data_3JXR # _entry.id 3JXR # _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 3JXR pdb_00003jxr 10.2210/pdb3jxr/pdb NDB NA0194 ? ? RCSB RCSB055292 ? ? WWPDB D_1000055292 ? ? # 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 2015-09-09 4 'Structure model' 1 3 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' 'Refinement description' 3 4 'Structure model' 'Data collection' 4 4 'Structure model' 'Database references' 5 4 '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 4 'Structure model' chem_comp_atom 2 4 'Structure model' chem_comp_bond 3 4 'Structure model' database_2 4 4 'Structure model' diffrn_source 5 4 'Structure model' struct_conn # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 4 'Structure model' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_diffrn_source.pdbx_synchrotron_site' 4 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3JXR _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.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 3JXQ _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 906 _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 3 ? ? ? ? 2 water nat water 18.015 60 ? ? ? ? # _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 _entity_poly.pdbx_target_identifier ? # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 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 # 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 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code D 2 HOH 1 7 3 HOH HOH A . D 2 HOH 2 8 4 HOH HOH A . D 2 HOH 3 9 9 HOH HOH A . D 2 HOH 4 10 5 HOH HOH A . D 2 HOH 5 13 13 HOH HOH A . D 2 HOH 6 14 14 HOH HOH A . D 2 HOH 7 15 15 HOH HOH A . D 2 HOH 8 16 16 HOH HOH A . D 2 HOH 9 17 17 HOH HOH A . D 2 HOH 10 18 18 HOH HOH A . D 2 HOH 11 19 19 HOH HOH A . D 2 HOH 12 21 21 HOH HOH A . D 2 HOH 13 23 23 HOH HOH A . D 2 HOH 14 26 26 HOH HOH A . D 2 HOH 15 31 31 HOH HOH A . D 2 HOH 16 32 32 HOH HOH A . D 2 HOH 17 33 33 HOH HOH A . D 2 HOH 18 34 34 HOH HOH A . D 2 HOH 19 35 35 HOH HOH A . D 2 HOH 20 37 37 HOH HOH A . D 2 HOH 21 40 40 HOH HOH A . D 2 HOH 22 41 41 HOH HOH A . D 2 HOH 23 42 42 HOH HOH A . D 2 HOH 24 44 44 HOH HOH A . D 2 HOH 25 45 45 HOH HOH A . D 2 HOH 26 52 52 HOH HOH A . D 2 HOH 27 54 54 HOH HOH A . D 2 HOH 28 55 55 HOH HOH A . D 2 HOH 29 56 56 HOH HOH A . D 2 HOH 30 58 58 HOH HOH A . D 2 HOH 31 59 59 HOH HOH A . E 2 HOH 1 7 7 HOH HOH B . E 2 HOH 2 8 8 HOH HOH B . E 2 HOH 3 9 1 HOH HOH B . E 2 HOH 4 10 10 HOH HOH B . E 2 HOH 5 11 11 HOH HOH B . E 2 HOH 6 12 12 HOH HOH B . E 2 HOH 7 13 2 HOH HOH B . E 2 HOH 8 14 6 HOH HOH B . E 2 HOH 9 20 20 HOH HOH B . E 2 HOH 10 22 22 HOH HOH B . E 2 HOH 11 24 24 HOH HOH B . E 2 HOH 12 25 25 HOH HOH B . E 2 HOH 13 27 27 HOH HOH B . E 2 HOH 14 28 28 HOH HOH B . E 2 HOH 15 29 29 HOH HOH B . E 2 HOH 16 36 36 HOH HOH B . E 2 HOH 17 43 43 HOH HOH B . E 2 HOH 18 47 47 HOH HOH B . E 2 HOH 19 48 48 HOH HOH B . E 2 HOH 20 50 50 HOH HOH B . E 2 HOH 21 51 51 HOH HOH B . E 2 HOH 22 57 57 HOH HOH B . E 2 HOH 23 60 60 HOH HOH B . F 2 HOH 1 30 30 HOH HOH K . F 2 HOH 2 38 38 HOH HOH K . F 2 HOH 3 39 39 HOH HOH K . F 2 HOH 4 46 46 HOH HOH K . F 2 HOH 5 49 49 HOH HOH K . F 2 HOH 6 53 53 HOH HOH K . # 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 3JXR _cell.length_a 41.116 _cell.length_b 41.116 _cell.length_c 143.285 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 54 _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 3JXR _symmetry.space_group_name_H-M 'H 3 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? # _exptl.entry_id 3JXR _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.02 _exptl_crystal.density_percent_sol 39.07 _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 7.0 _exptl_crystal_grow.pdbx_details '1.6M ammonium sulphate, 10mM magnesium chloride and 50mM HEPES, pH 7.0, 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 CCD _diffrn_detector.type 'MAR CCD 165 mm' _diffrn_detector.pdbx_collection_date 2002-03-22 _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)' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.8019 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'EMBL/DESY, HAMBURG BEAMLINE X13' _diffrn_source.pdbx_synchrotron_site 'EMBL/DESY, HAMBURG' _diffrn_source.pdbx_synchrotron_beamline X13 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.8019 # _reflns.entry_id 3JXR _reflns.observed_criterion_sigma_I 0 _reflns.observed_criterion_sigma_F 0 _reflns.d_resolution_low 25 _reflns.d_resolution_high 1.25 _reflns.number_obs 13169 _reflns.number_all 13169 _reflns.percent_possible_obs 99.1 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value 0.043 _reflns.pdbx_netI_over_sigmaI 26 _reflns.B_iso_Wilson_estimate 17 _reflns.pdbx_redundancy 8.6 _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 # _reflns_shell.d_res_high 1.25 _reflns_shell.d_res_low 1.27 _reflns_shell.percent_possible_all 99.8 _reflns_shell.Rmerge_I_obs ? _reflns_shell.pdbx_Rsym_value 0.476 _reflns_shell.meanI_over_sigI_obs 5.4 _reflns_shell.pdbx_redundancy 7.7 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 648 _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 # _refine.entry_id 3JXR _refine.ls_number_reflns_obs 12702 _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 20.00 _refine.ls_d_res_high 1.25 _refine.ls_percent_reflns_obs 100.00 _refine.ls_R_factor_obs 0.21992 _refine.ls_R_factor_all 0.21992 _refine.ls_R_factor_R_work 0.21892 _refine.ls_R_factor_R_free 0.27649 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 2.0 _refine.ls_number_reflns_R_free 253 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.958 _refine.correlation_coeff_Fo_to_Fc_free 0.936 _refine.B_iso_mean 21.270 _refine.aniso_B[1][1] 0.17 _refine.aniso_B[2][2] 0.17 _refine.aniso_B[3][3] -0.26 _refine.aniso_B[1][2] 0.09 _refine.aniso_B[1][3] 0.00 _refine.aniso_B[2][3] 0.00 _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 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS' _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 0.062 _refine.pdbx_overall_ESU_R_Free 0.065 _refine.overall_SU_ML 0.045 _refine.overall_SU_B 2.411 _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 3JXR _refine_analyze.Luzzati_coordinate_error_obs ? _refine_analyze.Luzzati_sigma_a_obs 0.062 _refine_analyze.Luzzati_d_res_low_obs ? _refine_analyze.Luzzati_coordinate_error_free 0.065 _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 381 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 60 _refine_hist.number_atoms_total 441 _refine_hist.d_res_high 1.25 _refine_hist.d_res_low 20.00 # 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 0.018 0.021 ? 423 'X-RAY DIFFRACTION' ? r_bond_other_d 0.002 0.020 ? 147 'X-RAY DIFFRACTION' ? r_angle_refined_deg 2.359 3.000 ? 651 'X-RAY DIFFRACTION' ? r_angle_other_deg 1.434 3.000 ? 381 'X-RAY DIFFRACTION' ? r_chiral_restr 0.101 0.200 ? 87 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.021 0.020 ? 189 'X-RAY DIFFRACTION' ? r_gen_planes_other 0.015 0.020 ? 36 'X-RAY DIFFRACTION' ? r_nbd_refined 0.100 0.200 ? 39 'X-RAY DIFFRACTION' ? r_nbd_other 0.278 0.200 ? 193 'X-RAY DIFFRACTION' ? r_nbtor_refined 0.251 0.200 ? 160 'X-RAY DIFFRACTION' ? r_nbtor_other 0.069 0.200 ? 104 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined 0.206 0.200 ? 26 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined 0.148 0.200 ? 16 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other 0.324 0.200 ? 30 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 0.588 0.200 ? 13 'X-RAY DIFFRACTION' ? r_scbond_it 2.440 3.000 ? 624 'X-RAY DIFFRACTION' ? r_scangle_it 3.119 5.000 ? 651 'X-RAY DIFFRACTION' ? r_rigid_bond_restr 1.911 3.000 ? 908 'X-RAY DIFFRACTION' ? r_sphericity_free 3.768 3.000 ? 63 'X-RAY DIFFRACTION' ? r_sphericity_bonded 3.308 3.000 ? 525 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 1.25 _refine_ls_shell.d_res_low 1.284 _refine_ls_shell.number_reflns_R_work 851 _refine_ls_shell.R_factor_R_work 0.272 _refine_ls_shell.percent_reflns_obs 100.00 _refine_ls_shell.R_factor_R_free 0.416 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 16 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.number_reflns_obs 851 _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _database_PDB_matrix.entry_id 3JXR _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 3JXR _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 3JXR _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 2 ? E N N 2 ? F N N 2 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 3JXR _struct_ref.pdbx_db_accession 3JXR _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 3JXR A 1 ? 6 ? 3JXR 1 ? 6 ? 1 6 2 1 3JXR B 1 ? 6 ? 3JXR 1 ? 6 ? 1 6 3 1 3JXR K 1 ? 6 ? 3JXR 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_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 660 ? 1 MORE -0 ? 1 'SSA (A^2)' 2410 ? 2 'ABSA (A^2)' 670 ? 2 MORE -1 ? 2 'SSA (A^2)' 2410 ? # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 1 A,B,D,E 2 1,2 C,F # 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' 12_555 -x+2/3,-x+y+1/3,-z+1/3 -0.5000000000 -0.8660254038 0.0000000000 20.5580000000 -0.8660254038 0.5000000000 0.0000000000 11.8691668340 0.0000000000 0.0000000000 -1.0000000000 47.7616666667 # _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 ? ? ? ? ? ? ? 1.592 ? ? covale2 covale one ? A 5CF 5 "O3'" ? ? ? 1_555 A G 6 P ? ? A 5CF 5 A G 6 1_555 ? ? ? ? ? ? ? 1.554 ? ? covale3 covale both ? B G 4 "O3'" ? ? ? 1_555 B 5CF 5 P ? ? B G 4 B 5CF 5 1_555 ? ? ? ? ? ? ? 1.591 ? ? covale4 covale one ? B 5CF 5 "O3'" ? ? ? 1_555 B G 6 P ? ? B 5CF 5 B G 6 1_555 ? ? ? ? ? ? ? 1.603 ? ? covale5 covale both ? C G 4 "O3'" ? ? ? 1_555 C 5CF 5 P ? ? K G 4 K 5CF 5 1_555 ? ? ? ? ? ? ? 1.635 ? ? covale6 covale one ? C 5CF 5 "O3'" ? ? ? 1_555 C G 6 P ? ? K 5CF 5 K G 6 1_555 ? ? ? ? ? ? ? 1.595 ? ? 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 C G 6 N1 ? ? K C 1 K G 6 12_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? C C 1 N4 ? ? ? 1_555 C G 6 O6 ? ? K C 1 K G 6 12_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? C C 1 O2 ? ? ? 1_555 C G 6 N2 ? ? K C 1 K G 6 12_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? C C 3 N3 ? ? ? 1_555 C G 4 N1 ? ? K C 3 K G 4 12_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? C C 3 N4 ? ? ? 1_555 C G 4 O6 ? ? K C 3 K G 4 12_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? C C 3 O2 ? ? ? 1_555 C G 4 N2 ? ? K C 3 K G 4 12_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? C G 4 N1 ? ? ? 1_555 C C 3 N3 ? ? K G 4 K C 3 12_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? C G 4 N2 ? ? ? 1_555 C C 3 O2 ? ? K G 4 K C 3 12_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? C G 4 O6 ? ? ? 1_555 C C 3 N4 ? ? K G 4 K C 3 12_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? C G 6 N1 ? ? ? 1_555 C C 1 N3 ? ? K G 6 K C 1 12_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? C G 6 N2 ? ? ? 1_555 C C 1 O2 ? ? K G 6 K C 1 12_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? C G 6 O6 ? ? ? 1_555 C C 1 N4 ? ? K G 6 K C 1 12_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # loop_ _pdbx_validate_symm_contact.id _pdbx_validate_symm_contact.PDB_model_num _pdbx_validate_symm_contact.auth_atom_id_1 _pdbx_validate_symm_contact.auth_asym_id_1 _pdbx_validate_symm_contact.auth_comp_id_1 _pdbx_validate_symm_contact.auth_seq_id_1 _pdbx_validate_symm_contact.PDB_ins_code_1 _pdbx_validate_symm_contact.label_alt_id_1 _pdbx_validate_symm_contact.site_symmetry_1 _pdbx_validate_symm_contact.auth_atom_id_2 _pdbx_validate_symm_contact.auth_asym_id_2 _pdbx_validate_symm_contact.auth_comp_id_2 _pdbx_validate_symm_contact.auth_seq_id_2 _pdbx_validate_symm_contact.PDB_ins_code_2 _pdbx_validate_symm_contact.label_alt_id_2 _pdbx_validate_symm_contact.site_symmetry_2 _pdbx_validate_symm_contact.dist 1 1 O A HOH 58 ? ? 1_555 O A HOH 58 ? ? 5_555 1.29 2 1 O B HOH 47 ? ? 1_555 O B HOH 47 ? ? 3_555 1.87 3 1 O K HOH 49 ? ? 1_555 O K HOH 49 ? ? 12_555 2.09 # loop_ _pdbx_validate_rmsd_bond.id _pdbx_validate_rmsd_bond.PDB_model_num _pdbx_validate_rmsd_bond.auth_atom_id_1 _pdbx_validate_rmsd_bond.auth_asym_id_1 _pdbx_validate_rmsd_bond.auth_comp_id_1 _pdbx_validate_rmsd_bond.auth_seq_id_1 _pdbx_validate_rmsd_bond.PDB_ins_code_1 _pdbx_validate_rmsd_bond.label_alt_id_1 _pdbx_validate_rmsd_bond.auth_atom_id_2 _pdbx_validate_rmsd_bond.auth_asym_id_2 _pdbx_validate_rmsd_bond.auth_comp_id_2 _pdbx_validate_rmsd_bond.auth_seq_id_2 _pdbx_validate_rmsd_bond.PDB_ins_code_2 _pdbx_validate_rmsd_bond.label_alt_id_2 _pdbx_validate_rmsd_bond.bond_value _pdbx_validate_rmsd_bond.bond_target_value _pdbx_validate_rmsd_bond.bond_deviation _pdbx_validate_rmsd_bond.bond_standard_deviation _pdbx_validate_rmsd_bond.linker_flag 1 1 "O5'" B C 1 ? ? "C5'" B C 1 ? ? 1.359 1.420 -0.061 0.009 N 2 1 C4 B C 3 ? ? N4 B C 3 ? ? 1.281 1.335 -0.054 0.009 N # 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 "C3'" A C 1 ? ? "C2'" A C 1 ? ? "C1'" A C 1 ? ? 96.00 101.30 -5.30 0.70 N 2 1 "O3'" A G 2 ? ? P A C 3 ? ? OP2 A C 3 ? ? 118.79 110.50 8.29 1.10 Y 3 1 "O5'" A C 3 ? ? P A C 3 ? ? OP2 A C 3 ? ? 98.10 105.70 -7.60 0.90 N 4 1 "C4'" A C 3 ? ? "C3'" A C 3 ? ? "C2'" A C 3 ? ? 93.69 102.60 -8.91 1.00 N 5 1 "C1'" A G 4 ? ? "O4'" A G 4 ? ? "C4'" A G 4 ? ? 105.25 109.70 -4.45 0.70 N 6 1 "O3'" B G 4 ? ? P B 5CF 5 ? ? OP2 B 5CF 5 ? ? 117.83 110.50 7.33 1.10 Y 7 1 C6 B G 6 ? ? C5 B G 6 ? ? N7 B G 6 ? ? 126.67 130.40 -3.73 0.60 N 8 1 C5 K G 2 ? ? C6 K G 2 ? ? O6 K G 2 ? ? 124.98 128.60 -3.62 0.60 N 9 1 "O5'" K C 3 ? ? "C5'" K C 3 ? ? "C4'" K C 3 ? ? 103.89 109.40 -5.51 0.80 N 10 1 "O4'" K C 3 ? ? "C1'" K C 3 ? ? N1 K C 3 ? ? 113.68 108.50 5.18 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 HOH 33 ? D HOH . 2 1 A HOH 34 ? D HOH . 3 1 A HOH 35 ? D HOH . 4 1 A HOH 42 ? D HOH . 5 1 B HOH 25 ? E HOH . 6 1 B HOH 36 ? E HOH . 7 1 B HOH 51 ? E HOH . 8 1 K HOH 30 ? F HOH . 9 1 K HOH 38 ? F HOH . # _pdbx_refine_tls.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine_tls.id 1 _pdbx_refine_tls.details ? _pdbx_refine_tls.method refined _pdbx_refine_tls.origin_x 9.9326 _pdbx_refine_tls.origin_y 10.2728 _pdbx_refine_tls.origin_z 12.7173 _pdbx_refine_tls.T[1][1] 0.0184 _pdbx_refine_tls.T[2][2] 0.0107 _pdbx_refine_tls.T[3][3] -0.0024 _pdbx_refine_tls.T[1][2] -0.0008 _pdbx_refine_tls.T[1][3] 0.0023 _pdbx_refine_tls.T[2][3] -0.0008 _pdbx_refine_tls.L[1][1] 0.3530 _pdbx_refine_tls.L[2][2] 0.5115 _pdbx_refine_tls.L[3][3] 0.9055 _pdbx_refine_tls.L[1][2] -0.0410 _pdbx_refine_tls.L[1][3] -0.2455 _pdbx_refine_tls.L[2][3] -0.0354 _pdbx_refine_tls.S[1][1] 0.0571 _pdbx_refine_tls.S[2][2] 0.0325 _pdbx_refine_tls.S[3][3] -0.0895 _pdbx_refine_tls.S[1][2] -0.0713 _pdbx_refine_tls.S[1][3] -0.0276 _pdbx_refine_tls.S[2][3] -0.0336 _pdbx_refine_tls.S[2][1] 0.1037 _pdbx_refine_tls.S[3][1] -0.0822 _pdbx_refine_tls.S[3][2] 0.0160 # loop_ _pdbx_refine_tls_group.pdbx_refine_id _pdbx_refine_tls_group.id _pdbx_refine_tls_group.refine_tls_id _pdbx_refine_tls_group.beg_auth_asym_id _pdbx_refine_tls_group.beg_auth_seq_id _pdbx_refine_tls_group.end_auth_asym_id _pdbx_refine_tls_group.end_auth_seq_id _pdbx_refine_tls_group.selection_details _pdbx_refine_tls_group.beg_label_asym_id _pdbx_refine_tls_group.beg_label_seq_id _pdbx_refine_tls_group.end_label_asym_id _pdbx_refine_tls_group.end_label_seq_id _pdbx_refine_tls_group.selection 'X-RAY DIFFRACTION' 1 1 B 7 B 60 ? . . . . ? 'X-RAY DIFFRACTION' 2 1 K 30 K 53 ? . . . . ? 'X-RAY DIFFRACTION' 3 1 A 7 A 59 ? . . . . ? 'X-RAY DIFFRACTION' 4 1 B 1 B 6 ? . . . . ? 'X-RAY DIFFRACTION' 5 1 K 1 K 6 ? . . . . ? 'X-RAY DIFFRACTION' 6 1 A 1 A 6 ? . . . . ? # 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 # 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 3JXR _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 C 1 1_555 B G 6 1_555 0.010 -0.214 0.013 9.077 -18.238 1.805 1 A_C1:G6_B A 1 ? B 6 ? 19 1 1 A C 3 1_555 B G 4 1_555 0.179 -0.187 0.089 3.734 -17.950 -1.680 2 A_C3:G4_B A 3 ? B 4 ? 19 1 1 A G 4 1_555 B C 3 1_555 -0.084 -0.141 0.014 -3.901 -13.511 -1.664 3 A_G4:C3_B A 4 ? B 3 ? 19 1 1 A G 6 1_555 B C 1 1_555 -0.095 -0.129 0.018 -9.730 -13.999 -2.090 4 A_G6:C1_B A 6 ? B 1 ? 19 1 1 C C 1 1_555 C G 6 12_555 0.033 -0.131 0.053 7.156 -11.250 2.333 5 K_C1:G6_K K 1 ? K 6 ? 19 1 1 C C 3 1_555 C G 4 12_555 0.697 -0.272 -0.137 2.919 -14.253 -1.632 6 K_C3:G4_K K 3 ? K 4 ? 19 1 1 C G 4 1_555 C C 3 12_555 -0.697 -0.272 -0.137 -2.919 -14.253 -1.632 7 K_G4:C3_K K 4 ? K 3 ? 19 1 1 C G 6 1_555 C C 1 12_555 -0.033 -0.131 0.053 -7.157 -11.250 2.333 8 K_G6:C1_K K 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 C 1 1_555 B G 6 1_555 A C 3 1_555 B G 4 1_555 -0.920 -2.911 6.404 -2.522 16.913 67.357 -3.718 0.637 5.653 15.003 2.237 69.245 1 AA_C1C3:G4G6_BB A 1 ? B 6 ? A 3 ? B 4 ? 1 A C 3 1_555 B G 4 1_555 A G 4 1_555 B C 3 1_555 0.146 -1.591 3.313 1.577 13.886 30.805 -4.801 -0.017 2.399 24.614 -2.796 33.757 2 AA_C3G4:C3G4_BB A 3 ? B 4 ? A 4 ? B 3 ? 1 A G 4 1_555 B C 3 1_555 A G 6 1_555 B C 1 1_555 0.304 -2.741 6.377 2.105 16.421 67.622 -3.524 -0.124 5.672 14.533 -1.863 69.384 3 AA_G4G6:C1C3_BB A 4 ? B 3 ? A 6 ? B 1 ? 1 C C 1 1_555 C G 6 12_555 C C 3 1_555 C G 4 12_555 -0.684 -2.416 6.542 -0.308 10.171 68.159 -2.872 0.583 6.176 9.024 0.274 68.824 4 KK_C1C3:G4G6_KK K 1 ? K 6 ? K 3 ? K 4 ? 1 C C 3 1_555 C G 4 12_555 C G 4 1_555 C C 3 12_555 0.000 -1.474 3.331 0.000 12.210 26.970 -5.288 0.000 2.448 24.639 0.000 29.558 5 KK_C3G4:C3G4_KK K 3 ? K 4 ? K 4 ? K 3 ? 1 C G 4 1_555 C C 3 12_555 C G 6 1_555 C C 1 12_555 0.684 -2.416 6.542 0.308 10.171 68.159 -2.872 -0.583 6.176 9.024 -0.274 68.824 6 KK_G4G6:C1C3_KK K 4 ? K 3 ? K 6 ? K 1 ? # _atom_sites.entry_id 3JXR _atom_sites.fract_transf_matrix[1][1] 0.024321 _atom_sites.fract_transf_matrix[1][2] 0.014042 _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] 0.028084 _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] 0.006979 _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 N O P # loop_