data_4XW0 # _entry.id 4XW0 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.383 _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 4XW0 pdb_00004xw0 10.2210/pdb4xw0/pdb WWPDB D_1000204236 ? ? # 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 2016-01-13 2 'Structure model' 1 1 2024-01-10 # _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' 'Data collection' 2 2 'Structure model' 'Database references' 3 2 'Structure model' 'Refinement description' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 2 'Structure model' chem_comp_atom 2 2 'Structure model' chem_comp_bond 3 2 'Structure model' database_2 4 2 'Structure model' pdbx_initial_refinement_model # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 2 'Structure model' '_database_2.pdbx_DOI' 2 2 'Structure model' '_database_2.pdbx_database_accession' # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 4XW0 _pdbx_database_status.recvd_initial_deposition_date 2015-01-28 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site PDBE _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Kiliszek, A.' 1 'Banaszak, K.' 2 'Rypniewski, W.' 3 # _citation.abstract ? _citation.abstract_id_CAS ? _citation.book_id_ISBN ? _citation.book_publisher ? _citation.book_publisher_city ? _citation.book_title ? _citation.coordinate_linkage ? _citation.country UK _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev Rna _citation.journal_id_ASTM RNARFU _citation.journal_id_CSD 2122 _citation.journal_id_ISSN 1469-9001 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 22 _citation.language ? _citation.page_first 22 _citation.page_last 31 _citation.title 'Watson-Crick-like pairs in CCUG repeats: evidence for tautomeric shifts or protonation.' _citation.year 2016 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1261/rna.052399.115 _citation.pdbx_database_id_PubMed 26543073 _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Rypniewski, W.' 1 ? primary 'Banaszak, K.' 2 ? primary 'Kulinski, T.' 3 ? primary 'Kiliszek, A.' 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 ;RNA (5'-R(*GP*CP*CP*UP*(LCG)P*CP*CP*UP*GP*C)-3') ; 3140.910 2 ? ? ? 'RNA oligomer' 2 non-polymer syn 'SULFATE ION' 96.063 2 ? ? ? ? 3 water nat water 18.015 22 ? ? ? ? # _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 'GCCU(LCG)CCUGC' _entity_poly.pdbx_seq_one_letter_code_can GCCUGCCUGC _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'SULFATE ION' SO4 3 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 G n 1 2 C n 1 3 C n 1 4 U n 1 5 LCG n 1 6 C n 1 7 C n 1 8 U n 1 9 G n 1 10 C 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 1 _pdbx_entity_src_syn.pdbx_end_seq_num 10 _pdbx_entity_src_syn.organism_scientific 'Homo sapiens' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 9606 _pdbx_entity_src_syn.details ? # 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 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 LCG 'RNA linking' n '[(1R,3R,4R,7S)-7-HYDROXY-3-(GUANIN-9-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL DIHYDROGEN PHOSPHATE' ? 'C11 H14 N5 O8 P' 375.231 SO4 non-polymer . 'SULFATE ION' ? 'O4 S -2' 96.063 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 G 1 1 1 G G A . n A 1 2 C 2 2 2 C C A . n A 1 3 C 3 3 3 C C A . n A 1 4 U 4 4 4 U U A . n A 1 5 LCG 5 5 5 LCG LCG A . n A 1 6 C 6 6 6 C C A . n A 1 7 C 7 7 7 C C A . n A 1 8 U 8 8 8 U U A . n A 1 9 G 9 9 9 G G A . n A 1 10 C 10 10 10 C C A . n B 1 1 G 1 1 1 G G B . n B 1 2 C 2 2 2 C C B . n B 1 3 C 3 3 3 C C B . n B 1 4 U 4 4 4 U U B . n B 1 5 LCG 5 5 5 LCG LCG B . n B 1 6 C 6 6 6 C C B . n B 1 7 C 7 7 7 C C B . n B 1 8 U 8 8 8 U U B . n B 1 9 G 9 9 9 G G B . n B 1 10 C 10 10 10 C C B . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code C 2 SO4 1 101 1 SO4 SO4 A . D 2 SO4 1 102 2 SO4 SO4 A . E 3 HOH 1 201 15 HOH HOH A . E 3 HOH 2 202 4 HOH HOH A . E 3 HOH 3 203 20 HOH HOH A . E 3 HOH 4 204 22 HOH HOH A . E 3 HOH 5 205 9 HOH HOH A . E 3 HOH 6 206 13 HOH HOH A . E 3 HOH 7 207 21 HOH HOH A . E 3 HOH 8 208 19 HOH HOH A . E 3 HOH 9 209 7 HOH HOH A . E 3 HOH 10 210 25 HOH HOH A . E 3 HOH 11 211 11 HOH HOH A . E 3 HOH 12 212 12 HOH HOH A . E 3 HOH 13 213 18 HOH HOH A . E 3 HOH 14 214 24 HOH HOH A . F 3 HOH 1 101 17 HOH HOH B . F 3 HOH 2 102 16 HOH HOH B . F 3 HOH 3 103 8 HOH HOH B . F 3 HOH 4 104 10 HOH HOH B . F 3 HOH 5 105 3 HOH HOH B . F 3 HOH 6 106 5 HOH HOH B . F 3 HOH 7 107 6 HOH HOH B . F 3 HOH 8 108 23 HOH HOH B . # loop_ _pdbx_unobs_or_zero_occ_atoms.id _pdbx_unobs_or_zero_occ_atoms.PDB_model_num _pdbx_unobs_or_zero_occ_atoms.polymer_flag _pdbx_unobs_or_zero_occ_atoms.occupancy_flag _pdbx_unobs_or_zero_occ_atoms.auth_asym_id _pdbx_unobs_or_zero_occ_atoms.auth_comp_id _pdbx_unobs_or_zero_occ_atoms.auth_seq_id _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code _pdbx_unobs_or_zero_occ_atoms.auth_atom_id _pdbx_unobs_or_zero_occ_atoms.label_alt_id _pdbx_unobs_or_zero_occ_atoms.label_asym_id _pdbx_unobs_or_zero_occ_atoms.label_comp_id _pdbx_unobs_or_zero_occ_atoms.label_seq_id _pdbx_unobs_or_zero_occ_atoms.label_atom_id 1 1 Y 1 B C 10 ? "O5'" ? B C 10 "O5'" 2 1 Y 1 B C 10 ? "C5'" ? B C 10 "C5'" 3 1 Y 1 B C 10 ? "C4'" ? B C 10 "C4'" 4 1 Y 1 B C 10 ? "O4'" ? B C 10 "O4'" 5 1 Y 1 B C 10 ? "C3'" ? B C 10 "C3'" 6 1 Y 1 B C 10 ? "O3'" ? B C 10 "O3'" 7 1 Y 1 B C 10 ? "C2'" ? B C 10 "C2'" 8 1 Y 1 B C 10 ? "O2'" ? B C 10 "O2'" 9 1 Y 1 B C 10 ? "C1'" ? B C 10 "C1'" 10 1 Y 1 B C 10 ? N1 ? B C 10 N1 11 1 Y 1 B C 10 ? C2 ? B C 10 C2 12 1 Y 1 B C 10 ? O2 ? B C 10 O2 13 1 Y 1 B C 10 ? N3 ? B C 10 N3 14 1 Y 1 B C 10 ? C4 ? B C 10 C4 15 1 Y 1 B C 10 ? N4 ? B C 10 N4 16 1 Y 1 B C 10 ? C5 ? B C 10 C5 17 1 Y 1 B C 10 ? C6 ? B C 10 C6 # loop_ _software.citation_id _software.classification _software.compiler_name _software.compiler_version _software.contact_author _software.contact_author_email _software.date _software.description _software.dependencies _software.hardware _software.language _software.location _software.mods _software.name _software.os _software.os_version _software.type _software.version _software.pdbx_ordinal ? refinement ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? '(phenix.refine: 1.8.2_1309)' 1 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? XDS ? ? ? . 2 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? XSCALE ? ? ? . 3 ? phasing ? ? ? ? ? ? ? ? ? ? ? PHASER ? ? ? . 4 # _cell.angle_alpha 90.00 _cell.angle_alpha_esd ? _cell.angle_beta 90.00 _cell.angle_beta_esd ? _cell.angle_gamma 90.00 _cell.angle_gamma_esd ? _cell.entry_id 4XW0 _cell.details ? _cell.formula_units_Z ? _cell.length_a 26.910 _cell.length_a_esd ? _cell.length_b 26.910 _cell.length_b_esd ? _cell.length_c 80.505 _cell.length_c_esd ? _cell.volume ? _cell.volume_esd ? _cell.Z_PDB 8 _cell.reciprocal_angle_alpha ? _cell.reciprocal_angle_beta ? _cell.reciprocal_angle_gamma ? _cell.reciprocal_angle_alpha_esd ? _cell.reciprocal_angle_beta_esd ? _cell.reciprocal_angle_gamma_esd ? _cell.reciprocal_length_a ? _cell.reciprocal_length_b ? _cell.reciprocal_length_c ? _cell.reciprocal_length_a_esd ? _cell.reciprocal_length_b_esd ? _cell.reciprocal_length_c_esd ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 4XW0 _symmetry.cell_setting ? _symmetry.Int_Tables_number 78 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43' _symmetry.pdbx_full_space_group_name_H-M ? # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.entry_id 4XW0 _exptl.crystals_number ? _exptl.details ? _exptl.method 'X-RAY DIFFRACTION' _exptl.method_details ? # _exptl_crystal.colour ? _exptl_crystal.density_diffrn ? _exptl_crystal.density_Matthews 2.32 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 46.98 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.id 1 _exptl_crystal.preparation ? _exptl_crystal.size_max ? _exptl_crystal.size_mid ? _exptl_crystal.size_min ? _exptl_crystal.size_rad ? _exptl_crystal.colour_lustre ? _exptl_crystal.colour_modifier ? _exptl_crystal.colour_primary ? _exptl_crystal.density_meas ? _exptl_crystal.density_meas_esd ? _exptl_crystal.density_meas_gt ? _exptl_crystal.density_meas_lt ? _exptl_crystal.density_meas_temp ? _exptl_crystal.density_meas_temp_esd ? _exptl_crystal.density_meas_temp_gt ? _exptl_crystal.density_meas_temp_lt ? _exptl_crystal.pdbx_crystal_image_url ? _exptl_crystal.pdbx_crystal_image_format ? _exptl_crystal.pdbx_mosaicity ? _exptl_crystal.pdbx_mosaicity_esd ? # _exptl_crystal_grow.apparatus ? _exptl_crystal_grow.atmosphere ? _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.details ? _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.method_ref ? _exptl_crystal_grow.pH ? _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp 292 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details '40 mM magnesium sulphate, HEPES and 1.3 M lithium sulphate' _exptl_crystal_grow.pdbx_pH_range 7.0 # _diffrn.ambient_environment ? _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.ambient_temp_esd ? _diffrn.crystal_id 1 _diffrn.crystal_support ? _diffrn.crystal_treatment ? _diffrn.details ? _diffrn.id 1 _diffrn.ambient_pressure ? _diffrn.ambient_pressure_esd ? _diffrn.ambient_pressure_gt ? _diffrn.ambient_pressure_lt ? _diffrn.ambient_temp_gt ? _diffrn.ambient_temp_lt ? # _diffrn_detector.details ? _diffrn_detector.detector CCD _diffrn_detector.diffrn_id 1 _diffrn_detector.type 'MAR CCD 165 mm' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2013-07-07 # _diffrn_radiation.collimation ? _diffrn_radiation.diffrn_id 1 _diffrn_radiation.filter_edge ? _diffrn_radiation.inhomogeneity ? _diffrn_radiation.monochromator ? _diffrn_radiation.polarisn_norm ? _diffrn_radiation.polarisn_ratio ? _diffrn_radiation.probe ? _diffrn_radiation.type ? _diffrn_radiation.xray_symbol ? _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_wavelength_list ? _diffrn_radiation.pdbx_wavelength ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_analyzer ? _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.91841 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.current ? _diffrn_source.details ? _diffrn_source.diffrn_id 1 _diffrn_source.power ? _diffrn_source.size ? _diffrn_source.source SYNCHROTRON _diffrn_source.target ? _diffrn_source.type 'BESSY BEAMLINE 14.2' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 0.91841 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline 14.2 _diffrn_source.pdbx_synchrotron_site BESSY # _reflns.B_iso_Wilson_estimate 40.3 _reflns.entry_id 4XW0 _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 1.81 _reflns.d_resolution_low 27.0 _reflns.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.number_all ? _reflns.number_obs 5249 _reflns.observed_criterion ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.observed_criterion_I_max ? _reflns.observed_criterion_I_min ? _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.percent_possible_obs 99.6 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 6.7 _reflns.pdbx_Rmerge_I_obs 0.057 _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 17.66 _reflns.pdbx_res_netI_over_av_sigmaI_2 ? _reflns.pdbx_res_netI_over_sigmaI_2 ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_d_res_high_opt ? _reflns.pdbx_d_res_low_opt ? _reflns.pdbx_d_res_opt_method ? _reflns.phase_calculation_details ? _reflns.pdbx_Rrim_I_all ? _reflns.pdbx_Rpim_I_all ? _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half ? _reflns.pdbx_R_split ? # _reflns_shell.d_res_high 1.81 _reflns_shell.d_res_low 1.92 _reflns_shell.meanI_over_sigI_all ? _reflns_shell.meanI_over_sigI_obs 1.96 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_possible ? _reflns_shell.number_unique_all ? _reflns_shell.number_unique_obs ? _reflns_shell.percent_possible_all 99.1 _reflns_shell.percent_possible_obs ? _reflns_shell.Rmerge_F_all ? _reflns_shell.Rmerge_F_obs ? _reflns_shell.Rmerge_I_all ? _reflns_shell.Rmerge_I_obs 1.355 _reflns_shell.meanI_over_sigI_gt ? _reflns_shell.meanI_over_uI_all ? _reflns_shell.meanI_over_uI_gt ? _reflns_shell.number_measured_gt ? _reflns_shell.number_unique_gt ? _reflns_shell.percent_possible_gt ? _reflns_shell.Rmerge_F_gt ? _reflns_shell.Rmerge_I_gt ? _reflns_shell.pdbx_redundancy 6.6 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_netI_over_sigmaI_all ? _reflns_shell.pdbx_netI_over_sigmaI_obs ? _reflns_shell.pdbx_Rrim_I_all ? _reflns_shell.pdbx_Rpim_I_all ? _reflns_shell.pdbx_rejects ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_CC_half ? _reflns_shell.pdbx_R_split ? # _refine.aniso_B[1][1] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][2] ? _refine.aniso_B[2][3] ? _refine.aniso_B[3][3] ? _refine.B_iso_max ? _refine.B_iso_mean 47.30 _refine.B_iso_min ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.details ? _refine.diff_density_max ? _refine.diff_density_max_esd ? _refine.diff_density_min ? _refine.diff_density_min_esd ? _refine.diff_density_rms ? _refine.diff_density_rms_esd ? _refine.entry_id 4XW0 _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.ls_abs_structure_details ? _refine.ls_abs_structure_Flack ? _refine.ls_abs_structure_Flack_esd ? _refine.ls_abs_structure_Rogers ? _refine.ls_abs_structure_Rogers_esd ? _refine.ls_d_res_high 1.81 _refine.ls_d_res_low 26.910 _refine.ls_extinction_coef ? _refine.ls_extinction_coef_esd ? _refine.ls_extinction_expression ? _refine.ls_extinction_method ? _refine.ls_goodness_of_fit_all ? _refine.ls_goodness_of_fit_all_esd ? _refine.ls_goodness_of_fit_obs ? _refine.ls_goodness_of_fit_obs_esd ? _refine.ls_hydrogen_treatment ? _refine.ls_matrix_type ? _refine.ls_number_constraints ? _refine.ls_number_parameters ? _refine.ls_number_reflns_all ? _refine.ls_number_reflns_obs 5239 _refine.ls_number_reflns_R_free 524 _refine.ls_number_reflns_R_work ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 99.43 _refine.ls_percent_reflns_R_free 10.00 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.2298 _refine.ls_R_factor_R_free 0.2984 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.2237 _refine.ls_R_Fsqd_factor_obs ? _refine.ls_R_I_factor_obs ? _refine.ls_redundancy_reflns_all ? _refine.ls_redundancy_reflns_obs ? _refine.ls_restrained_S_all ? _refine.ls_restrained_S_obs ? _refine.ls_shift_over_esd_max ? _refine.ls_shift_over_esd_mean ? _refine.ls_structure_factor_coef ? _refine.ls_weighting_details ? _refine.ls_weighting_scheme ? _refine.ls_wR_factor_all ? _refine.ls_wR_factor_obs ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.ls_R_factor_gt ? _refine.ls_goodness_of_fit_gt ? _refine.ls_goodness_of_fit_ref ? _refine.ls_shift_over_su_max ? _refine.ls_shift_over_su_max_lt ? _refine.ls_shift_over_su_mean ? _refine.ls_shift_over_su_mean_lt ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 1.37 _refine.pdbx_ls_sigma_Fsqd ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_ls_cross_valid_method 'FREE R-VALUE' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_starting_model 3GLP _refine.pdbx_stereochemistry_target_values TWIN_LSQ_F _refine.pdbx_R_Free_selection_details 'Random selection' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_solvent_vdw_probe_radii 1.11 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.90 _refine.pdbx_real_space_R ? _refine.pdbx_density_correlation ? _refine.pdbx_pd_number_of_powder_patterns ? _refine.pdbx_pd_number_of_points ? _refine.pdbx_pd_meas_number_of_points ? _refine.pdbx_pd_proc_ls_prof_R_factor ? _refine.pdbx_pd_proc_ls_prof_wR_factor ? _refine.pdbx_pd_Marquardt_correlation_coeff ? _refine.pdbx_pd_Fsqrd_R_factor ? _refine.pdbx_pd_ls_matrix_band_width ? _refine.pdbx_overall_phase_error 36.36 _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_diffrn_id 1 _refine.overall_SU_B ? _refine.overall_SU_ML ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_average_fsc_overall ? _refine.pdbx_average_fsc_work ? _refine.pdbx_average_fsc_free ? # _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 397 _refine_hist.pdbx_number_atoms_ligand 10 _refine_hist.number_atoms_solvent 22 _refine_hist.number_atoms_total 429 _refine_hist.d_res_high 1.81 _refine_hist.d_res_low 26.910 # loop_ _refine_ls_restr.pdbx_refine_id _refine_ls_restr.criterion _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.number _refine_ls_restr.rejects _refine_ls_restr.type _refine_ls_restr.weight _refine_ls_restr.pdbx_restraint_function 'X-RAY DIFFRACTION' ? 0.007 ? 478 ? f_bond_d ? ? 'X-RAY DIFFRACTION' ? 1.497 ? 743 ? f_angle_d ? ? 'X-RAY DIFFRACTION' ? 13.957 ? 224 ? f_dihedral_angle_d ? ? 'X-RAY DIFFRACTION' ? 0.051 ? 96 ? f_chiral_restr ? ? 'X-RAY DIFFRACTION' ? 0.008 ? 20 ? f_plane_restr ? ? # loop_ _refine_ls_shell.pdbx_refine_id _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.number_reflns_all _refine_ls_shell.number_reflns_obs _refine_ls_shell.number_reflns_R_free _refine_ls_shell.number_reflns_R_work _refine_ls_shell.percent_reflns_obs _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.R_factor_all _refine_ls_shell.R_factor_obs _refine_ls_shell.R_factor_R_free _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.R_factor_R_work _refine_ls_shell.redundancy_reflns_all _refine_ls_shell.redundancy_reflns_obs _refine_ls_shell.wR_factor_all _refine_ls_shell.wR_factor_obs _refine_ls_shell.wR_factor_R_free _refine_ls_shell.wR_factor_R_work _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.pdbx_phase_error _refine_ls_shell.pdbx_fsc_work _refine_ls_shell.pdbx_fsc_free 'X-RAY DIFFRACTION' 1.8066 1.9882 . . 129 1156 89.00 . . . 0.3712 . 0.3495 . . . . . . . . . . 'X-RAY DIFFRACTION' 1.9882 2.2755 . . 131 1181 90.00 . . . 0.3189 . 0.2962 . . . . . . . . . . 'X-RAY DIFFRACTION' 2.2755 2.8653 . . 131 1183 90.00 . . . 0.3786 . 0.2981 . . . . . . . . . . 'X-RAY DIFFRACTION' 2.8653 19.00 . . 133 1189 89.00 . . . 0.2566 . 0.1729 . . . . . . . . . . # _struct.entry_id 4XW0 _struct.title 'Crystal structure of (GCCU(G-LNA)CCUGC)2 duplex' _struct.pdbx_model_details ? _struct.pdbx_formula_weight ? _struct.pdbx_formula_weight_method ? _struct.pdbx_model_type_details ? _struct.pdbx_CASP_flag ? # _struct_keywords.entry_id 4XW0 _struct_keywords.text ;CCUG repeats, RNA duplex, Myotonic Dystrophy type 2, tautomery, LNA residue, 3' overhanging nucleotides, 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 1 ? C N N 2 ? D N N 2 ? E N N 3 ? F N N 3 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 4XW0 _struct_ref.pdbx_db_accession 4XW0 _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin 1 # 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 4XW0 A 1 ? 10 ? 4XW0 1 ? 10 ? 1 10 2 1 4XW0 B 1 ? 10 ? 4XW0 1 ? 10 ? 1 10 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details 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)' 2190 ? 1 MORE -24 ? 1 'SSA (A^2)' 3790 ? # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F # _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 # 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 U 4 "O3'" ? ? ? 1_555 A LCG 5 P ? ? A U 4 A LCG 5 1_555 ? ? ? ? ? ? ? 1.599 ? ? covale2 covale both ? A LCG 5 "O3'" ? ? ? 1_555 A C 6 P ? ? A LCG 5 A C 6 1_555 ? ? ? ? ? ? ? 1.602 ? ? covale3 covale both ? B U 4 "O3'" ? ? ? 1_555 B LCG 5 P ? ? B U 4 B LCG 5 1_555 ? ? ? ? ? ? ? 1.602 ? ? covale4 covale both ? B LCG 5 "O3'" ? ? ? 1_555 B C 6 P ? ? B LCG 5 B C 6 1_555 ? ? ? ? ? ? ? 1.603 ? ? hydrog1 hydrog ? ? A G 1 N1 ? ? ? 1_555 B C 6 N3 ? ? A G 1 B C 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 B C 6 O2 ? ? A G 1 B C 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 B C 6 N4 ? ? A G 1 B C 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A C 2 N3 ? ? ? 1_555 B LCG 5 N1 ? ? A C 2 B LCG 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A C 2 N4 ? ? ? 1_555 B LCG 5 O6 ? ? A C 2 B LCG 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A C 2 O2 ? ? ? 1_555 B LCG 5 N2 ? ? A C 2 B LCG 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A C 3 N3 ? ? ? 1_555 B U 4 N3 ? ? A C 3 B U 4 1_555 ? ? ? ? ? ? TYPE_18_PAIR ? ? ? hydrog8 hydrog ? ? A C 3 N4 ? ? ? 1_555 B U 4 O4 ? ? A C 3 B U 4 1_555 ? ? ? ? ? ? TYPE_18_PAIR ? ? ? hydrog9 hydrog ? ? A U 4 N3 ? ? ? 1_555 B C 3 N3 ? ? A U 4 B C 3 1_555 ? ? ? ? ? ? TYPE_18_PAIR ? ? ? hydrog10 hydrog ? ? A U 4 O4 ? ? ? 1_555 B C 3 N4 ? ? A U 4 B C 3 1_555 ? ? ? ? ? ? TYPE_18_PAIR ? ? ? hydrog11 hydrog ? ? A LCG 5 N1 ? ? ? 1_555 B C 2 N3 ? ? A LCG 5 B C 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A LCG 5 N2 ? ? ? 1_555 B C 2 O2 ? ? A LCG 5 B C 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A LCG 5 O6 ? ? ? 1_555 B C 2 N4 ? ? A LCG 5 B C 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A C 6 N3 ? ? ? 1_555 B G 1 N1 ? ? A C 6 B G 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A C 6 N4 ? ? ? 1_555 B G 1 O6 ? ? A C 6 B G 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A C 6 O2 ? ? ? 1_555 B G 1 N2 ? ? A C 6 B G 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A U 8 O2 ? ? ? 1_555 A C 10 N4 ? ? A U 8 A C 10 1_555 ? ? ? ? ? ? 'U-C MISPAIR' ? ? ? # 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 SO4 101 ? 2 'binding site for residue SO4 A 101' AC2 Software A SO4 102 ? 4 'binding site for residue SO4 A 102' AC3 Software B LCG 5 ? 8 'binding site for Di-nucleotide LCG B 5 and C B 6' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 2 C A 6 ? C A 6 . ? 1_555 ? 2 AC1 2 C A 7 ? C A 7 . ? 1_555 ? 3 AC2 4 C A 2 ? C A 2 . ? 1_555 ? 4 AC2 4 C A 3 ? C A 3 . ? 1_555 ? 5 AC2 4 HOH E . ? HOH A 202 . ? 1_555 ? 6 AC2 4 HOH E . ? HOH A 210 . ? 1_555 ? 7 AC3 8 G A 1 ? G A 1 . ? 1_555 ? 8 AC3 8 C A 2 ? C A 2 . ? 1_555 ? 9 AC3 8 C A 3 ? C A 3 . ? 1_555 ? 10 AC3 8 LCG A 5 ? LCG A 5 . ? 4_465 ? 11 AC3 8 C A 6 ? C A 6 . ? 4_465 ? 12 AC3 8 U B 4 ? U B 4 . ? 1_555 ? 13 AC3 8 C B 7 ? C B 7 . ? 1_555 ? 14 AC3 8 HOH F . ? HOH B 106 . ? 1_555 ? # 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 C 10 ? ? C2 A C 10 ? ? O2 A C 10 ? ? 124.99 118.90 6.09 0.60 N 2 1 N3 A C 10 ? ? C2 A C 10 ? ? O2 A C 10 ? ? 116.53 121.90 -5.37 0.70 N 3 1 C2 A C 10 ? ? N1 A C 10 ? ? "C1'" A C 10 ? ? 127.60 118.80 8.80 1.10 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 C OP3 O N N 1 C P P N N 2 C OP1 O N N 3 C OP2 O N N 4 C "O5'" O N N 5 C "C5'" C N N 6 C "C4'" C N R 7 C "O4'" O N N 8 C "C3'" C N S 9 C "O3'" O N N 10 C "C2'" C N R 11 C "O2'" O N N 12 C "C1'" C N R 13 C N1 N N N 14 C C2 C N N 15 C O2 O N N 16 C N3 N N N 17 C C4 C N N 18 C N4 N N N 19 C C5 C N N 20 C C6 C N N 21 C HOP3 H N N 22 C HOP2 H N N 23 C "H5'" H N N 24 C "H5''" H N N 25 C "H4'" H N N 26 C "H3'" H N N 27 C "HO3'" H N N 28 C "H2'" H N N 29 C "HO2'" H N N 30 C "H1'" H N N 31 C H41 H N N 32 C H42 H N N 33 C H5 H N N 34 C H6 H N N 35 G OP3 O N N 36 G P P N N 37 G OP1 O N N 38 G OP2 O N N 39 G "O5'" O N N 40 G "C5'" C N N 41 G "C4'" C N R 42 G "O4'" O N N 43 G "C3'" C N S 44 G "O3'" O N N 45 G "C2'" C N R 46 G "O2'" O N N 47 G "C1'" C N R 48 G N9 N Y N 49 G C8 C Y N 50 G N7 N Y N 51 G C5 C Y N 52 G C6 C N N 53 G O6 O N N 54 G N1 N N N 55 G C2 C N N 56 G N2 N N N 57 G N3 N N N 58 G C4 C Y N 59 G HOP3 H N N 60 G HOP2 H N N 61 G "H5'" H N N 62 G "H5''" H N N 63 G "H4'" H N N 64 G "H3'" H N N 65 G "HO3'" H N N 66 G "H2'" H N N 67 G "HO2'" H N N 68 G "H1'" H N N 69 G H8 H N N 70 G H1 H N N 71 G H21 H N N 72 G H22 H N N 73 HOH O O N N 74 HOH H1 H N N 75 HOH H2 H N N 76 LCG P P N N 77 LCG OP1 O N N 78 LCG "O5'" O N N 79 LCG "C5'" C N N 80 LCG "C3'" C N S 81 LCG "C6'" C N N 82 LCG N9 N Y N 83 LCG C8 C Y N 84 LCG C4 C Y N 85 LCG N7 N Y N 86 LCG C5 C Y N 87 LCG C6 C N N 88 LCG "C2'" C N R 89 LCG O6 O N N 90 LCG "C4'" C N R 91 LCG "C1'" C N R 92 LCG C2 C N N 93 LCG N1 N N N 94 LCG "O4'" O N N 95 LCG OP2 O N N 96 LCG N2 N N N 97 LCG N3 N N N 98 LCG "O2'" O N N 99 LCG "O3'" O N N 100 LCG OP3 O N N 101 LCG "H5'" H N N 102 LCG "H5''" H N N 103 LCG "H3'" H N N 104 LCG "H6'1" H N N 105 LCG "H6'2" H N N 106 LCG H8 H N N 107 LCG "H2'" H N N 108 LCG "H1'" H N N 109 LCG H1 H N N 110 LCG HOP2 H N N 111 LCG H21 H N N 112 LCG H22 H N N 113 LCG "HO3'" H N N 114 LCG HOP3 H N N 115 SO4 S S N N 116 SO4 O1 O N N 117 SO4 O2 O N N 118 SO4 O3 O N N 119 SO4 O4 O N N 120 U OP3 O N N 121 U P P N N 122 U OP1 O N N 123 U OP2 O N N 124 U "O5'" O N N 125 U "C5'" C N N 126 U "C4'" C N R 127 U "O4'" O N N 128 U "C3'" C N S 129 U "O3'" O N N 130 U "C2'" C N R 131 U "O2'" O N N 132 U "C1'" C N R 133 U N1 N N N 134 U C2 C N N 135 U O2 O N N 136 U N3 N N N 137 U C4 C N N 138 U O4 O N N 139 U C5 C N N 140 U C6 C N N 141 U HOP3 H N N 142 U HOP2 H N N 143 U "H5'" H N N 144 U "H5''" H N N 145 U "H4'" H N N 146 U "H3'" H N N 147 U "HO3'" H N N 148 U "H2'" H N N 149 U "HO2'" H N N 150 U "H1'" H N N 151 U H3 H N N 152 U H5 H N N 153 U H6 H N N 154 # 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 C OP3 P sing N N 1 C OP3 HOP3 sing N N 2 C P OP1 doub N N 3 C P OP2 sing N N 4 C P "O5'" sing N N 5 C OP2 HOP2 sing N N 6 C "O5'" "C5'" sing N N 7 C "C5'" "C4'" sing N N 8 C "C5'" "H5'" sing N N 9 C "C5'" "H5''" sing N N 10 C "C4'" "O4'" sing N N 11 C "C4'" "C3'" sing N N 12 C "C4'" "H4'" sing N N 13 C "O4'" "C1'" sing N N 14 C "C3'" "O3'" sing N N 15 C "C3'" "C2'" sing N N 16 C "C3'" "H3'" sing N N 17 C "O3'" "HO3'" sing N N 18 C "C2'" "O2'" sing N N 19 C "C2'" "C1'" sing N N 20 C "C2'" "H2'" sing N N 21 C "O2'" "HO2'" sing N N 22 C "C1'" N1 sing N N 23 C "C1'" "H1'" sing N N 24 C N1 C2 sing N N 25 C N1 C6 sing N N 26 C C2 O2 doub N N 27 C C2 N3 sing N N 28 C N3 C4 doub N N 29 C C4 N4 sing N N 30 C C4 C5 sing N N 31 C N4 H41 sing N N 32 C N4 H42 sing N N 33 C C5 C6 doub N N 34 C C5 H5 sing N N 35 C C6 H6 sing N N 36 G OP3 P sing N N 37 G OP3 HOP3 sing N N 38 G P OP1 doub N N 39 G P OP2 sing N N 40 G P "O5'" sing N N 41 G OP2 HOP2 sing N N 42 G "O5'" "C5'" sing N N 43 G "C5'" "C4'" sing N N 44 G "C5'" "H5'" sing N N 45 G "C5'" "H5''" sing N N 46 G "C4'" "O4'" sing N N 47 G "C4'" "C3'" sing N N 48 G "C4'" "H4'" sing N N 49 G "O4'" "C1'" sing N N 50 G "C3'" "O3'" sing N N 51 G "C3'" "C2'" sing N N 52 G "C3'" "H3'" sing N N 53 G "O3'" "HO3'" sing N N 54 G "C2'" "O2'" sing N N 55 G "C2'" "C1'" sing N N 56 G "C2'" "H2'" sing N N 57 G "O2'" "HO2'" sing N N 58 G "C1'" N9 sing N N 59 G "C1'" "H1'" sing N N 60 G N9 C8 sing Y N 61 G N9 C4 sing Y N 62 G C8 N7 doub Y N 63 G C8 H8 sing N N 64 G N7 C5 sing Y N 65 G C5 C6 sing N N 66 G C5 C4 doub Y N 67 G C6 O6 doub N N 68 G C6 N1 sing N N 69 G N1 C2 sing N N 70 G N1 H1 sing N N 71 G C2 N2 sing N N 72 G C2 N3 doub N N 73 G N2 H21 sing N N 74 G N2 H22 sing N N 75 G N3 C4 sing N N 76 HOH O H1 sing N N 77 HOH O H2 sing N N 78 LCG P OP1 doub N N 79 LCG P "O5'" sing N N 80 LCG P OP2 sing N N 81 LCG P OP3 sing N N 82 LCG "O5'" "C5'" sing N N 83 LCG "C5'" "C4'" sing N N 84 LCG "C5'" "H5'" sing N N 85 LCG "C5'" "H5''" sing N N 86 LCG "C3'" "C2'" sing N N 87 LCG "C3'" "C4'" sing N N 88 LCG "C3'" "O3'" sing N N 89 LCG "C3'" "H3'" sing N N 90 LCG "C6'" "C4'" sing N N 91 LCG "C6'" "O2'" sing N N 92 LCG "C6'" "H6'1" sing N N 93 LCG "C6'" "H6'2" sing N N 94 LCG N9 C8 sing Y N 95 LCG N9 C4 sing Y N 96 LCG N9 "C1'" sing N N 97 LCG C8 N7 doub Y N 98 LCG C8 H8 sing N N 99 LCG C4 C5 doub Y N 100 LCG C4 N3 sing N N 101 LCG N7 C5 sing Y N 102 LCG C5 C6 sing N N 103 LCG C6 O6 doub N N 104 LCG C6 N1 sing N N 105 LCG "C2'" "C1'" sing N N 106 LCG "C2'" "O2'" sing N N 107 LCG "C2'" "H2'" sing N N 108 LCG "C4'" "O4'" sing N N 109 LCG "C1'" "O4'" sing N N 110 LCG "C1'" "H1'" sing N N 111 LCG C2 N1 sing N N 112 LCG C2 N2 sing N N 113 LCG C2 N3 doub N N 114 LCG N1 H1 sing N N 115 LCG OP2 HOP2 sing N N 116 LCG N2 H21 sing N N 117 LCG N2 H22 sing N N 118 LCG "O3'" "HO3'" sing N N 119 LCG OP3 HOP3 sing N N 120 SO4 S O1 doub N N 121 SO4 S O2 doub N N 122 SO4 S O3 sing N N 123 SO4 S O4 sing N N 124 U OP3 P sing N N 125 U OP3 HOP3 sing N N 126 U P OP1 doub N N 127 U P OP2 sing N N 128 U P "O5'" sing N N 129 U OP2 HOP2 sing N N 130 U "O5'" "C5'" sing N N 131 U "C5'" "C4'" sing N N 132 U "C5'" "H5'" sing N N 133 U "C5'" "H5''" sing N N 134 U "C4'" "O4'" sing N N 135 U "C4'" "C3'" sing N N 136 U "C4'" "H4'" sing N N 137 U "O4'" "C1'" sing N N 138 U "C3'" "O3'" sing N N 139 U "C3'" "C2'" sing N N 140 U "C3'" "H3'" sing N N 141 U "O3'" "HO3'" sing N N 142 U "C2'" "O2'" sing N N 143 U "C2'" "C1'" sing N N 144 U "C2'" "H2'" sing N N 145 U "O2'" "HO2'" sing N N 146 U "C1'" N1 sing N N 147 U "C1'" "H1'" sing N N 148 U N1 C2 sing N N 149 U N1 C6 sing N N 150 U C2 O2 doub N N 151 U C2 N3 sing N N 152 U N3 C4 sing N N 153 U N3 H3 sing N N 154 U C4 O4 doub N N 155 U C4 C5 sing N N 156 U C5 C6 doub N N 157 U C5 H5 sing N N 158 U C6 H6 sing N N 159 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 4XW0 'double helix' 4XW0 '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 G 1 1_555 B C 6 1_555 -0.258 -0.321 -0.141 -2.037 -3.495 -2.974 1 A_G1:C6_B A 1 ? B 6 ? 19 1 1 A C 2 1_555 B LCG 5 1_555 0.445 -0.037 -0.228 0.605 -7.346 0.370 2 A_C2:LCG5_B A 2 ? B 5 ? 19 1 1 A C 3 1_555 B U 4 1_555 0.386 -1.668 0.382 7.195 -5.746 15.043 3 A_C3:U4_B A 3 ? B 4 ? 18 1 1 A U 4 1_555 B C 3 1_555 -0.318 -1.431 0.239 -4.976 -8.928 18.064 4 A_U4:C3_B A 4 ? B 3 ? 18 1 1 A LCG 5 1_555 B C 2 1_555 -0.219 -0.092 -0.095 1.805 -5.834 1.916 5 A_LCG5:C2_B A 5 ? B 2 ? 19 1 1 A C 6 1_555 B G 1 1_555 0.420 -0.099 -0.013 1.248 -0.406 -0.706 6 A_C6:G1_B A 6 ? B 1 ? 19 1 1 A U 8 1_555 A C 10 1_555 6.510 0.839 -0.820 12.141 -18.660 -6.151 7 A_U8:C10_A A 8 ? A 10 ? ? 9 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A G 1 1_555 B C 6 1_555 A C 2 1_555 B LCG 5 1_555 -0.420 -1.859 3.322 -1.502 3.377 31.628 -3.998 0.494 3.128 6.170 2.745 31.838 1 AA_G1C2:LCG5C6_BB A 1 ? B 6 ? A 2 ? B 5 ? 1 A C 2 1_555 B LCG 5 1_555 A C 3 1_555 B U 4 1_555 0.384 -1.626 3.117 -6.445 11.705 25.931 -5.382 -1.947 2.056 24.150 13.298 29.119 2 AA_C2C3:U4LCG5_BB A 2 ? B 5 ? A 3 ? B 4 ? 1 A C 3 1_555 B U 4 1_555 A U 4 1_555 B C 3 1_555 0.151 -1.123 3.618 3.225 18.678 34.364 -3.994 0.175 2.685 29.040 -5.014 39.106 3 AA_C3U4:C3U4_BB A 3 ? B 4 ? A 4 ? B 3 ? 1 A U 4 1_555 B C 3 1_555 A LCG 5 1_555 B C 2 1_555 -0.451 -1.378 3.079 3.747 12.534 25.653 -5.139 1.615 2.105 26.171 -7.824 28.746 4 AA_U4LCG5:C2C3_BB A 4 ? B 3 ? A 5 ? B 2 ? 1 A LCG 5 1_555 B C 2 1_555 A C 6 1_555 B G 1 1_555 0.409 -1.935 3.354 0.314 3.523 31.801 -4.143 -0.685 3.131 6.404 -0.570 31.992 5 AA_LCG5C6:G1C2_BB A 5 ? B 2 ? A 6 ? B 1 ? # _pdbx_audit_support.funding_organization 'National Science Centre' _pdbx_audit_support.country Poland _pdbx_audit_support.grant_number UMO-2011/01/B/NZ1/04429 _pdbx_audit_support.ordinal 1 # _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.accession_code 3GLP _pdbx_initial_refinement_model.details ? # _atom_sites.entry_id 4XW0 _atom_sites.fract_transf_matrix[1][1] 0.037161 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.037161 _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] 0.012422 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C N O P S # loop_