data_4RKV # _entry.id 4RKV # _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 4RKV pdb_00004rkv 10.2210/pdb4rkv/pdb NDB NA3254 ? ? RCSB RCSB087472 ? ? WWPDB D_1000087472 ? ? # 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 2014-11-19 2 'Structure model' 1 1 2015-06-24 3 'Structure model' 1 2 2024-02-28 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Database references' 2 3 'Structure model' 'Data collection' 3 3 'Structure model' 'Database references' 4 3 'Structure model' 'Derived calculations' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 3 'Structure model' chem_comp_atom 2 3 'Structure model' chem_comp_bond 3 3 'Structure model' database_2 4 3 'Structure model' pdbx_struct_conn_angle 5 3 'Structure model' struct_conn 6 3 'Structure model' struct_site # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 3 'Structure model' '_database_2.pdbx_DOI' 2 3 'Structure model' '_database_2.pdbx_database_accession' 3 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_asym_id' 4 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_comp_id' 5 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 6 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_alt_id' 7 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_asym_id' 8 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_atom_id' 9 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_comp_id' 10 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_seq_id' 11 3 'Structure model' '_pdbx_struct_conn_angle.ptnr2_auth_asym_id' 12 3 'Structure model' '_pdbx_struct_conn_angle.ptnr2_auth_comp_id' 13 3 'Structure model' '_pdbx_struct_conn_angle.ptnr2_auth_seq_id' 14 3 'Structure model' '_pdbx_struct_conn_angle.ptnr2_label_alt_id' 15 3 'Structure model' '_pdbx_struct_conn_angle.ptnr2_label_asym_id' 16 3 'Structure model' '_pdbx_struct_conn_angle.ptnr2_label_atom_id' 17 3 'Structure model' '_pdbx_struct_conn_angle.ptnr2_label_comp_id' 18 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_asym_id' 19 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_comp_id' 20 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 21 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_alt_id' 22 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id' 23 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_atom_id' 24 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_comp_id' 25 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_seq_id' 26 3 'Structure model' '_pdbx_struct_conn_angle.value' 27 3 'Structure model' '_struct_conn.pdbx_dist_value' 28 3 'Structure model' '_struct_conn.pdbx_ptnr1_label_alt_id' 29 3 'Structure model' '_struct_conn.pdbx_ptnr2_label_alt_id' 30 3 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 31 3 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 32 3 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 33 3 'Structure model' '_struct_conn.ptnr1_label_asym_id' 34 3 'Structure model' '_struct_conn.ptnr1_label_atom_id' 35 3 'Structure model' '_struct_conn.ptnr1_label_comp_id' 36 3 'Structure model' '_struct_conn.ptnr1_label_seq_id' 37 3 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 38 3 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 39 3 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 40 3 'Structure model' '_struct_conn.ptnr2_label_asym_id' 41 3 'Structure model' '_struct_conn.ptnr2_label_atom_id' 42 3 'Structure model' '_struct_conn.ptnr2_label_comp_id' 43 3 'Structure model' '_struct_site.pdbx_auth_asym_id' 44 3 'Structure model' '_struct_site.pdbx_auth_comp_id' 45 3 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 4RKV _pdbx_database_status.recvd_initial_deposition_date 2014-10-14 _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 ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 1J8G . unspecified PDB 4RJ1 . unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Fyfe, A.C.' 1 'Dunten, P.W.' 2 'Scott, W.G.' 3 # _citation.id primary _citation.title 'Structural Variations and Solvent Structure of r(UGGGGU) Quadruplexes Stabilized by Sr(2+) Ions.' _citation.journal_abbrev J.Mol.Biol. _citation.journal_volume 427 _citation.page_first 2205 _citation.page_last 2219 _citation.year 2015 _citation.journal_id_ASTM JMOBAK _citation.country UK _citation.journal_id_ISSN 0022-2836 _citation.journal_id_CSD 0070 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 25861762 _citation.pdbx_database_id_DOI 10.1016/j.jmb.2015.03.022 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Fyfe, A.C.' 1 ? primary 'Dunten, P.W.' 2 ? primary 'Martick, M.M.' 3 ? primary 'Scott, W.G.' 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(*UP*GP*GP*GP*GP*U)-3') ; 1948.197 2 ? ? ? ? 2 non-polymer syn 'STRONTIUM ION' 87.620 6 ? ? ? ? 3 non-polymer syn 'SODIUM ION' 22.990 2 ? ? ? ? 4 non-polymer syn 'CALCIUM ION' 40.078 2 ? ? ? ? 5 water nat water 18.015 54 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code UGGGGU _entity_poly.pdbx_seq_one_letter_code_can UGGGGU _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 'STRONTIUM ION' SR 3 'SODIUM ION' NA 4 'CALCIUM ION' CA 5 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 U n 1 2 G n 1 3 G n 1 4 G n 1 5 G n 1 6 U n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num ? _pdbx_entity_src_syn.pdbx_end_seq_num ? _pdbx_entity_src_syn.organism_scientific 'synthetic construct' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 32630 _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 CA non-polymer . 'CALCIUM ION' ? 'Ca 2' 40.078 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 HOH non-polymer . WATER ? 'H2 O' 18.015 NA non-polymer . 'SODIUM ION' ? 'Na 1' 22.990 SR non-polymer . 'STRONTIUM ION' ? 'Sr 2' 87.620 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 U 1 1001 1001 U U A . n A 1 2 G 2 1002 1002 G G A . n A 1 3 G 3 1003 1003 G G A . n A 1 4 G 4 1004 1004 G G A . n A 1 5 G 5 1005 1005 G G A . n A 1 6 U 6 1006 1006 U U A . n B 1 1 U 1 2001 2001 U U B . n B 1 2 G 2 2002 2002 G G B . n B 1 3 G 3 2003 2003 G G B . n B 1 4 G 4 2004 2004 G G B . n B 1 5 G 5 2005 2005 G G B . n B 1 6 U 6 2006 2006 U U 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 SR 1 9001 9001 SR SR A . D 2 SR 1 9002 9002 SR SR A . E 3 NA 1 9003 9005 NA NA A . F 2 SR 1 9004 9101 SR SR A . G 2 SR 1 9005 9105 SR SR A . H 2 SR 1 2101 9003 SR SR B . I 2 SR 1 2102 9004 SR SR B . J 3 NA 1 2103 9006 NA NA B . K 4 CA 1 2104 9103 CA CA B . L 4 CA 1 2105 9104 CA CA B . M 5 HOH 1 9101 9108 HOH HOH A . M 5 HOH 2 9102 9502 HOH HOH A . M 5 HOH 3 9103 9503 HOH HOH A . M 5 HOH 4 9104 9505 HOH HOH A . M 5 HOH 5 9105 9506 HOH HOH A . M 5 HOH 6 9106 9510 HOH HOH A . M 5 HOH 7 9107 9512 HOH HOH A . M 5 HOH 8 9108 9513 HOH HOH A . M 5 HOH 9 9109 9517 HOH HOH A . M 5 HOH 10 9110 9520 HOH HOH A . M 5 HOH 11 9111 9524 HOH HOH A . M 5 HOH 12 9112 9525 HOH HOH A . M 5 HOH 13 9113 9536 HOH HOH A . M 5 HOH 14 9114 9537 HOH HOH A . M 5 HOH 15 9115 9540 HOH HOH A . M 5 HOH 16 9116 9545 HOH HOH A . M 5 HOH 17 9117 9547 HOH HOH A . M 5 HOH 18 9118 9556 HOH HOH A . M 5 HOH 19 9119 9567 HOH HOH A . M 5 HOH 20 9120 9571 HOH HOH A . M 5 HOH 21 9121 9574 HOH HOH A . M 5 HOH 22 9122 9576 HOH HOH A . M 5 HOH 23 9123 9581 HOH HOH A . M 5 HOH 24 9124 9585 HOH HOH A . M 5 HOH 25 9125 9586 HOH HOH A . M 5 HOH 26 9126 9591 HOH HOH A . N 5 HOH 1 2201 9504 HOH HOH B . N 5 HOH 2 2202 9532 HOH HOH B . N 5 HOH 3 2203 9106 HOH HOH B . N 5 HOH 4 2204 9107 HOH HOH B . N 5 HOH 5 2205 9501 HOH HOH B . N 5 HOH 6 2206 9508 HOH HOH B . N 5 HOH 7 2207 9509 HOH HOH B . N 5 HOH 8 2208 9511 HOH HOH B . N 5 HOH 9 2209 9515 HOH HOH B . N 5 HOH 10 2210 9516 HOH HOH B . N 5 HOH 11 2211 9518 HOH HOH B . N 5 HOH 12 2212 9521 HOH HOH B . N 5 HOH 13 2213 9523 HOH HOH B . N 5 HOH 14 2214 9526 HOH HOH B . N 5 HOH 15 2215 9529 HOH HOH B . N 5 HOH 16 2216 9534 HOH HOH B . N 5 HOH 17 2217 9538 HOH HOH B . N 5 HOH 18 2218 9543 HOH HOH B . N 5 HOH 19 2219 9546 HOH HOH B . N 5 HOH 20 2220 9548 HOH HOH B . N 5 HOH 21 2221 9549 HOH HOH B . N 5 HOH 22 2222 9561 HOH HOH B . N 5 HOH 23 2223 9563 HOH HOH B . N 5 HOH 24 2224 9565 HOH HOH B . N 5 HOH 25 2225 9573 HOH HOH B . N 5 HOH 26 2226 9583 HOH HOH B . N 5 HOH 27 2227 9588 HOH HOH B . N 5 HOH 28 2228 9590 HOH HOH B . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal MOSFLM 'data reduction' . ? 1 PHASER phasing . ? 2 REFMAC refinement 5.8.0073 ? 3 SCALA 'data scaling' . ? 4 # _cell.entry_id 4RKV _cell.length_a 36.645 _cell.length_b 36.645 _cell.length_c 37.078 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 16 _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 4RKV _symmetry.space_group_name_H-M 'P 4 21 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 90 _symmetry.space_group_name_Hall ? # _exptl.entry_id 4RKV _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 1.60 _exptl_crystal.density_percent_sol 23.00 _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 298 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.0 _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.pdbx_details ;MgCl2 20mM, SrCl2 80mM, CaCl2 40mM, SPM 4Cl 12mM, Sodium cacodylate 20mM, 35% MPD, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K ; # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector PIXEL _diffrn_detector.type 'PSI PILATUS 6M' _diffrn_detector.pdbx_collection_date ? _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.979 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'SSRL BEAMLINE BL11-1' _diffrn_source.pdbx_synchrotron_site SSRL _diffrn_source.pdbx_synchrotron_beamline BL11-1 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.979 # _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.entry_id 4RKV _reflns.observed_criterion_sigma_I 0 _reflns.observed_criterion_sigma_F 0 _reflns.d_resolution_low 37.08 _reflns.d_resolution_high 0.88 _reflns.number_obs 19031 _reflns.number_all 19031 _reflns.percent_possible_obs 93.5 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy ? _reflns.R_free_details ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? # _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_ordinal 1 _reflns_shell.d_res_high 0.88 _reflns_shell.d_res_low 0.93 _reflns_shell.percent_possible_all 58.8 _reflns_shell.Rmerge_I_obs ? _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs ? _reflns_shell.pdbx_redundancy ? _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all ? _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 4RKV _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.ls_number_reflns_obs 18036 _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 37.08 _refine.ls_d_res_high 0.88 _refine.ls_percent_reflns_obs 93.31 _refine.ls_R_factor_obs 0.09299 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.09272 _refine.ls_R_factor_R_free 0.09811 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 5.1 _refine.ls_number_reflns_R_free 975 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.989 _refine.correlation_coeff_Fo_to_Fc_free 0.989 _refine.B_iso_mean 12.663 _refine.aniso_B[1][1] -0.01 _refine.aniso_B[2][2] -0.01 _refine.aniso_B[3][3] 0.01 _refine.aniso_B[1][2] 0.00 _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 USED IF PRESENT IN THE INPUT' _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 0.013 _refine.pdbx_overall_ESU_R_Free 0.012 _refine.overall_SU_ML 0.009 _refine.pdbx_overall_phase_error ? _refine.overall_SU_B 0.331 _refine.overall_SU_R_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? _refine.ls_redundancy_reflns_obs ? _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_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 258 _refine_hist.pdbx_number_atoms_ligand 10 _refine_hist.number_atoms_solvent 54 _refine_hist.number_atoms_total 322 _refine_hist.d_res_high 0.88 _refine_hist.d_res_low 37.08 # 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 0.013 0.011 ? 294 'X-RAY DIFFRACTION' ? r_bond_other_d 0.002 0.020 ? 116 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1.744 1.248 ? 459 'X-RAY DIFFRACTION' ? r_angle_other_deg 1.882 3.000 ? 287 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_chiral_restr 0.106 0.200 ? 49 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.052 0.020 ? 132 'X-RAY DIFFRACTION' ? r_gen_planes_other 0.002 0.020 ? 44 'X-RAY DIFFRACTION' ? r_nbd_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcangle_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_scbond_it 1.079 . ? 293 'X-RAY DIFFRACTION' ? r_scbond_other 1.073 ? ? 292 'X-RAY DIFFRACTION' ? r_scangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_scangle_other 1.496 ? ? 459 'X-RAY DIFFRACTION' ? r_long_range_B_refined 1.939 ? ? 533 'X-RAY DIFFRACTION' ? r_long_range_B_other 1.713 ? ? 500 'X-RAY DIFFRACTION' ? r_rigid_bond_restr 5.433 3.000 ? 284 'X-RAY DIFFRACTION' ? r_sphericity_free 22.921 6.800 ? 22 'X-RAY DIFFRACTION' ? r_sphericity_bonded 9.673 6.800 ? 307 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 0.88 _refine_ls_shell.d_res_low 0.907 _refine_ls_shell.number_reflns_R_work 529 _refine_ls_shell.R_factor_R_work 0.441 _refine_ls_shell.percent_reflns_obs 37.77 _refine_ls_shell.R_factor_R_free 0.440 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 22 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.number_reflns_obs ? # _database_PDB_matrix.entry_id 4RKV _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 4RKV _struct.title 'Structural variations and solvent structure of UGGGGU quadruplexes stabilized by Sr2+ ions' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 4RKV _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'RNA quadruplexes, parallel-stranded, 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 2 ? G N N 2 ? H N N 2 ? I N N 2 ? J N N 3 ? K N N 4 ? L N N 4 ? M N N 5 ? N N N 5 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 4RKV _struct_ref.pdbx_db_accession 4RKV _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code UGGGGU _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 4RKV A 1 ? 6 ? 4RKV 1001 ? 1006 ? 1001 1006 2 1 4RKV B 1 ? 6 ? 4RKV 2001 ? 2006 ? 2001 2006 # _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 octameric _pdbx_struct_assembly.oligomeric_count 8 # 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)' 8250 ? 1 MORE -85 ? 1 'SSA (A^2)' 4400 ? # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N # 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' 2_655 -x+1,-y,z -1.0000000000 0.0000000000 0.0000000000 36.6450000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 3 'crystal symmetry operation' 3_545 -y+1/2,x-1/2,z 0.0000000000 -1.0000000000 0.0000000000 18.3225000000 1.0000000000 0.0000000000 0.0000000000 -18.3225000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 4 'crystal symmetry operation' 4_555 y+1/2,-x+1/2,z 0.0000000000 1.0000000000 0.0000000000 18.3225000000 -1.0000000000 0.0000000000 0.0000000000 18.3225000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 # _struct_biol.id 1 _struct_biol.details ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role metalc1 metalc ? ? A G 2 O6 ? ? ? 1_555 D SR . SR ? ? A G 1002 A SR 9002 1_555 ? ? ? ? ? ? ? 2.610 ? ? metalc2 metalc ? ? A G 3 O6 ? ? ? 1_555 D SR . SR ? ? A G 1003 A SR 9002 1_555 ? ? ? ? ? ? ? 2.620 ? ? metalc3 metalc ? ? A G 4 O6 ? ? ? 1_555 C SR . SR ? ? A G 1004 A SR 9001 1_555 ? ? ? ? ? ? ? 2.605 ? ? metalc4 metalc ? ? A G 5 O6 ? ? ? 1_555 C SR . SR ? ? A G 1005 A SR 9001 1_555 ? ? ? ? ? ? ? 2.625 ? ? metalc5 metalc ? ? A G 5 OP1 ? ? ? 1_555 G SR . SR A ? A G 1005 A SR 9005 1_555 ? ? ? ? ? ? ? 2.637 ? ? metalc6 metalc ? ? A U 6 O4 ? ? ? 1_555 E NA . NA B ? A U 1006 A NA 9003 1_555 ? ? ? ? ? ? ? 2.313 ? ? metalc7 metalc ? ? A U 6 "O3'" ? ? ? 1_555 F SR . SR ? ? A U 1006 A SR 9004 1_555 ? ? ? ? ? ? ? 2.457 ? ? metalc8 metalc ? ? A U 6 "O2'" ? ? ? 1_555 F SR . SR ? ? A U 1006 A SR 9004 1_555 ? ? ? ? ? ? ? 2.790 ? ? metalc9 metalc ? ? F SR . SR ? ? ? 1_555 M HOH . O ? ? A SR 9004 A HOH 9103 1_555 ? ? ? ? ? ? ? 2.627 ? ? metalc10 metalc ? ? F SR . SR ? ? ? 1_555 M HOH . O ? ? A SR 9004 A HOH 9108 1_555 ? ? ? ? ? ? ? 2.684 ? ? metalc11 metalc ? ? F SR . SR ? ? ? 1_555 M HOH . O ? ? A SR 9004 A HOH 9110 1_555 ? ? ? ? ? ? ? 2.448 ? ? metalc12 metalc ? ? F SR . SR ? ? ? 1_555 M HOH . O ? ? A SR 9004 A HOH 9111 1_555 ? ? ? ? ? ? ? 2.458 ? ? metalc13 metalc ? ? F SR . SR ? ? ? 1_555 M HOH . O ? ? A SR 9004 A HOH 9124 1_555 ? ? ? ? ? ? ? 2.442 ? ? metalc14 metalc ? ? G SR . SR A ? ? 1_555 M HOH . O ? ? A SR 9005 A HOH 9115 1_555 ? ? ? ? ? ? ? 2.695 ? ? metalc15 metalc ? ? G SR . SR A ? ? 1_555 M HOH . O ? ? A SR 9005 A HOH 9116 1_555 ? ? ? ? ? ? ? 2.627 ? ? metalc16 metalc ? ? B G 2 O6 ? ? ? 1_555 H SR . SR ? ? B G 2002 B SR 2101 1_555 ? ? ? ? ? ? ? 2.596 ? ? metalc17 metalc ? ? B G 2 "O3'" ? ? ? 1_555 K CA . CA A ? B G 2002 B CA 2104 1_555 ? ? ? ? ? ? ? 3.110 ? ? metalc18 metalc ? ? B G 2 OP2 ? ? ? 1_555 L CA . CA A ? B G 2002 B CA 2105 1_555 ? ? ? ? ? ? ? 2.443 ? ? metalc19 metalc ? ? B G 3 O6 ? ? ? 1_555 H SR . SR ? ? B G 2003 B SR 2101 1_555 ? ? ? ? ? ? ? 2.610 ? ? metalc20 metalc ? ? B G 3 OP1 ? ? ? 1_555 K CA . CA A ? B G 2003 B CA 2104 1_555 ? ? ? ? ? ? ? 2.512 ? ? metalc21 metalc ? ? B G 4 O6 ? ? ? 1_555 I SR . SR ? ? B G 2004 B SR 2102 1_555 ? ? ? ? ? ? ? 2.598 ? ? metalc22 metalc ? ? B G 5 O6 ? ? ? 1_555 I SR . SR ? ? B G 2005 B SR 2102 1_555 ? ? ? ? ? ? ? 2.611 ? ? metalc23 metalc ? ? B U 6 O4 ? ? ? 1_555 J NA . NA B ? B U 2006 B NA 2103 1_555 ? ? ? ? ? ? ? 2.347 ? ? metalc24 metalc ? ? J NA . NA A ? ? 1_555 N HOH . O ? ? B NA 2103 B HOH 2225 1_555 ? ? ? ? ? ? ? 3.199 ? ? metalc25 metalc ? ? K CA . CA A ? ? 1_555 N HOH . O ? ? B CA 2104 B HOH 2210 1_555 ? ? ? ? ? ? ? 2.441 ? ? metalc26 metalc ? ? K CA . CA A ? ? 1_555 N HOH . O ? ? B CA 2104 B HOH 2215 1_555 ? ? ? ? ? ? ? 2.662 ? ? metalc27 metalc ? ? L CA . CA A ? ? 1_555 N HOH . O A ? B CA 2105 B HOH 2207 1_555 ? ? ? ? ? ? ? 2.291 ? ? metalc28 metalc ? ? L CA . CA A ? ? 1_555 N HOH . O ? ? B CA 2105 B HOH 2214 1_555 ? ? ? ? ? ? ? 2.306 ? ? metalc29 metalc ? ? L CA . CA A ? ? 1_555 N HOH . O A ? B CA 2105 B HOH 2224 1_555 ? ? ? ? ? ? ? 2.450 ? ? hydrog1 hydrog ? ? A G 3 N2 ? ? ? 1_555 B U 1 O2 ? ? A G 1003 B U 2001 1_555 ? ? ? ? ? ? 'G-U MISPAIR' ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference metalc ? ? hydrog ? ? # loop_ _pdbx_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 O6 ? A G 2 ? A G 1002 ? 1_555 SR ? D SR . ? A SR 9002 ? 1_555 O6 ? A G 3 ? A G 1003 ? 1_555 68.8 ? 2 O6 ? A G 4 ? A G 1004 ? 1_555 SR ? C SR . ? A SR 9001 ? 1_555 O6 ? A G 5 ? A G 1005 ? 1_555 68.2 ? 3 OP1 ? A G 5 ? A G 1005 ? 1_555 SR A G SR . ? A SR 9005 ? 1_555 O ? M HOH . ? A HOH 9115 ? 1_555 70.7 ? 4 OP1 ? A G 5 ? A G 1005 ? 1_555 SR A G SR . ? A SR 9005 ? 1_555 O ? M HOH . ? A HOH 9116 ? 1_555 68.0 ? 5 O ? M HOH . ? A HOH 9115 ? 1_555 SR A G SR . ? A SR 9005 ? 1_555 O ? M HOH . ? A HOH 9116 ? 1_555 127.9 ? 6 "O3'" ? A U 6 ? A U 1006 ? 1_555 SR ? F SR . ? A SR 9004 ? 1_555 "O2'" ? A U 6 ? A U 1006 ? 1_555 60.8 ? 7 "O3'" ? A U 6 ? A U 1006 ? 1_555 SR ? F SR . ? A SR 9004 ? 1_555 O ? M HOH . ? A HOH 9103 ? 1_555 97.5 ? 8 "O2'" ? A U 6 ? A U 1006 ? 1_555 SR ? F SR . ? A SR 9004 ? 1_555 O ? M HOH . ? A HOH 9103 ? 1_555 80.4 ? 9 "O3'" ? A U 6 ? A U 1006 ? 1_555 SR ? F SR . ? A SR 9004 ? 1_555 O ? M HOH . ? A HOH 9108 ? 1_555 131.2 ? 10 "O2'" ? A U 6 ? A U 1006 ? 1_555 SR ? F SR . ? A SR 9004 ? 1_555 O ? M HOH . ? A HOH 9108 ? 1_555 70.4 ? 11 O ? M HOH . ? A HOH 9103 ? 1_555 SR ? F SR . ? A SR 9004 ? 1_555 O ? M HOH . ? A HOH 9108 ? 1_555 73.0 ? 12 "O3'" ? A U 6 ? A U 1006 ? 1_555 SR ? F SR . ? A SR 9004 ? 1_555 O ? M HOH . ? A HOH 9110 ? 1_555 101.2 ? 13 "O2'" ? A U 6 ? A U 1006 ? 1_555 SR ? F SR . ? A SR 9004 ? 1_555 O ? M HOH . ? A HOH 9110 ? 1_555 79.7 ? 14 O ? M HOH . ? A HOH 9103 ? 1_555 SR ? F SR . ? A SR 9004 ? 1_555 O ? M HOH . ? A HOH 9110 ? 1_555 141.2 ? 15 O ? M HOH . ? A HOH 9108 ? 1_555 SR ? F SR . ? A SR 9004 ? 1_555 O ? M HOH . ? A HOH 9110 ? 1_555 69.1 ? 16 "O3'" ? A U 6 ? A U 1006 ? 1_555 SR ? F SR . ? A SR 9004 ? 1_555 O ? M HOH . ? A HOH 9111 ? 1_555 74.6 ? 17 "O2'" ? A U 6 ? A U 1006 ? 1_555 SR ? F SR . ? A SR 9004 ? 1_555 O ? M HOH . ? A HOH 9111 ? 1_555 121.2 ? 18 O ? M HOH . ? A HOH 9103 ? 1_555 SR ? F SR . ? A SR 9004 ? 1_555 O ? M HOH . ? A HOH 9111 ? 1_555 69.1 ? 19 O ? M HOH . ? A HOH 9108 ? 1_555 SR ? F SR . ? A SR 9004 ? 1_555 O ? M HOH . ? A HOH 9111 ? 1_555 136.7 ? 20 O ? M HOH . ? A HOH 9110 ? 1_555 SR ? F SR . ? A SR 9004 ? 1_555 O ? M HOH . ? A HOH 9111 ? 1_555 148.9 ? 21 "O3'" ? A U 6 ? A U 1006 ? 1_555 SR ? F SR . ? A SR 9004 ? 1_555 O ? M HOH . ? A HOH 9124 ? 1_555 152.1 ? 22 "O2'" ? A U 6 ? A U 1006 ? 1_555 SR ? F SR . ? A SR 9004 ? 1_555 O ? M HOH . ? A HOH 9124 ? 1_555 145.9 ? 23 O ? M HOH . ? A HOH 9103 ? 1_555 SR ? F SR . ? A SR 9004 ? 1_555 O ? M HOH . ? A HOH 9124 ? 1_555 84.2 ? 24 O ? M HOH . ? A HOH 9108 ? 1_555 SR ? F SR . ? A SR 9004 ? 1_555 O ? M HOH . ? A HOH 9124 ? 1_555 76.0 ? 25 O ? M HOH . ? A HOH 9110 ? 1_555 SR ? F SR . ? A SR 9004 ? 1_555 O ? M HOH . ? A HOH 9124 ? 1_555 94.2 ? 26 O ? M HOH . ? A HOH 9111 ? 1_555 SR ? F SR . ? A SR 9004 ? 1_555 O ? M HOH . ? A HOH 9124 ? 1_555 80.2 ? 27 O6 ? B G 2 ? B G 2002 ? 1_555 SR ? H SR . ? B SR 2101 ? 1_555 O6 ? B G 3 ? B G 2003 ? 1_555 69.3 ? 28 "O3'" ? B G 2 ? B G 2002 ? 1_555 CA A K CA . ? B CA 2104 ? 1_555 OP1 ? B G 3 ? B G 2003 ? 1_555 49.7 ? 29 "O3'" ? B G 2 ? B G 2002 ? 1_555 CA A K CA . ? B CA 2104 ? 1_555 O ? N HOH . ? B HOH 2210 ? 1_555 64.6 ? 30 OP1 ? B G 3 ? B G 2003 ? 1_555 CA A K CA . ? B CA 2104 ? 1_555 O ? N HOH . ? B HOH 2210 ? 1_555 102.9 ? 31 "O3'" ? B G 2 ? B G 2002 ? 1_555 CA A K CA . ? B CA 2104 ? 1_555 O ? N HOH . ? B HOH 2215 ? 1_555 143.3 ? 32 OP1 ? B G 3 ? B G 2003 ? 1_555 CA A K CA . ? B CA 2104 ? 1_555 O ? N HOH . ? B HOH 2215 ? 1_555 166.9 ? 33 O ? N HOH . ? B HOH 2210 ? 1_555 CA A K CA . ? B CA 2104 ? 1_555 O ? N HOH . ? B HOH 2215 ? 1_555 88.2 ? 34 OP2 ? B G 2 ? B G 2002 ? 1_555 CA A L CA . ? B CA 2105 ? 1_555 O A N HOH . ? B HOH 2207 ? 1_555 88.7 ? 35 OP2 ? B G 2 ? B G 2002 ? 1_555 CA A L CA . ? B CA 2105 ? 1_555 O ? N HOH . ? B HOH 2214 ? 1_555 165.1 ? 36 O A N HOH . ? B HOH 2207 ? 1_555 CA A L CA . ? B CA 2105 ? 1_555 O ? N HOH . ? B HOH 2214 ? 1_555 98.5 ? 37 OP2 ? B G 2 ? B G 2002 ? 1_555 CA A L CA . ? B CA 2105 ? 1_555 O A N HOH . ? B HOH 2224 ? 1_555 88.6 ? 38 O A N HOH . ? B HOH 2207 ? 1_555 CA A L CA . ? B CA 2105 ? 1_555 O A N HOH . ? B HOH 2224 ? 1_555 172.8 ? 39 O ? N HOH . ? B HOH 2214 ? 1_555 CA A L CA . ? B CA 2105 ? 1_555 O A N HOH . ? B HOH 2224 ? 1_555 85.7 ? 40 O6 ? B G 4 ? B G 2004 ? 1_555 SR ? I SR . ? B SR 2102 ? 1_555 O6 ? B G 5 ? B G 2005 ? 1_555 69.4 ? # 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 SR 9001 ? 8 'BINDING SITE FOR RESIDUE SR A 9001' AC2 Software A SR 9002 ? 8 'BINDING SITE FOR RESIDUE SR A 9002' AC3 Software A NA 9003 ? 8 'BINDING SITE FOR RESIDUE NA A 9003' AC4 Software A SR 9004 ? 7 'BINDING SITE FOR RESIDUE SR A 9004' AC5 Software A SR 9005 ? 9 'BINDING SITE FOR RESIDUE SR A 9005' AC6 Software B SR 2101 ? 8 'BINDING SITE FOR RESIDUE SR B 2101' AC7 Software B SR 2102 ? 8 'BINDING SITE FOR RESIDUE SR B 2102' AC8 Software B NA 2103 ? 8 'BINDING SITE FOR RESIDUE NA B 2103' AC9 Software B CA 2104 ? 8 'BINDING SITE FOR RESIDUE CA B 2104' BC1 Software B CA 2105 ? 7 'BINDING SITE FOR RESIDUE CA B 2105' # 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 8 G A 4 ? G A 1004 . ? 2_655 ? 2 AC1 8 G A 4 ? G A 1004 . ? 4_555 ? 3 AC1 8 G A 4 ? G A 1004 . ? 1_555 ? 4 AC1 8 G A 4 ? G A 1004 . ? 3_545 ? 5 AC1 8 G A 5 ? G A 1005 . ? 3_545 ? 6 AC1 8 G A 5 ? G A 1005 . ? 1_555 ? 7 AC1 8 G A 5 ? G A 1005 . ? 4_555 ? 8 AC1 8 G A 5 ? G A 1005 . ? 2_655 ? 9 AC2 8 G A 2 ? G A 1002 . ? 2_655 ? 10 AC2 8 G A 2 ? G A 1002 . ? 4_555 ? 11 AC2 8 G A 2 ? G A 1002 . ? 1_555 ? 12 AC2 8 G A 2 ? G A 1002 . ? 3_545 ? 13 AC2 8 G A 3 ? G A 1003 . ? 1_555 ? 14 AC2 8 G A 3 ? G A 1003 . ? 3_545 ? 15 AC2 8 G A 3 ? G A 1003 . ? 4_555 ? 16 AC2 8 G A 3 ? G A 1003 . ? 2_655 ? 17 AC3 8 U A 6 ? U A 1006 . ? 2_654 ? 18 AC3 8 U A 6 ? U A 1006 . ? 3_544 ? 19 AC3 8 U A 6 ? U A 1006 . ? 1_554 ? 20 AC3 8 U A 6 ? U A 1006 . ? 4_554 ? 21 AC3 8 U A 6 ? U A 1006 . ? 2_655 ? 22 AC3 8 U A 6 ? U A 1006 . ? 3_545 ? 23 AC3 8 U A 6 ? U A 1006 . ? 1_555 ? 24 AC3 8 U A 6 ? U A 1006 . ? 4_555 ? 25 AC4 7 U A 6 ? U A 1006 . ? 1_555 ? 26 AC4 7 HOH M . ? HOH A 9102 . ? 8_667 ? 27 AC4 7 HOH M . ? HOH A 9103 . ? 1_555 ? 28 AC4 7 HOH M . ? HOH A 9108 . ? 1_555 ? 29 AC4 7 HOH M . ? HOH A 9110 . ? 1_555 ? 30 AC4 7 HOH M . ? HOH A 9111 . ? 1_555 ? 31 AC4 7 HOH M . ? HOH A 9124 . ? 1_555 ? 32 AC5 9 G A 4 ? G A 1004 . ? 8_667 ? 33 AC5 9 G A 5 ? G A 1005 . ? 1_555 ? 34 AC5 9 G A 5 ? G A 1005 . ? 8_667 ? 35 AC5 9 U A 6 ? U A 1006 . ? 1_555 ? 36 AC5 9 HOH M . ? HOH A 9115 . ? 1_555 ? 37 AC5 9 HOH M . ? HOH A 9116 . ? 8_667 ? 38 AC5 9 HOH M . ? HOH A 9116 . ? 1_555 ? 39 AC5 9 HOH N . ? HOH B 2201 . ? 8_667 ? 40 AC5 9 HOH N . ? HOH B 2202 . ? 8_667 ? 41 AC6 8 G B 2 ? G B 2002 . ? 2_655 ? 42 AC6 8 G B 2 ? G B 2002 . ? 1_555 ? 43 AC6 8 G B 2 ? G B 2002 . ? 3_545 ? 44 AC6 8 G B 2 ? G B 2002 . ? 4_555 ? 45 AC6 8 G B 3 ? G B 2003 . ? 3_545 ? 46 AC6 8 G B 3 ? G B 2003 . ? 1_555 ? 47 AC6 8 G B 3 ? G B 2003 . ? 4_555 ? 48 AC6 8 G B 3 ? G B 2003 . ? 2_655 ? 49 AC7 8 G B 4 ? G B 2004 . ? 4_555 ? 50 AC7 8 G B 4 ? G B 2004 . ? 1_555 ? 51 AC7 8 G B 4 ? G B 2004 . ? 3_545 ? 52 AC7 8 G B 4 ? G B 2004 . ? 2_655 ? 53 AC7 8 G B 5 ? G B 2005 . ? 3_545 ? 54 AC7 8 G B 5 ? G B 2005 . ? 2_655 ? 55 AC7 8 G B 5 ? G B 2005 . ? 4_555 ? 56 AC7 8 G B 5 ? G B 2005 . ? 1_555 ? 57 AC8 8 G B 5 ? G B 2005 . ? 1_555 ? 58 AC8 8 G B 5 ? G B 2005 . ? 3_545 ? 59 AC8 8 G B 5 ? G B 2005 . ? 2_655 ? 60 AC8 8 G B 5 ? G B 2005 . ? 4_555 ? 61 AC8 8 U B 6 ? U B 2006 . ? 3_545 ? 62 AC8 8 U B 6 ? U B 2006 . ? 2_655 ? 63 AC8 8 U B 6 ? U B 2006 . ? 1_555 ? 64 AC8 8 U B 6 ? U B 2006 . ? 4_555 ? 65 AC9 8 G B 2 ? G B 2002 . ? 1_555 ? 66 AC9 8 G B 3 ? G B 2003 . ? 1_555 ? 67 AC9 8 G B 3 ? G B 2003 . ? 8_666 ? 68 AC9 8 HOH N . ? HOH B 2203 . ? 1_555 ? 69 AC9 8 HOH N . ? HOH B 2205 . ? 8_666 ? 70 AC9 8 HOH N . ? HOH B 2210 . ? 1_555 ? 71 AC9 8 HOH N . ? HOH B 2215 . ? 1_555 ? 72 AC9 8 HOH N . ? HOH B 2222 . ? 8_666 ? 73 BC1 7 G A 2 ? G A 1002 . ? 3_545 ? 74 BC1 7 G B 2 ? G B 2002 . ? 1_555 ? 75 BC1 7 G B 4 ? G B 2004 . ? 5_656 ? 76 BC1 7 G B 5 ? G B 2005 . ? 5_656 ? 77 BC1 7 HOH N . ? HOH B 2207 . ? 1_555 ? 78 BC1 7 HOH N . ? HOH B 2214 . ? 1_555 ? 79 BC1 7 HOH N . ? HOH B 2224 . ? 1_555 ? # _pdbx_validate_rmsd_angle.id 1 _pdbx_validate_rmsd_angle.PDB_model_num 1 _pdbx_validate_rmsd_angle.auth_atom_id_1 "O5'" _pdbx_validate_rmsd_angle.auth_asym_id_1 B _pdbx_validate_rmsd_angle.auth_comp_id_1 U _pdbx_validate_rmsd_angle.auth_seq_id_1 2006 _pdbx_validate_rmsd_angle.PDB_ins_code_1 ? _pdbx_validate_rmsd_angle.label_alt_id_1 ? _pdbx_validate_rmsd_angle.auth_atom_id_2 "C5'" _pdbx_validate_rmsd_angle.auth_asym_id_2 B _pdbx_validate_rmsd_angle.auth_comp_id_2 U _pdbx_validate_rmsd_angle.auth_seq_id_2 2006 _pdbx_validate_rmsd_angle.PDB_ins_code_2 ? _pdbx_validate_rmsd_angle.label_alt_id_2 ? _pdbx_validate_rmsd_angle.auth_atom_id_3 "C4'" _pdbx_validate_rmsd_angle.auth_asym_id_3 B _pdbx_validate_rmsd_angle.auth_comp_id_3 U _pdbx_validate_rmsd_angle.auth_seq_id_3 2006 _pdbx_validate_rmsd_angle.PDB_ins_code_3 ? _pdbx_validate_rmsd_angle.label_alt_id_3 ? _pdbx_validate_rmsd_angle.angle_value 103.87 _pdbx_validate_rmsd_angle.angle_target_value 109.40 _pdbx_validate_rmsd_angle.angle_deviation -5.53 _pdbx_validate_rmsd_angle.angle_standard_deviation 0.80 _pdbx_validate_rmsd_angle.linker_flag N # loop_ _pdbx_validate_planes.id _pdbx_validate_planes.PDB_model_num _pdbx_validate_planes.auth_comp_id _pdbx_validate_planes.auth_asym_id _pdbx_validate_planes.auth_seq_id _pdbx_validate_planes.PDB_ins_code _pdbx_validate_planes.label_alt_id _pdbx_validate_planes.rmsd _pdbx_validate_planes.type 1 1 G A 1002 ? ? 0.074 'SIDE CHAIN' 2 1 G A 1003 ? ? 0.056 'SIDE CHAIN' 3 1 G A 1004 ? ? 0.069 'SIDE CHAIN' 4 1 G B 2002 ? ? 0.063 'SIDE CHAIN' 5 1 G B 2003 ? ? 0.057 'SIDE CHAIN' 6 1 G B 2004 ? ? 0.057 'SIDE CHAIN' 7 1 U B 2006 ? ? 0.068 'SIDE CHAIN' # 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 SR 9001 ? C SR . 2 1 A SR 9002 ? D SR . 3 1 A NA 9003 ? E NA . 4 1 B SR 2101 ? H SR . 5 1 B SR 2102 ? I SR . 6 1 B NA 2103 ? J NA . 7 1 A HOH 9116 ? M HOH . 8 1 A HOH 9125 ? M HOH . # 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 CA CA CA N N 1 G OP3 O N N 2 G P P N N 3 G OP1 O N N 4 G OP2 O N N 5 G "O5'" O N N 6 G "C5'" C N N 7 G "C4'" C N R 8 G "O4'" O N N 9 G "C3'" C N S 10 G "O3'" O N N 11 G "C2'" C N R 12 G "O2'" O N N 13 G "C1'" C N R 14 G N9 N Y N 15 G C8 C Y N 16 G N7 N Y N 17 G C5 C Y N 18 G C6 C N N 19 G O6 O N N 20 G N1 N N N 21 G C2 C N N 22 G N2 N N N 23 G N3 N N N 24 G C4 C Y N 25 G HOP3 H N N 26 G HOP2 H N N 27 G "H5'" H N N 28 G "H5''" H N N 29 G "H4'" H N N 30 G "H3'" H N N 31 G "HO3'" H N N 32 G "H2'" H N N 33 G "HO2'" H N N 34 G "H1'" H N N 35 G H8 H N N 36 G H1 H N N 37 G H21 H N N 38 G H22 H N N 39 HOH O O N N 40 HOH H1 H N N 41 HOH H2 H N N 42 NA NA NA N N 43 SR SR SR N N 44 U OP3 O N N 45 U P P N N 46 U OP1 O N N 47 U OP2 O N N 48 U "O5'" O N N 49 U "C5'" C N N 50 U "C4'" C N R 51 U "O4'" O N N 52 U "C3'" C N S 53 U "O3'" O N N 54 U "C2'" C N R 55 U "O2'" O N N 56 U "C1'" C N R 57 U N1 N N N 58 U C2 C N N 59 U O2 O N N 60 U N3 N N N 61 U C4 C N N 62 U O4 O N N 63 U C5 C N N 64 U C6 C N N 65 U HOP3 H N N 66 U HOP2 H N N 67 U "H5'" H N N 68 U "H5''" H N N 69 U "H4'" H N N 70 U "H3'" H N N 71 U "HO3'" H N N 72 U "H2'" H N N 73 U "HO2'" H N N 74 U "H1'" H N N 75 U H3 H N N 76 U H5 H N N 77 U H6 H N N 78 # 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 G OP3 P sing N N 1 G OP3 HOP3 sing N N 2 G P OP1 doub N N 3 G P OP2 sing N N 4 G P "O5'" sing N N 5 G OP2 HOP2 sing N N 6 G "O5'" "C5'" sing N N 7 G "C5'" "C4'" sing N N 8 G "C5'" "H5'" sing N N 9 G "C5'" "H5''" sing N N 10 G "C4'" "O4'" sing N N 11 G "C4'" "C3'" sing N N 12 G "C4'" "H4'" sing N N 13 G "O4'" "C1'" sing N N 14 G "C3'" "O3'" sing N N 15 G "C3'" "C2'" sing N N 16 G "C3'" "H3'" sing N N 17 G "O3'" "HO3'" sing N N 18 G "C2'" "O2'" sing N N 19 G "C2'" "C1'" sing N N 20 G "C2'" "H2'" sing N N 21 G "O2'" "HO2'" sing N N 22 G "C1'" N9 sing N N 23 G "C1'" "H1'" sing N N 24 G N9 C8 sing Y N 25 G N9 C4 sing Y N 26 G C8 N7 doub Y N 27 G C8 H8 sing N N 28 G N7 C5 sing Y N 29 G C5 C6 sing N N 30 G C5 C4 doub Y N 31 G C6 O6 doub N N 32 G C6 N1 sing N N 33 G N1 C2 sing N N 34 G N1 H1 sing N N 35 G C2 N2 sing N N 36 G C2 N3 doub N N 37 G N2 H21 sing N N 38 G N2 H22 sing N N 39 G N3 C4 sing N N 40 HOH O H1 sing N N 41 HOH O H2 sing N N 42 U OP3 P sing N N 43 U OP3 HOP3 sing N N 44 U P OP1 doub N N 45 U P OP2 sing N N 46 U P "O5'" sing N N 47 U OP2 HOP2 sing N N 48 U "O5'" "C5'" sing N N 49 U "C5'" "C4'" sing N N 50 U "C5'" "H5'" sing N N 51 U "C5'" "H5''" sing N N 52 U "C4'" "O4'" sing N N 53 U "C4'" "C3'" sing N N 54 U "C4'" "H4'" sing N N 55 U "O4'" "C1'" sing N N 56 U "C3'" "O3'" sing N N 57 U "C3'" "C2'" sing N N 58 U "C3'" "H3'" sing N N 59 U "O3'" "HO3'" sing N N 60 U "C2'" "O2'" sing N N 61 U "C2'" "C1'" sing N N 62 U "C2'" "H2'" sing N N 63 U "O2'" "HO2'" sing N N 64 U "C1'" N1 sing N N 65 U "C1'" "H1'" sing N N 66 U N1 C2 sing N N 67 U N1 C6 sing N N 68 U C2 O2 doub N N 69 U C2 N3 sing N N 70 U N3 C4 sing N N 71 U N3 H3 sing N N 72 U C4 O4 doub N N 73 U C4 C5 sing N N 74 U C5 C6 doub N N 75 U C5 H5 sing N N 76 U C6 H6 sing N N 77 # _ndb_struct_conf_na.entry_id 4RKV _ndb_struct_conf_na.feature 'double helix' # _ndb_struct_na_base_pair.model_number 1 _ndb_struct_na_base_pair.i_label_asym_id A _ndb_struct_na_base_pair.i_label_comp_id G _ndb_struct_na_base_pair.i_label_seq_id 3 _ndb_struct_na_base_pair.i_symmetry 1_555 _ndb_struct_na_base_pair.j_label_asym_id B _ndb_struct_na_base_pair.j_label_comp_id U _ndb_struct_na_base_pair.j_label_seq_id 1 _ndb_struct_na_base_pair.j_symmetry 1_555 _ndb_struct_na_base_pair.shear -1.679 _ndb_struct_na_base_pair.stretch 7.837 _ndb_struct_na_base_pair.stagger 0.997 _ndb_struct_na_base_pair.buckle 18.580 _ndb_struct_na_base_pair.propeller 14.472 _ndb_struct_na_base_pair.opening 179.146 _ndb_struct_na_base_pair.pair_number 1 _ndb_struct_na_base_pair.pair_name A_G1003:U2001_B _ndb_struct_na_base_pair.i_auth_asym_id A _ndb_struct_na_base_pair.i_auth_seq_id 1003 _ndb_struct_na_base_pair.i_PDB_ins_code ? _ndb_struct_na_base_pair.j_auth_asym_id B _ndb_struct_na_base_pair.j_auth_seq_id 2001 _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 ? # _atom_sites.entry_id 4RKV _atom_sites.fract_transf_matrix[1][1] 0.027289 _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] 0.027289 _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] 0.026970 _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 CA H N NA O P SR # loop_