data_6IBQ # _entry.id 6IBQ # _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 6IBQ pdb_00006ibq 10.2210/pdb6ibq/pdb WWPDB D_1200013099 ? ? # 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 2019-05-01 2 'Structure model' 1 1 2019-05-29 3 'Structure model' 1 2 2024-01-24 # _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 3 'Structure model' 'Data collection' 4 3 'Structure model' 'Database references' 5 3 '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' citation 2 2 'Structure model' citation_author 3 2 'Structure model' pdbx_database_proc 4 2 'Structure model' pdbx_seq_map_depositor_info 5 3 'Structure model' chem_comp_atom 6 3 'Structure model' chem_comp_bond 7 3 'Structure model' database_2 8 3 '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' '_citation.journal_volume' 2 2 'Structure model' '_citation.page_first' 3 2 'Structure model' '_citation.page_last' 4 2 'Structure model' '_citation.pdbx_database_id_PubMed' 5 2 'Structure model' '_citation.title' 6 2 'Structure model' '_pdbx_seq_map_depositor_info.one_letter_code_mod' 7 3 'Structure model' '_database_2.pdbx_DOI' 8 3 '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 6IBQ _pdbx_database_status.recvd_initial_deposition_date 2018-11-30 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site PDBE _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 _audit_author.identifier_ORCID 'de Wijn, R.' 1 0000-0002-8342-1008 'Olieric, V.' 2 0000-0002-0533-7222 'Lorber, B.' 3 0000-0002-4672-9652 'Sauter, C.' 4 0000-0002-8766-287X # loop_ _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 _citation.database_id_Medline _citation.details _citation.id _citation.journal_abbrev _citation.journal_id_ASTM _citation.journal_id_CSD _citation.journal_id_ISSN _citation.journal_full _citation.journal_issue _citation.journal_volume _citation.language _citation.page_first _citation.page_last _citation.title _citation.year _citation.database_id_CSD _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.unpublished_flag ? ? ? ? ? ? ? UK ? ? primary Iucrj ? ? 2052-2525 ? ? 6 ? 454 464 ;A simple and versatile microfluidic device for efficient biomacromolecule crystallization and structural analysis by serial crystallography. ; 2019 ? 10.1107/S2052252519003622 31098026 ? ? ? ? ? ? ? ? UK ? ? 1 RNA RNARFU 2122 1355-8382 ? ? 5 ? 1384 1395 'A sulfate pocket formed by three GoU pairs in the 0.97 A resolution X-ray structure of a nonameric RNA.' 1999 ? ? 10573129 ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'de Wijn, R.' 1 ? primary 'Hennig, O.' 2 ? primary 'Roche, J.' 3 ? primary 'Engilberge, S.' 4 ? primary 'Rollet, K.' 5 ? primary 'Fernandez-Millan, P.' 6 ? primary 'Brillet, K.' 7 ? primary 'Betat, H.' 8 ? primary 'Morl, M.' 9 ? primary 'Roussel, A.' 10 ? primary 'Girard, E.' 11 ? primary 'Mueller-Dieckmann, C.' 12 ? primary 'Fox, G.C.' 13 ? primary 'Olieric, V.' 14 ? primary 'Gavira, J.A.' 15 ? primary 'Lorber, B.' 16 ? primary 'Sauter, C.' 17 ? 1 'Masquida, B.' 18 ? 1 'Sauter, C.' 19 0000-0002-8766-287X 1 'Westhof, E.' 20 ? # 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 ;DNA/RNA (5'-R(*CP*GP*UP*GP*AP*UP*CP*G)-D(P*C)-3') ; 2831.743 2 ? ? ? ? 2 non-polymer syn 'SULFATE ION' 96.063 1 ? ? ? ? 3 water nat water 18.015 43 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type 'polydeoxyribonucleotide/polyribonucleotide hybrid' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code 'CGUGAUCG(DC)' _entity_poly.pdbx_seq_one_letter_code_can CGUGAUCGC _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 C n 1 2 G n 1 3 U n 1 4 G n 1 5 A n 1 6 U n 1 7 C n 1 8 G n 1 9 DC 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 9 _pdbx_entity_src_syn.organism_scientific Rattus _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 10114 _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 A 'RNA linking' y "ADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 HOH non-polymer . WATER ? 'H2 O' 18.015 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 C 1 1 1 C C A . n A 1 2 G 2 2 2 G G A . n A 1 3 U 3 3 3 U U A . n A 1 4 G 4 4 4 G G A . n A 1 5 A 5 5 5 A A A . n A 1 6 U 6 6 6 U U A . n A 1 7 C 7 7 7 C C A . n A 1 8 G 8 8 8 G G A . n A 1 9 DC 9 9 9 DC DC A . n B 1 1 C 1 11 11 C C B . n B 1 2 G 2 12 12 G G B . n B 1 3 U 3 13 13 U U B . n B 1 4 G 4 14 14 G G B . n B 1 5 A 5 15 15 A A B . n B 1 6 U 6 16 16 U U B . n B 1 7 C 7 17 17 C C B . n B 1 8 G 8 18 18 G G B . n B 1 9 DC 9 19 19 DC DC 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 B . D 3 HOH 1 101 30 HOH HOH A . D 3 HOH 2 102 17 HOH HOH A . D 3 HOH 3 103 39 HOH HOH A . D 3 HOH 4 104 29 HOH HOH A . D 3 HOH 5 105 8 HOH HOH A . D 3 HOH 6 106 47 HOH HOH A . D 3 HOH 7 107 9 HOH HOH A . D 3 HOH 8 108 27 HOH HOH A . D 3 HOH 9 109 25 HOH HOH A . D 3 HOH 10 110 15 HOH HOH A . D 3 HOH 11 111 41 HOH HOH A . D 3 HOH 12 112 32 HOH HOH A . D 3 HOH 13 113 22 HOH HOH A . D 3 HOH 14 114 31 HOH HOH A . D 3 HOH 15 115 24 HOH HOH A . D 3 HOH 16 116 43 HOH HOH A . E 3 HOH 1 201 10 HOH HOH B . E 3 HOH 2 202 12 HOH HOH B . E 3 HOH 3 203 7 HOH HOH B . E 3 HOH 4 204 13 HOH HOH B . E 3 HOH 5 205 34 HOH HOH B . E 3 HOH 6 206 48 HOH HOH B . E 3 HOH 7 207 16 HOH HOH B . E 3 HOH 8 208 28 HOH HOH B . E 3 HOH 9 209 5 HOH HOH B . E 3 HOH 10 210 35 HOH HOH B . E 3 HOH 11 211 6 HOH HOH B . E 3 HOH 12 212 33 HOH HOH B . E 3 HOH 13 213 49 HOH HOH B . E 3 HOH 14 214 11 HOH HOH B . E 3 HOH 15 215 3 HOH HOH B . E 3 HOH 16 216 36 HOH HOH B . E 3 HOH 17 217 14 HOH HOH B . E 3 HOH 18 218 18 HOH HOH B . E 3 HOH 19 219 40 HOH HOH B . E 3 HOH 20 220 2 HOH HOH B . E 3 HOH 21 221 26 HOH HOH B . E 3 HOH 22 222 21 HOH HOH B . E 3 HOH 23 223 19 HOH HOH B . E 3 HOH 24 224 46 HOH HOH B . E 3 HOH 25 225 45 HOH HOH B . E 3 HOH 26 226 44 HOH HOH B . E 3 HOH 27 227 42 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 A C 1 ? "O5'" ? A C 1 "O5'" 2 1 Y 1 A C 1 ? "C5'" ? A C 1 "C5'" 3 1 Y 1 A C 1 ? "C4'" ? A C 1 "C4'" 4 1 Y 1 A C 1 ? "O4'" ? A C 1 "O4'" 5 1 Y 1 A C 1 ? "C3'" ? A C 1 "C3'" 6 1 Y 1 A C 1 ? "C2'" ? A C 1 "C2'" 7 1 Y 1 A C 1 ? "O2'" ? A C 1 "O2'" 8 1 Y 1 A C 1 ? "C1'" ? A C 1 "C1'" 9 1 Y 1 A C 1 ? N1 ? A C 1 N1 10 1 Y 1 A C 1 ? C2 ? A C 1 C2 11 1 Y 1 A C 1 ? O2 ? A C 1 O2 12 1 Y 1 A C 1 ? N3 ? A C 1 N3 13 1 Y 1 A C 1 ? C4 ? A C 1 C4 14 1 Y 1 A C 1 ? N4 ? A C 1 N4 15 1 Y 1 A C 1 ? C5 ? A C 1 C5 16 1 Y 1 A C 1 ? C6 ? A C 1 C6 17 1 Y 1 B C 11 ? "O5'" ? B C 1 "O5'" 18 1 Y 1 B C 11 ? "C5'" ? B C 1 "C5'" 19 1 Y 1 B C 11 ? "C4'" ? B C 1 "C4'" 20 1 Y 1 B C 11 ? "O4'" ? B C 1 "O4'" 21 1 Y 1 B C 11 ? "C3'" ? B C 1 "C3'" 22 1 Y 1 B C 11 ? "C2'" ? B C 1 "C2'" 23 1 Y 1 B C 11 ? "O2'" ? B C 1 "O2'" 24 1 Y 1 B C 11 ? "C1'" ? B C 1 "C1'" 25 1 Y 1 B C 11 ? N1 ? B C 1 N1 26 1 Y 1 B C 11 ? C2 ? B C 1 C2 27 1 Y 1 B C 11 ? O2 ? B C 1 O2 28 1 Y 1 B C 11 ? N3 ? B C 1 N3 29 1 Y 1 B C 11 ? C4 ? B C 1 C4 30 1 Y 1 B C 11 ? N4 ? B C 1 N4 31 1 Y 1 B C 11 ? C5 ? B C 1 C5 32 1 Y 1 B C 11 ? C6 ? B C 1 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 ? ? ? 1.13_2998 1 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? XDS ? ? ? 20180808 2 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? XSCALE ? ? ? 20180808 3 ? phasing ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? 1.13_2998 4 # _cell.angle_alpha 90.00 _cell.angle_alpha_esd ? _cell.angle_beta 90.00 _cell.angle_beta_esd ? _cell.angle_gamma 120.00 _cell.angle_gamma_esd ? _cell.entry_id 6IBQ _cell.details ? _cell.formula_units_Z ? _cell.length_a 40.000 _cell.length_a_esd ? _cell.length_b 40.000 _cell.length_b_esd ? _cell.length_c 69.110 _cell.length_c_esd ? _cell.volume ? _cell.volume_esd ? _cell.Z_PDB 18 _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 6IBQ _symmetry.cell_setting ? _symmetry.Int_Tables_number 146 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3' _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 6IBQ _exptl.crystals_number 1 _exptl.details ? _exptl.method 'X-RAY DIFFRACTION' _exptl.method_details ? # _exptl_crystal.colour ? _exptl_crystal.density_diffrn ? _exptl_crystal.density_Matthews 1.83 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 54.7 _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 COUNTER-DIFFUSION _exptl_crystal_grow.method_ref ? _exptl_crystal_grow.pH 6.0 _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp 300 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details ;RNA solution: 10 mg/mL in 10 mM Na-cacodylate pH 6.0, 5 mM MgCl2. Reservoir solution: 2.6 M ammonium sulfate, 50 mM Na-cacodylate pH 6.0, 5 mM MgSO4, 1 mM spermine. Crystallization and crystallographic analysis were performed using the ChipX microfluidic device. ; _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.ambient_environment ? _diffrn.ambient_temp 293 _diffrn.ambient_temp_details 'in situ' _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.pdbx_serial_crystal_experiment N # _diffrn_detector.details ? _diffrn_detector.detector CCD _diffrn_detector.diffrn_id 1 _diffrn_detector.type 'MARMOSAIC 225 mm CCD' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2011-08-31 _diffrn_detector.pdbx_frequency ? # _diffrn_radiation.collimation ? _diffrn_radiation.diffrn_id 1 _diffrn_radiation.filter_edge ? _diffrn_radiation.inhomogeneity ? _diffrn_radiation.monochromator 'Bartel monochromator with dual channel cut crystals (DCCM)' _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 1.000 _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 'SLS BEAMLINE X06DA' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 1.000 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline X06DA _diffrn_source.pdbx_synchrotron_site SLS # _reflns.B_iso_Wilson_estimate 23.6 _reflns.entry_id 6IBQ _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 1.55 _reflns.d_resolution_low 24. _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 5485 _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 -3 _reflns.percent_possible_obs 91.5 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 3.9 _reflns.pdbx_Rmerge_I_obs 0.157 _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 6.1 _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 0.179 _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 0.988 _reflns.pdbx_R_split ? # _reflns_shell.d_res_high 1.55 _reflns_shell.d_res_low 1.59 _reflns_shell.meanI_over_sigI_all ? _reflns_shell.meanI_over_sigI_obs 1.8 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_possible ? _reflns_shell.number_unique_all ? _reflns_shell.number_unique_obs 304 _reflns_shell.percent_possible_all 69.7 _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 0.367 _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 2.0 _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 0.455 _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 0.755 _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 ? _refine.B_iso_min ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.details ;The structure was refined using data collected on four crystals at room temperature. The first nucleotide of each chain was not visible in the electron density and is not included in the model. ; _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 6IBQ _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 1.550 _refine.ls_d_res_low 23.037 _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 5484 _refine.ls_number_reflns_R_free 382 _refine.ls_number_reflns_R_work ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 91.52 _refine.ls_percent_reflns_R_free 6.97 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.2073 _refine.ls_R_factor_R_free 0.2228 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.1924 _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 ? _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 2.55 _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 THROUGHOUT _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_starting_model 485D _refine.pdbx_stereochemistry_target_values ? _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 25.79 _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 342 _refine_hist.pdbx_number_atoms_ligand 5 _refine_hist.number_atoms_solvent 43 _refine_hist.number_atoms_total 390 _refine_hist.d_res_high 1.550 _refine_hist.d_res_low 23.037 # 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' ? 0.004 ? 384 ? f_bond_d ? ? 'X-RAY DIFFRACTION' ? 0.680 ? 596 ? f_angle_d ? ? 'X-RAY DIFFRACTION' ? 8.740 ? 182 ? f_dihedral_angle_d ? ? 'X-RAY DIFFRACTION' ? 0.031 ? 78 ? f_chiral_restr ? ? 'X-RAY DIFFRACTION' ? 0.003 ? 16 ? f_plane_restr ? ? # _struct.entry_id 6IBQ _struct.title 'Structure of a nonameric RNA duplex at room temperature in ChipX microfluidic device' _struct.pdbx_model_details ? _struct.pdbx_formula_weight ? _struct.pdbx_formula_weight_method ? _struct.pdbx_model_type_details ? _struct.pdbx_CASP_flag N # _struct_keywords.entry_id 6IBQ _struct_keywords.text 'RNA duplex, GoU pair, chipx, 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 3 ? E N N 3 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 6IBQ _struct_ref.pdbx_db_accession 6IBQ _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 6IBQ A 1 ? 9 ? 6IBQ 1 ? 9 ? 1 9 2 1 6IBQ B 1 ? 9 ? 6IBQ 11 ? 19 ? 11 19 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 860 ? 1 MORE -9 ? 1 'SSA (A^2)' 3360 ? # _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 # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support 'native gel electrophoresis' _pdbx_struct_assembly_auth_evidence.details ? # _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 hydrog1 hydrog ? ? A G 2 N1 ? ? ? 1_555 B DC 9 N3 ? ? A G 2 B DC 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 2 N2 ? ? ? 1_555 B DC 9 O2 ? ? A G 2 B DC 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 2 O6 ? ? ? 1_555 B DC 9 N4 ? ? A G 2 B DC 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A U 3 N3 ? ? ? 1_555 B G 8 O6 ? ? A U 3 B G 18 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog5 hydrog ? ? A U 3 O2 ? ? ? 1_555 B G 8 N1 ? ? A U 3 B G 18 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog6 hydrog ? ? A G 4 N1 ? ? ? 1_555 B C 7 N3 ? ? A G 4 B C 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A G 4 N2 ? ? ? 1_555 B C 7 O2 ? ? A G 4 B C 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A G 4 O6 ? ? ? 1_555 B C 7 N4 ? ? A G 4 B C 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A A 5 N1 ? ? ? 1_555 B U 6 N3 ? ? A A 5 B U 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A A 5 N6 ? ? ? 1_555 B U 6 O4 ? ? A A 5 B U 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A U 6 N3 ? ? ? 1_555 B A 5 N1 ? ? A U 6 B A 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A U 6 O4 ? ? ? 1_555 B A 5 N6 ? ? A U 6 B A 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A C 7 N3 ? ? ? 1_555 B G 4 N1 ? ? A C 7 B G 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A C 7 N4 ? ? ? 1_555 B G 4 O6 ? ? A C 7 B G 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A C 7 O2 ? ? ? 1_555 B G 4 N2 ? ? A C 7 B G 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A G 8 N1 ? ? ? 1_555 B U 3 O2 ? ? A G 8 B U 13 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog17 hydrog ? ? A G 8 O6 ? ? ? 1_555 B U 3 N3 ? ? A G 8 B U 13 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog18 hydrog ? ? A DC 9 N3 ? ? ? 1_555 B G 2 N1 ? ? A DC 9 B G 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DC 9 N4 ? ? ? 1_555 B G 2 O6 ? ? A DC 9 B G 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DC 9 O2 ? ? ? 1_555 B G 2 N2 ? ? A DC 9 B G 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _struct_site.pdbx_auth_asym_id B _struct_site.pdbx_auth_comp_id SO4 _struct_site.pdbx_auth_seq_id 101 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 9 _struct_site.details 'binding site for residue SO4 B 101' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 9 HOH D . ? HOH A 106 . ? 2_655 ? 2 AC1 9 G B 8 ? G B 18 . ? 3_665 ? 3 AC1 9 G B 8 ? G B 18 . ? 2_655 ? 4 AC1 9 G B 8 ? G B 18 . ? 1_555 ? 5 AC1 9 DC B 9 ? DC B 19 . ? 2_655 ? 6 AC1 9 DC B 9 ? DC B 19 . ? 3_665 ? 7 AC1 9 HOH E . ? HOH B 202 . ? 3_665 ? 8 AC1 9 HOH E . ? HOH B 202 . ? 1_555 ? 9 AC1 9 HOH E . ? HOH B 202 . ? 2_655 ? # 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 "O3'" A C 1 ? ? P A G 2 ? ? 1.482 1.607 -0.125 0.012 Y 2 1 "O3'" B C 11 ? ? P B G 12 ? ? 1.474 1.607 -0.133 0.012 Y # 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 B SO4 101 ? C SO4 . 2 1 A HOH 102 ? D HOH . 3 1 A HOH 107 ? D HOH . 4 1 B HOH 211 ? E HOH . 5 1 B HOH 220 ? E HOH . # _pdbx_distant_solvent_atoms.id 1 _pdbx_distant_solvent_atoms.PDB_model_num 1 _pdbx_distant_solvent_atoms.auth_atom_id O _pdbx_distant_solvent_atoms.label_alt_id ? _pdbx_distant_solvent_atoms.auth_asym_id B _pdbx_distant_solvent_atoms.auth_comp_id HOH _pdbx_distant_solvent_atoms.auth_seq_id 227 _pdbx_distant_solvent_atoms.PDB_ins_code ? _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance 6.39 _pdbx_distant_solvent_atoms.neighbor_ligand_distance . # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal A OP3 O N N 1 A P P N N 2 A OP1 O N N 3 A OP2 O N N 4 A "O5'" O N N 5 A "C5'" C N N 6 A "C4'" C N R 7 A "O4'" O N N 8 A "C3'" C N S 9 A "O3'" O N N 10 A "C2'" C N R 11 A "O2'" O N N 12 A "C1'" C N R 13 A N9 N Y N 14 A C8 C Y N 15 A N7 N Y N 16 A C5 C Y N 17 A C6 C Y N 18 A N6 N N N 19 A N1 N Y N 20 A C2 C Y N 21 A N3 N Y N 22 A C4 C Y N 23 A HOP3 H N N 24 A HOP2 H N N 25 A "H5'" H N N 26 A "H5''" H N N 27 A "H4'" H N N 28 A "H3'" H N N 29 A "HO3'" H N N 30 A "H2'" H N N 31 A "HO2'" H N N 32 A "H1'" H N N 33 A H8 H N N 34 A H61 H N N 35 A H62 H N N 36 A H2 H N N 37 C OP3 O N N 38 C P P N N 39 C OP1 O N N 40 C OP2 O N N 41 C "O5'" O N N 42 C "C5'" C N N 43 C "C4'" C N R 44 C "O4'" O N N 45 C "C3'" C N S 46 C "O3'" O N N 47 C "C2'" C N R 48 C "O2'" O N N 49 C "C1'" C N R 50 C N1 N N N 51 C C2 C N N 52 C O2 O N N 53 C N3 N N N 54 C C4 C N N 55 C N4 N N N 56 C C5 C N N 57 C C6 C N N 58 C HOP3 H N N 59 C HOP2 H N N 60 C "H5'" H N N 61 C "H5''" H N N 62 C "H4'" H N N 63 C "H3'" H N N 64 C "HO3'" H N N 65 C "H2'" H N N 66 C "HO2'" H N N 67 C "H1'" H N N 68 C H41 H N N 69 C H42 H N N 70 C H5 H N N 71 C H6 H N N 72 DC OP3 O N N 73 DC P P N N 74 DC OP1 O N N 75 DC OP2 O N N 76 DC "O5'" O N N 77 DC "C5'" C N N 78 DC "C4'" C N R 79 DC "O4'" O N N 80 DC "C3'" C N S 81 DC "O3'" O N N 82 DC "C2'" C N N 83 DC "C1'" C N R 84 DC N1 N N N 85 DC C2 C N N 86 DC O2 O N N 87 DC N3 N N N 88 DC C4 C N N 89 DC N4 N N N 90 DC C5 C N N 91 DC C6 C N N 92 DC HOP3 H N N 93 DC HOP2 H N N 94 DC "H5'" H N N 95 DC "H5''" H N N 96 DC "H4'" H N N 97 DC "H3'" H N N 98 DC "HO3'" H N N 99 DC "H2'" H N N 100 DC "H2''" H N N 101 DC "H1'" H N N 102 DC H41 H N N 103 DC H42 H N N 104 DC H5 H N N 105 DC H6 H N N 106 G OP3 O N N 107 G P P N N 108 G OP1 O N N 109 G OP2 O N N 110 G "O5'" O N N 111 G "C5'" C N N 112 G "C4'" C N R 113 G "O4'" O N N 114 G "C3'" C N S 115 G "O3'" O N N 116 G "C2'" C N R 117 G "O2'" O N N 118 G "C1'" C N R 119 G N9 N Y N 120 G C8 C Y N 121 G N7 N Y N 122 G C5 C Y N 123 G C6 C N N 124 G O6 O N N 125 G N1 N N N 126 G C2 C N N 127 G N2 N N N 128 G N3 N N N 129 G C4 C Y N 130 G HOP3 H N N 131 G HOP2 H N N 132 G "H5'" H N N 133 G "H5''" H N N 134 G "H4'" H N N 135 G "H3'" H N N 136 G "HO3'" H N N 137 G "H2'" H N N 138 G "HO2'" H N N 139 G "H1'" H N N 140 G H8 H N N 141 G H1 H N N 142 G H21 H N N 143 G H22 H N N 144 HOH O O N N 145 HOH H1 H N N 146 HOH H2 H N N 147 SO4 S S N N 148 SO4 O1 O N N 149 SO4 O2 O N N 150 SO4 O3 O N N 151 SO4 O4 O N N 152 U OP3 O N N 153 U P P N N 154 U OP1 O N N 155 U OP2 O N N 156 U "O5'" O N N 157 U "C5'" C N N 158 U "C4'" C N R 159 U "O4'" O N N 160 U "C3'" C N S 161 U "O3'" O N N 162 U "C2'" C N R 163 U "O2'" O N N 164 U "C1'" C N R 165 U N1 N N N 166 U C2 C N N 167 U O2 O N N 168 U N3 N N N 169 U C4 C N N 170 U O4 O N N 171 U C5 C N N 172 U C6 C N N 173 U HOP3 H N N 174 U HOP2 H N N 175 U "H5'" H N N 176 U "H5''" H N N 177 U "H4'" H N N 178 U "H3'" H N N 179 U "HO3'" H N N 180 U "H2'" H N N 181 U "HO2'" H N N 182 U "H1'" H N N 183 U H3 H N N 184 U H5 H N N 185 U H6 H N N 186 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal A OP3 P sing N N 1 A OP3 HOP3 sing N N 2 A P OP1 doub N N 3 A P OP2 sing N N 4 A P "O5'" sing N N 5 A OP2 HOP2 sing N N 6 A "O5'" "C5'" sing N N 7 A "C5'" "C4'" sing N N 8 A "C5'" "H5'" sing N N 9 A "C5'" "H5''" sing N N 10 A "C4'" "O4'" sing N N 11 A "C4'" "C3'" sing N N 12 A "C4'" "H4'" sing N N 13 A "O4'" "C1'" sing N N 14 A "C3'" "O3'" sing N N 15 A "C3'" "C2'" sing N N 16 A "C3'" "H3'" sing N N 17 A "O3'" "HO3'" sing N N 18 A "C2'" "O2'" sing N N 19 A "C2'" "C1'" sing N N 20 A "C2'" "H2'" sing N N 21 A "O2'" "HO2'" sing N N 22 A "C1'" N9 sing N N 23 A "C1'" "H1'" sing N N 24 A N9 C8 sing Y N 25 A N9 C4 sing Y N 26 A C8 N7 doub Y N 27 A C8 H8 sing N N 28 A N7 C5 sing Y N 29 A C5 C6 sing Y N 30 A C5 C4 doub Y N 31 A C6 N6 sing N N 32 A C6 N1 doub Y N 33 A N6 H61 sing N N 34 A N6 H62 sing N N 35 A N1 C2 sing Y N 36 A C2 N3 doub Y N 37 A C2 H2 sing N N 38 A N3 C4 sing Y N 39 C OP3 P sing N N 40 C OP3 HOP3 sing N N 41 C P OP1 doub N N 42 C P OP2 sing N N 43 C P "O5'" sing N N 44 C OP2 HOP2 sing N N 45 C "O5'" "C5'" sing N N 46 C "C5'" "C4'" sing N N 47 C "C5'" "H5'" sing N N 48 C "C5'" "H5''" sing N N 49 C "C4'" "O4'" sing N N 50 C "C4'" "C3'" sing N N 51 C "C4'" "H4'" sing N N 52 C "O4'" "C1'" sing N N 53 C "C3'" "O3'" sing N N 54 C "C3'" "C2'" sing N N 55 C "C3'" "H3'" sing N N 56 C "O3'" "HO3'" sing N N 57 C "C2'" "O2'" sing N N 58 C "C2'" "C1'" sing N N 59 C "C2'" "H2'" sing N N 60 C "O2'" "HO2'" sing N N 61 C "C1'" N1 sing N N 62 C "C1'" "H1'" sing N N 63 C N1 C2 sing N N 64 C N1 C6 sing N N 65 C C2 O2 doub N N 66 C C2 N3 sing N N 67 C N3 C4 doub N N 68 C C4 N4 sing N N 69 C C4 C5 sing N N 70 C N4 H41 sing N N 71 C N4 H42 sing N N 72 C C5 C6 doub N N 73 C C5 H5 sing N N 74 C C6 H6 sing N N 75 DC OP3 P sing N N 76 DC OP3 HOP3 sing N N 77 DC P OP1 doub N N 78 DC P OP2 sing N N 79 DC P "O5'" sing N N 80 DC OP2 HOP2 sing N N 81 DC "O5'" "C5'" sing N N 82 DC "C5'" "C4'" sing N N 83 DC "C5'" "H5'" sing N N 84 DC "C5'" "H5''" sing N N 85 DC "C4'" "O4'" sing N N 86 DC "C4'" "C3'" sing N N 87 DC "C4'" "H4'" sing N N 88 DC "O4'" "C1'" sing N N 89 DC "C3'" "O3'" sing N N 90 DC "C3'" "C2'" sing N N 91 DC "C3'" "H3'" sing N N 92 DC "O3'" "HO3'" sing N N 93 DC "C2'" "C1'" sing N N 94 DC "C2'" "H2'" sing N N 95 DC "C2'" "H2''" sing N N 96 DC "C1'" N1 sing N N 97 DC "C1'" "H1'" sing N N 98 DC N1 C2 sing N N 99 DC N1 C6 sing N N 100 DC C2 O2 doub N N 101 DC C2 N3 sing N N 102 DC N3 C4 doub N N 103 DC C4 N4 sing N N 104 DC C4 C5 sing N N 105 DC N4 H41 sing N N 106 DC N4 H42 sing N N 107 DC C5 C6 doub N N 108 DC C5 H5 sing N N 109 DC C6 H6 sing N N 110 G OP3 P sing N N 111 G OP3 HOP3 sing N N 112 G P OP1 doub N N 113 G P OP2 sing N N 114 G P "O5'" sing N N 115 G OP2 HOP2 sing N N 116 G "O5'" "C5'" sing N N 117 G "C5'" "C4'" sing N N 118 G "C5'" "H5'" sing N N 119 G "C5'" "H5''" sing N N 120 G "C4'" "O4'" sing N N 121 G "C4'" "C3'" sing N N 122 G "C4'" "H4'" sing N N 123 G "O4'" "C1'" sing N N 124 G "C3'" "O3'" sing N N 125 G "C3'" "C2'" sing N N 126 G "C3'" "H3'" sing N N 127 G "O3'" "HO3'" sing N N 128 G "C2'" "O2'" sing N N 129 G "C2'" "C1'" sing N N 130 G "C2'" "H2'" sing N N 131 G "O2'" "HO2'" sing N N 132 G "C1'" N9 sing N N 133 G "C1'" "H1'" sing N N 134 G N9 C8 sing Y N 135 G N9 C4 sing Y N 136 G C8 N7 doub Y N 137 G C8 H8 sing N N 138 G N7 C5 sing Y N 139 G C5 C6 sing N N 140 G C5 C4 doub Y N 141 G C6 O6 doub N N 142 G C6 N1 sing N N 143 G N1 C2 sing N N 144 G N1 H1 sing N N 145 G C2 N2 sing N N 146 G C2 N3 doub N N 147 G N2 H21 sing N N 148 G N2 H22 sing N N 149 G N3 C4 sing N N 150 HOH O H1 sing N N 151 HOH O H2 sing N N 152 SO4 S O1 doub N N 153 SO4 S O2 doub N N 154 SO4 S O3 sing N N 155 SO4 S O4 sing N N 156 U OP3 P sing N N 157 U OP3 HOP3 sing N N 158 U P OP1 doub N N 159 U P OP2 sing N N 160 U P "O5'" sing N N 161 U OP2 HOP2 sing N N 162 U "O5'" "C5'" sing N N 163 U "C5'" "C4'" sing N N 164 U "C5'" "H5'" sing N N 165 U "C5'" "H5''" sing N N 166 U "C4'" "O4'" sing N N 167 U "C4'" "C3'" sing N N 168 U "C4'" "H4'" sing N N 169 U "O4'" "C1'" sing N N 170 U "C3'" "O3'" sing N N 171 U "C3'" "C2'" sing N N 172 U "C3'" "H3'" sing N N 173 U "O3'" "HO3'" sing N N 174 U "C2'" "O2'" sing N N 175 U "C2'" "C1'" sing N N 176 U "C2'" "H2'" sing N N 177 U "O2'" "HO2'" sing N N 178 U "C1'" N1 sing N N 179 U "C1'" "H1'" sing N N 180 U N1 C2 sing N N 181 U N1 C6 sing N N 182 U C2 O2 doub N N 183 U C2 N3 sing N N 184 U N3 C4 sing N N 185 U N3 H3 sing N N 186 U C4 O4 doub N N 187 U C4 C5 sing N N 188 U C5 C6 doub N N 189 U C5 H5 sing N N 190 U C6 H6 sing N N 191 # _ndb_struct_conf_na.entry_id 6IBQ _ndb_struct_conf_na.feature 'a-form double helix' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A G 2 1_555 B DC 9 1_555 -0.798 -0.129 0.304 -2.339 -4.400 -9.721 1 A_G2:DC19_B A 2 ? B 19 ? 19 1 1 A U 3 1_555 B G 8 1_555 2.407 -0.211 -0.440 10.162 -14.672 6.666 2 A_U3:G18_B A 3 ? B 18 ? 28 1 1 A G 4 1_555 B C 7 1_555 -0.603 0.179 -0.105 -3.547 -4.151 6.926 3 A_G4:C17_B A 4 ? B 17 ? 19 1 1 A A 5 1_555 B U 6 1_555 0.209 -0.113 -0.180 6.627 -8.225 -4.403 4 A_A5:U16_B A 5 ? B 16 ? 20 1 1 A U 6 1_555 B A 5 1_555 -0.699 -0.144 0.217 0.394 -4.902 -3.811 5 A_U6:A15_B A 6 ? B 15 ? 20 1 1 A C 7 1_555 B G 4 1_555 0.613 -0.206 -0.513 14.648 -11.301 5.266 6 A_C7:G14_B A 7 ? B 14 ? 19 1 1 A G 8 1_555 B U 3 1_555 -2.288 -0.173 -0.177 -3.397 -9.686 8.726 7 A_G8:U13_B A 8 ? B 13 ? 28 1 1 A DC 9 1_555 B G 2 1_555 0.699 -0.026 -0.124 9.212 -10.036 0.950 8 A_DC9:G12_B A 9 ? B 12 ? 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 2 1_555 B DC 9 1_555 A U 3 1_555 B G 8 1_555 0.598 -1.272 3.113 7.670 4.083 46.086 -1.921 -0.148 3.052 5.162 -9.696 46.854 1 AA_G2U3:G18DC19_BB A 2 ? B 19 ? A 3 ? B 18 ? 1 A U 3 1_555 B G 8 1_555 A G 4 1_555 B C 7 1_555 0.570 -2.043 3.513 -0.528 9.180 21.377 -8.063 -1.586 2.423 23.403 1.346 23.250 2 AA_U3G4:C17G18_BB A 3 ? B 18 ? A 4 ? B 17 ? 1 A G 4 1_555 B C 7 1_555 A A 5 1_555 B U 6 1_555 -0.544 -1.847 3.010 1.493 5.257 30.155 -4.396 1.286 2.628 10.001 -2.840 30.635 3 AA_G4A5:U16C17_BB A 4 ? B 17 ? A 5 ? B 16 ? 1 A A 5 1_555 B U 6 1_555 A U 6 1_555 B A 5 1_555 0.004 -2.214 3.454 -5.230 4.370 29.400 -5.152 -1.082 3.054 8.469 10.135 30.162 4 AA_A5U6:A15U16_BB A 5 ? B 16 ? A 6 ? B 15 ? 1 A U 6 1_555 B A 5 1_555 A C 7 1_555 B G 4 1_555 -0.030 -1.337 3.024 6.109 3.651 34.044 -2.742 0.894 2.822 6.153 -10.295 34.758 5 AA_U6C7:G14A15_BB A 6 ? B 15 ? A 7 ? B 14 ? 1 A C 7 1_555 B G 4 1_555 A G 8 1_555 B U 3 1_555 0.956 -1.908 3.653 -3.447 13.121 19.997 -8.451 -3.307 1.872 33.284 8.745 24.126 6 AA_C7G8:U13G14_BB A 7 ? B 14 ? A 8 ? B 13 ? 1 A G 8 1_555 B U 3 1_555 A DC 9 1_555 B G 2 1_555 -0.103 -1.576 3.090 1.290 1.186 44.709 -2.172 0.246 3.045 1.558 -1.696 44.742 7 AA_G8DC9:G12U13_BB A 8 ? B 13 ? A 9 ? B 12 ? # loop_ _pdbx_audit_support.funding_organization _pdbx_audit_support.country _pdbx_audit_support.grant_number _pdbx_audit_support.ordinal 'French National Research Agency' France ANR-11-LABX-0057_MITOCROSS 1 'French National Research Agency' France ANR-10-LABX-0036_NETRNA 2 ? France ? 3 # _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 485D _pdbx_initial_refinement_model.details ? # _atom_sites.entry_id 6IBQ _atom_sites.fract_transf_matrix[1][1] 0.025000 _atom_sites.fract_transf_matrix[1][2] 0.014434 _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] 0.028868 _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] 0.014470 _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_