HOH B . J 3 HOH 10 30 30 HOH HOH B . J 3 HOH 11 33 33 HOH HOH B . J 3 HOH 12 34 34 HOH HOH B . J 3 HOH 13 40 40 HOH HOH B . J 3 HOH 14 43 43 HOH HOH B . J 3 HOH 15 50 50 HOH HOH B . J 3 HOH 16 53 53 HOH HOH B . J 3 HOH 17 55 55 HOH HOH B . J 3 HOH 18 61 61 HOH HOH B . J 3 HOH 19 63 63 HOH HOH B . J 3 HOH 20 66 66 HOH HOH B . J 3 HOH 21 71 71 HOH HOH B . J 3 HOH 22 77 77 HOH HOH B . J 3 HOH 23 80 80 HOH HOH B . J 3 HOH 24 84 84 HOH HOH B . J 3 HOH 25 91 91 HOH HOH B . J 3 HOH 26 93 93 HOH HOH B . J 3 HOH 27 94 94 HOH HOH B . J 3 HOH 28 96 96 HOH HOH B . J 3 HOH 29 101 101 HOH HOH B . J 3 HOH 30 102 102 HOH HOH B . J 3 HOH 31 104 104 HOH HOH B . J 3 HOH 32 106 106 HOH HOH B . J 3 HOH 33 108 108 HOH HOH B . J 3 HOH 34 110 110 HOH HOH B . J 3 HOH 35 113 113 HOH HOH B . J 3 HOH 36 120 120 HOH HOH B . J 3 HOH 37 121 121 HOH HOH B . J 3 HOH 38 124 124 HOH HOH B . J 3 HOH 39 132 132 HOH HOH B . K 3 HOH 1 8 1 HOH HOH K . K 3 HOH 2 9 2 HOH HOH K . K 3 HOH 3 20 20 HOH HOH K . K 3 HOH 4 26 26 HOH HOH K . K 3 HOH 5 27 27 HOH HOH K . K 3 HOH 6 29 29 HOH HOH K . K 3 HOH 7 36 36 HOH HOH K . K 3 HOH 8 37 37 HOH HOH K . K 3 HOH 9 41 41 HOH HOH K . K 3 HOH 10 42 42 HOH HOH K . K 3 HOH 11 44 44 HOH HOH K . K 3 HOH 12 46 46 HOH HOH K . K 3 HOH 13 47 47 HOH HOH K . K 3 HOH 14 52 52 HOH HOH K . K 3 HOH 15 57 57 HOH HOH K . K 3 HOH 16 58 58 HOH HOH K . K 3 HOH 17 59 59 HOH HOH K . K 3 HOH 18 64 64 HOH HOH K . K 3 HOH 19 69 69 HOH HOH K . K 3 HOH 20 70 70 HOH HOH K . K 3 HOH 21 73 73 HOH HOH K . K 3 HOH 22 82 82 HOH HOH K . K 3 HOH 23 85 85 HOH HOH K . K 3 HOH 24 88 88 HOH HOH K . K 3 HOH 25 95 95 HOH HOH K . K 3 HOH 26 98 98 HOH HOH K . K 3 HOH 27 103 103 HOH HOH K . K 3 HOH 28 105 105 HOH HOH K . K 3 HOH 29 114 114 HOH HOH K . K 3 HOH 30 115 115 HOH HOH K . K 3 HOH 31 126 126 HOH HOH K . L 3 HOH 1 9 7 HOH HOH L . L 3 HOH 2 16 16 HOH HOH L . L 3 HOH 3 35 35 HOH HOH L . L 3 HOH 4 38 38 HOH HOH L . L 3 HOH 5 39 39 HOH HOH L . L 3 HOH 6 45 45 HOH HOH L . L 3 HOH 7 48 48 HOH HOH L . L 3 HOH 8 54 54 HOH HOH L . L 3 HOH 9 56 56 HOH HOH L . L 3 HOH 10 67 67 HOH HOH L . L 3 HOH 11 68 68 HOH HOH L . L 3 HOH 12 72 72 HOH HOH L . L 3 HOH 13 74 74 HOH HOH L . L 3 HOH 14 75 75 HOH HOH L . L 3 HOH 15 76 76 HOH HOH L . L 3 HOH 16 86 86 HOH HOH L . L 3 HOH 17 92 92 HOH HOH L . L 3 HOH 18 99 99 HOH HOH L . L 3 HOH 19 107 107 HOH HOH L . L 3 HOH 20 111 111 HOH HOH L . L 3 HOH 21 112 112 HOH HOH L . L 3 HOH 22 116 116 HOH HOH L . L 3 HOH 23 117 117 HOH HOH L . L 3 HOH 24 122 122 HOH HOH L . L 3 HOH 25 123 123 HOH HOH L . L 3 HOH 26 128 128 HOH HOH L . L 3 HOH 27 131 131 HOH HOH L . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal MAR345dtb 'data collection' . ? 1 MOLREP phasing . ? 2 REFMAC refinement 5.2.0019 ? 3 DENZO 'data reduction' . ? 4 SCALEPACK 'data scaling' . ? 5 # _cell.entry_id 3JXQ _cell.length_a 21.224 _cell.length_b 26.486 _cell.length_c 29.310 _cell.angle_alpha 97.56 _cell.angle_beta 105.47 _cell.angle_gamma 109.38 _cell.Z_PDB 4 _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 3JXQ _symmetry.space_group_name_H-M 'P 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? # _exptl.entry_id 3JXQ _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 1.89 _exptl_crystal.density_percent_sol 34.86 _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.temp 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 5.6 _exptl_crystal_grow.pdbx_details '2.0M lithium sulfate, 10mM magnesium chloride and 50mM MES, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K' _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 'MAR scanner 345 mm plate' _diffrn_detector.pdbx_collection_date 2001-11-17 _diffrn_detector.details 'Si(111)' # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'Si(111) channel' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.1000 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'EMBL/DESY, HAMBURG BEAMLINE BW7A' _diffrn_source.pdbx_synchrotron_site 'EMBL/DESY, HAMBURG' _diffrn_source.pdbx_synchrotron_beamline BW7A _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.1000 # _reflns.entry_id 3JXQ _reflns.observed_criterion_sigma_I 0 _reflns.observed_criterion_sigma_F 0 _reflns.d_resolution_low 20 _reflns.d_resolution_high 1.45 _reflns.number_obs 9439 _reflns.number_all 9439 _reflns.percent_possible_obs 93.7 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value 0.041 _reflns.pdbx_netI_over_sigmaI 30 _reflns.B_iso_Wilson_estimate 14 _reflns.pdbx_redundancy 3.1 _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_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 1.45 _reflns_shell.d_res_low 1.47 _reflns_shell.percent_possible_all 80 _reflns_shell.Rmerge_I_obs ? _reflns_shell.pdbx_Rsym_value 0.296 _reflns_shell.meanI_over_sigI_obs 2.6 _reflns_shell.pdbx_redundancy 2.2 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 409 _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 3JXQ _refine.ls_number_reflns_obs 9199 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 15.00 _refine.ls_d_res_high 1.45 _refine.ls_percent_reflns_obs 100.00 _refine.ls_R_factor_obs 0.17181 _refine.ls_R_factor_all 0.17181 _refine.ls_R_factor_R_work 0.17115 _refine.ls_R_factor_R_free 0.20517 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 1.9 _refine.ls_number_reflns_R_free 174 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.973 _refine.correlation_coeff_Fo_to_Fc_free 0.948 _refine.B_iso_mean 20.307 _refine.aniso_B[1][1] -0.25 _refine.aniso_B[2][2] -0.47 _refine.aniso_B[3][3] 0.09 _refine.aniso_B[1][2] -0.41 _refine.aniso_B[1][3] -0.32 _refine.aniso_B[2][3] -0.74 _refine.solvent_model_details 'BABINET MODEL WITH MASK' _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.20 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R 0.078 _refine.pdbx_overall_ESU_R_Free 0.079 _refine.overall_SU_ML 0.059 _refine.overall_SU_B 1.655 _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _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_overall_phase_error ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _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_analyze.entry_id 3JXQ _refine_analyze.Luzzati_coordinate_error_obs ? _refine_analyze.Luzzati_sigma_a_obs 0.059 _refine_analyze.Luzzati_d_res_low_obs ? _refine_analyze.Luzzati_coordinate_error_free 0.079 _refine_analyze.Luzzati_sigma_a_free ? _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_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 508 _refine_hist.pdbx_number_atoms_ligand 4 _refine_hist.number_atoms_solvent 132 _refine_hist.number_atoms_total 644 _refine_hist.d_res_high 1.45 _refine_hist.d_res_low 15.00 # 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_refine_id _refine_ls_restr.pdbx_restraint_function r_bond_refined_d 0.011 0.021 ? 567 'X-RAY DIFFRACTION' ? r_angle_refined_deg 2.022 3.000 ? 870 'X-RAY DIFFRACTION' ? r_chiral_restr 0.078 0.200 ? 116 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.011 0.020 ? 252 'X-RAY DIFFRACTION' ? r_nbd_refined 0.176 0.200 ? 195 'X-RAY DIFFRACTION' ? r_nbtor_refined 0.276 0.200 ? 364 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined 0.113 0.200 ? 92 'X-RAY DIFFRACTION' ? r_metal_ion_refined 0.169 0.200 ? 3 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined 0.148 0.200 ? 47 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 0.130 0.200 ? 18 'X-RAY DIFFRACTION' ? r_scbond_it 2.479 7.000 ? 827 'X-RAY DIFFRACTION' ? r_scangle_it 3.098 9.000 ? 870 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 1.450 _refine_ls_shell.d_res_low 1.487 _refine_ls_shell.number_reflns_R_work 596 _refine_ls_shell.R_factor_R_work 0.259 _refine_ls_shell.percent_reflns_obs 100.00 _refine_ls_shell.R_factor_R_free 0.331 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 13 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.number_reflns_obs 596 _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _database_PDB_matrix.entry_id 3JXQ _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 3JXQ _struct.title 'X-Ray structure of r[CGCG(5-fluoro)CG]2' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3JXQ _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'RNA, double helix' # 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 1 ? E N N 2 ? F N N 2 ? G N N 2 ? H N N 2 ? I N N 3 ? J N N 3 ? K N N 3 ? L N N 3 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 3JXQ _struct_ref.pdbx_db_accession 3JXQ _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code CGCGXG _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 3JXQ A 1 ? 6 ? 3JXQ 1 ? 6 ? 1 6 2 1 3JXQ B 1 ? 6 ? 3JXQ 1 ? 6 ? 1 6 3 1 3JXQ K 1 ? 6 ? 3JXQ 1 ? 6 ? 1 6 4 1 3JXQ L 1 ? 6 ? 3JXQ 1 ? 6 ? 1 6 # 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,E,F,I,J 2 1 C,D,G,H,K,L # _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 covale1 covale both ? A G 4 "O3'" ? ? ? 1_555 A 5CF 5 P ? ? A G 4 A 5CF 5 1_555 ? ? ? ? ? ? ? 1.598 ? ? covale2 covale one ? A 5CF 5 "O3'" ? ? ? 1_555 A G 6 P ? ? A 5CF 5 A G 6 1_555 ? ? ? ? ? ? ? 1.597 ? ? covale3 covale both ? B G 4 "O3'" ? ? ? 1_555 B 5CF 5 P ? ? B G 4 B 5CF 5 1_555 ? ? ? ? ? ? ? 1.611 ? ? covale4 covale one ? B 5CF 5 "O3'" ? ? ? 1_555 B G 6 P ? ? B 5CF 5 B G 6 1_555 ? ? ? ? ? ? ? 1.625 ? ? covale5 covale both ? C G 4 "O3'" ? ? ? 1_555 C 5CF 5 P ? ? K G 4 K 5CF 5 1_555 ? ? ? ? ? ? ? 1.600 ? ? covale6 covale one ? C 5CF 5 "O3'" ? ? ? 1_555 C G 6 P ? ? K 5CF 5 K G 6 1_555 ? ? ? ? ? ? ? 1.585 ? ? covale7 covale both ? D G 4 "O3'" ? ? ? 1_555 D 5CF 5 P ? ? L G 4 L 5CF 5 1_555 ? ? ? ? ? ? ? 1.612 ? ? covale8 covale one ? D 5CF 5 "O3'" ? ? ? 1_555 D G 6 P ? ? L 5CF 5 L G 6 1_555 ? ? ? ? ? ? ? 1.597 ? ? hydrog1 hydrog ? ? A C 1 N3 ? ? ? 1_555 B G 6 N1 ? ? A C 1 B G 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A C 1 N4 ? ? ? 1_555 B G 6 O6 ? ? A C 1 B G 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A C 1 O2 ? ? ? 1_555 B G 6 N2 ? ? A C 1 B G 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A C 3 N3 ? ? ? 1_555 B G 4 N1 ? ? A C 3 B G 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A C 3 N4 ? ? ? 1_555 B G 4 O6 ? ? A C 3 B G 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A C 3 O2 ? ? ? 1_555 B G 4 N2 ? ? A C 3 B G 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A G 4 N1 ? ? ? 1_555 B C 3 N3 ? ? A G 4 B C 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A G 4 N2 ? ? ? 1_555 B C 3 O2 ? ? A G 4 B C 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G 4 O6 ? ? ? 1_555 B C 3 N4 ? ? A G 4 B C 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A G 6 N1 ? ? ? 1_555 B C 1 N3 ? ? A G 6 B C 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A G 6 N2 ? ? ? 1_555 B C 1 O2 ? ? A G 6 B C 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A G 6 O6 ? ? ? 1_555 B C 1 N4 ? ? A G 6 B C 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? C C 1 N3 ? ? ? 1_555 D G 6 N1 ? ? K C 1 L G 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? C C 1 N4 ? ? ? 1_555 D G 6 O6 ? ? K C 1 L G 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? C C 1 O2 ? ? ? 1_555 D G 6 N2 ? ? K C 1 L G 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? C C 3 N3 ? ? ? 1_555 D G 4 N1 ? ? K C 3 L G 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? C C 3 N4 ? ? ? 1_555 D G 4 O6 ? ? K C 3 L G 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? C C 3 O2 ? ? ? 1_555 D G 4 N2 ? ? K C 3 L G 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? C G 4 N1 ? ? ? 1_555 D C 3 N3 ? ? K G 4 L C 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? C G 4 N2 ? ? ? 1_555 D C 3 O2 ? ? K G 4 L C 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? C G 4 O6 ? ? ? 1_555 D C 3 N4 ? ? K G 4 L C 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? C G 6 N1 ? ? ? 1_555 D C 1 N3 ? ? K G 6 L C 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? C G 6 N2 ? ? ? 1_555 D C 1 O2 ? ? K G 6 L C 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? C G 6 O6 ? ? ? 1_555 D C 1 N4 ? ? K G 6 L C 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software A MG 7 ? 4 'BINDING SITE FOR RESIDUE MG A 7' AC2 Software B MG 7 ? 6 'BINDING SITE FOR RESIDUE MG B 7' AC3 Software K MG 7 ? 5 'BINDING SITE FOR RESIDUE MG K 7' AC4 Software L MG 7 ? 5 'BINDING SITE FOR RESIDUE MG L 7' # 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 4 HOH I . ? HOH A 18 . ? 1_555 ? 2 AC1 4 HOH I . ? HOH A 109 . ? 1_555 ? 3 AC1 4 HOH I . ? HOH A 118 . ? 1_555 ? 4 AC1 4 HOH I . ? HOH A 119 . ? 1_555 ? 5 AC2 6 HOH J . ? HOH B 10 . ? 1_555 ? 6 AC2 6 HOH J . ? HOH B 71 . ? 1_555 ? 7 AC2 6 HOH J . ? HOH B 108 . ? 1_555 ? 8 AC2 6 HOH J . ? HOH B 120 . ? 1_555 ? 9 AC2 6 HOH J . ? HOH B 121 . ? 1_555 ? 10 AC2 6 HOH J . ? HOH B 132 . ? 1_555 ? 11 AC3 5 HOH J . ? HOH B 53 . ? 1_555 ? 12 AC3 5 HOH J . ? HOH B 94 . ? 1_555 ? 13 AC3 5 HOH J . ? HOH B 96 . ? 1_555 ? 14 AC3 5 HOH K . ? HOH K 41 . ? 1_555 ? 15 AC3 5 HOH K . ? HOH K 115 . ? 1_555 ? 16 AC4 5 G D 6 ? G L 6 . ? 1_555 ? 17 AC4 5 HOH L . ? HOH L 112 . ? 1_555 ? 18 AC4 5 HOH L . ? HOH L 116 . ? 1_555 ? 19 AC4 5 HOH L . ? HOH L 122 . ? 1_555 ? 20 AC4 5 HOH L . ? HOH L 123 . ? 1_555 ? # _pdbx_validate_rmsd_angle.id 1 _pdbx_validate_rmsd_angle.PDB_model_num 1 _pdbx_validate_rmsd_angle.auth_atom_id_1 "O5'" _pdbx_validate_rmsd_angle.auth_asym_id_1 A _pdbx_validate_rmsd_angle.auth_comp_id_1 G _pdbx_validate_rmsd_angle.auth_seq_id_1 4 _pdbx_validate_rmsd_angle.PDB_ins_code_1 ? _pdbx_validate_rmsd_angle.label_alt_id_1 ? _pdbx_validate_rmsd_angle.auth_atom_id_2 P _pdbx_validate_rmsd_angle.auth_asym_id_2 A _pdbx_validate_rmsd_angle.auth_comp_id_2 G _pdbx_validate_rmsd_angle.auth_seq_id_2 4 _pdbx_validate_rmsd_angle.PDB_ins_code_2 ? _pdbx_validate_rmsd_angle.label_alt_id_2 ? _pdbx_validate_rmsd_angle.auth_atom_id_3 OP2 _pdbx_validate_rmsd_angle.auth_asym_id_3 A _pdbx_validate_rmsd_angle.auth_comp_id_3 G _pdbx_validate_rmsd_angle.auth_seq_id_3 4 _pdbx_validate_rmsd_angle.PDB_ins_code_3 ? _pdbx_validate_rmsd_angle.label_alt_id_3 ? _pdbx_validate_rmsd_angle.angle_value 97.26 _pdbx_validate_rmsd_angle.angle_target_value 105.70 _pdbx_validate_rmsd_angle.angle_deviation -8.44 _pdbx_validate_rmsd_angle.angle_standard_deviation 0.90 _pdbx_validate_rmsd_angle.linker_flag N # 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 5CF OP3 O N N 1 5CF P P N N 2 5CF N1 N N N 3 5CF C2 C N N 4 5CF O2 O N N 5 5CF N3 N N N 6 5CF C4 C N N 7 5CF N4 N N N 8 5CF C5 C N N 9 5CF F5 F N N 10 5CF C6 C N N 11 5CF "C1'" C N R 12 5CF "C2'" C N R 13 5CF "O2'" O N N 14 5CF "C3'" C N S 15 5CF "O3'" O N N 16 5CF "C4'" C N R 17 5CF "O4'" O N N 18 5CF "C5'" C N N 19 5CF "O5'" O N N 20 5CF OP1 O N N 21 5CF OP2 O N N 22 5CF HOP3 H N N 23 5CF HN4 H N N 24 5CF HN4A H N N 25 5CF H6 H N N 26 5CF "H1'" H N N 27 5CF "H2'" H N N 28 5CF "HO2'" H N N 29 5CF "H3'" H N N 30 5CF "HO3'" H N N 31 5CF "H4'" H N N 32 5CF "H5'" H N N 33 5CF "H5'A" H N N 34 5CF HOP1 H N N 35 C OP3 O N N 36 C P P N N 37 C OP1 O N N 38 C OP2 O N N 39 C "O5'" O N N 40 C "C5'" C N N 41 C "C4'" C N R 42 C "O4'" O N N 43 C "C3'" C N S 44 C "O3'" O N N 45 C "C2'" C N R 46 C "O2'" O N N 47 C "C1'" C N R 48 C N1 N N N 49 C C2 C N N 50 C O2 O N N 51 C N3 N N N 52 C C4 C N N 53 C N4 N N N 54 C C5 C N N 55 C C6 C N N 56 C HOP3 H N N 57 C HOP2 H N N 58 C "H5'" H N N 59 C "H5''" H N N 60 C "H4'" H N N 61 C "H3'" H N N 62 C "HO3'" H N N 63 C "H2'" H N N 64 C "HO2'" H N N 65 C "H1'" H N N 66 C H41 H N N 67 C H42 H N N 68 C H5 H N N 69 C H6 H N N 70 G OP3 O N N 71 G P P N N 72 G OP1 O N N 73 G OP2 O N N 74 G "O5'" O N N 75 G "C5'" C N N 76 G "C4'" C N R 77 G "O4'" O N N 78 G "C3'" C N S 79 G "O3'" O N N 80 G "C2'" C N R 81 G "O2'" O N N 82 G "C1'" C N R 83 G N9 N Y N 84 G C8 C Y N 85 G N7 N Y N 86 G C5 C Y N 87 G C6 C N N 88 G O6 O N N 89 G N1 N N N 90 G C2 C N N 91 G N2 N N N 92 G N3 N N N 93 G C4 C Y N 94 G HOP3 H N N 95 G HOP2 H N N 96 G "H5'" H N N 97 G "H5''" H N N 98 G "H4'" H N N 99 G "H3'" H N N 100 G "HO3'" H N N 101 G "H2'" H N N 102 G "HO2'" H N N 103 G "H1'" H N N 104 G H8 H N N 105 G H1 H N N 106 G H21 H N N 107 G H22 H N N 108 HOH O O N N 109 HOH H1 H N N 110 HOH H2 H N N 111 MG MG MG N N 112 # 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 5CF P OP3 sing N N 1 5CF OP3 HOP3 sing N N 2 5CF OP2 P doub N N 3 5CF OP1 P sing N N 4 5CF P "O5'" sing N N 5 5CF C6 N1 sing N N 6 5CF "C1'" N1 sing N N 7 5CF N1 C2 sing N N 8 5CF C2 N3 sing N N 9 5CF C2 O2 doub N N 10 5CF C4 N3 doub N N 11 5CF C5 C4 sing N N 12 5CF C4 N4 sing N N 13 5CF N4 HN4 sing N N 14 5CF N4 HN4A sing N N 15 5CF F5 C5 sing N N 16 5CF C6 C5 doub N N 17 5CF C6 H6 sing N N 18 5CF "C2'" "C1'" sing N N 19 5CF "O4'" "C1'" sing N N 20 5CF "C1'" "H1'" sing N N 21 5CF "C3'" "C2'" sing N N 22 5CF "C2'" "O2'" sing N N 23 5CF "C2'" "H2'" sing N N 24 5CF "O2'" "HO2'" sing N N 25 5CF "O3'" "C3'" sing N N 26 5CF "C3'" "C4'" sing N N 27 5CF "C3'" "H3'" sing N N 28 5CF "O3'" "HO3'" sing N N 29 5CF "C5'" "C4'" sing N N 30 5CF "C4'" "O4'" sing N N 31 5CF "C4'" "H4'" sing N N 32 5CF "O5'" "C5'" sing N N 33 5CF "C5'" "H5'" sing N N 34 5CF "C5'" "H5'A" sing N N 35 5CF OP1 HOP1 sing N N 36 C OP3 P sing N N 37 C OP3 HOP3 sing N N 38 C P OP1 doub N N 39 C P OP2 sing N N 40 C P "O5'" sing N N 41 C OP2 HOP2 sing N N 42 C "O5'" "C5'" sing N N 43 C "C5'" "C4'" sing N N 44 C "C5'" "H5'" sing N N 45 C "C5'" "H5''" sing N N 46 C "C4'" "O4'" sing N N 47 C "C4'" "C3'" sing N N 48 C "C4'" "H4'" sing N N 49 C "O4'" "C1'" sing N N 50 C "C3'" "O3'" sing N N 51 C "C3'" "C2'" sing N N 52 C "C3'" "H3'" sing N N 53 C "O3'" "HO3'" sing N N 54 C "C2'" "O2'" sing N N 55 C "C2'" "C1'" sing N N 56 C "C2'" "H2'" sing N N 57 C "O2'" "HO2'" sing N N 58 C "C1'" N1 sing N N 59 C "C1'" "H1'" sing N N 60 C N1 C2 sing N N 61 C N1 C6 sing N N 62 C C2 O2 doub N N 63 C C2 N3 sing N N 64 C N3 C4 doub N N 65 C C4 N4 sing N N 66 C C4 C5 sing N N 67 C N4 H41 sing N N 68 C N4 H42 sing N N 69 C C5 C6 doub N N 70 C C5 H5 sing N N 71 C C6 H6 sing N N 72 G OP3 P sing N N 73 G OP3 HOP3 sing N N 74 G P OP1 doub N N 75 G P OP2 sing N N 76 G P "O5'" sing N N 77 G OP2 HOP2 sing N N 78 G "O5'" "C5'" sing N N 79 G "C5'" "C4'" sing N N 80 G "C5'" "H5'" sing N N 81 G "C5'" "H5''" sing N N 82 G "C4'" "O4'" sing N N 83 G "C4'" "C3'" sing N N 84 G "C4'" "H4'" sing N N 85 G "O4'" "C1'" sing N N 86 G "C3'" "O3'" sing N N 87 G "C3'" "C2'" sing N N 88 G "C3'" "H3'" sing N N 89 G "O3'" "HO3'" sing N N 90 G "C2'" "O2'" sing N N 91 G "C2'" "C1'" sing N N 92 G "C2'" "H2'" sing N N 93 G "O2'" "HO2'" sing N N 94 G "C1'" N9 sing N N 95 G "C1'" "H1'" sing N N 96 G N9 C8 sing Y N 97 G N9 C4 sing Y N 98 G C8 N7 doub Y N 99 G C8 H8 sing N N 100 G N7 C5 sing Y N 101 G C5 C6 sing N N 102 G C5 C4 doub Y N 103 G C6 O6 doub N N 104 G C6 N1 sing N N 105 G N1 C2 sing N N 106 G N1 H1 sing N N 107 G C2 N2 sing N N 108 G C2 N3 doub N N 109 G N2 H21 sing N N 110 G N2 H22 sing N N 111 G N3 C4 sing N N 112 HOH O H1 sing N N 113 HOH O H2 sing N N 114 # _ndb_struct_conf_na.entry_id 3JXQ _ndb_struct_conf_na.feature '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 G 6 1_555 B C 1 1_555 -0.060 -0.130 -0.075 -2.884 -7.239 -1.060 1 A_G6:C1_B A 6 ? B 1 ? 19 1 1 A G 4 1_555 B C 3 1_555 -0.287 -0.157 0.145 -0.779 -10.413 -1.164 2 A_G4:C3_B A 4 ? B 3 ? 19 1 1 A C 3 1_555 B G 4 1_555 0.174 -0.145 0.092 -0.627 -9.767 -2.015 3 A_C3:G4_B A 3 ? B 4 ? 19 1 1 B G 6 1_555 A C 1 1_555 -0.096 -0.232 0.036 3.506 -9.389 1.680 4 B_G6:C1_A B 6 ? A 1 ? 19 1 1 D C 1 1_555 C G 6 1_555 0.098 -0.157 0.089 2.603 -15.342 -0.217 5 L_C1:G6_K L 1 ? K 6 ? 19 1 1 D C 3 1_555 C G 4 1_555 0.204 -0.113 0.018 2.460 -10.578 0.161 6 L_C3:G4_K L 3 ? K 4 ? 19 1 1 D G 4 1_555 C C 3 1_555 -0.252 -0.222 0.018 -0.695 -11.027 0.585 7 L_G4:C3_K L 4 ? K 3 ? 19 1 1 D G 6 1_555 C C 1 1_555 -0.231 -0.156 -0.005 -5.882 -7.692 0.138 8 L_G6:C1_K L 6 ? K 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 6 1_555 B C 1 1_555 A G 4 1_555 B C 3 1_555 -0.107 2.863 -6.323 0.562 -14.209 -67.356 -3.519 -0.134 -5.694 12.667 0.501 -68.667 1 AA_G6G4:C3C1_BB A 6 ? B 1 ? A 4 ? B 3 ? 1 A G 4 1_555 B C 3 1_555 A C 3 1_555 B G 4 1_555 -0.965 1.808 -3.142 -1.046 -11.489 -27.256 -5.638 -1.701 -2.247 23.110 -2.104 -29.554 2 AA_G4C3:G4C3_BB A 4 ? B 3 ? A 3 ? B 4 ? 1 A C 3 1_555 B G 4 1_555 B G 6 1_555 A C 1 1_555 -0.601 -7.019 1.049 141.166 -86.450 174.329 -3.495 0.324 1.203 -43.229 -70.590 179.286 3 AB_C3G6:C1G4_AB A 3 ? B 4 ? B 6 ? A 1 ? 1 B G 6 1_555 A C 1 1_555 D C 1 1_555 C G 6 1_555 1.101 -1.257 3.155 -0.165 5.215 52.023 -1.753 -1.260 3.021 5.928 0.187 52.266 4 BL_G6C1:G6C1_KA B 6 ? A 1 ? L 1 ? K 6 ? 1 D C 1 1_555 C G 6 1_555 D C 3 1_555 C G 4 1_555 0.547 -2.578 6.169 5.325 21.918 63.229 -3.895 -0.121 5.160 20.239 -4.917 66.737 5 LL_C1C3:G4G6_KK L 1 ? K 6 ? L 3 ? K 4 ? 1 D C 3 1_555 C G 4 1_555 D G 4 1_555 C C 3 1_555 0.621 -2.240 3.263 0.827 9.167 23.281 -7.554 -1.219 2.252 21.661 -1.954 25.012 6 LL_C3G4:C3G4_KK L 3 ? K 4 ? L 4 ? K 3 ? 1 D G 4 1_555 C C 3 1_555 D G 6 1_555 C C 1 1_555 -0.927 -3.508 6.476 -2.786 10.271 65.174 -4.019 0.636 5.957 9.469 2.568 65.943 7 LL_G4G6:C1C3_KK L 4 ? K 3 ? L 6 ? K 1 ? # _atom_sites.entry_id 3JXQ _atom_sites.fract_transf_matrix[1][1] 0.047116 _atom_sites.fract_transf_matrix[1][2] 0.016571 _atom_sites.fract_transf_matrix[1][3] 0.017574 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.040023 _atom_sites.fract_transf_matrix[2][3] 0.009985 _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] 0.036486 _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 F MG N O P # loop_