data_4MCE # _entry.id 4MCE # _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 4MCE pdb_00004mce 10.2210/pdb4mce/pdb NDB NA2700 ? ? RCSB RCSB081735 ? ? WWPDB D_1000081735 ? ? # 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 2014-09-24 2 'Structure model' 1 1 2014-12-03 3 'Structure model' 1 2 2018-03-28 4 'Structure model' 1 3 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' Advisory 3 3 'Structure model' 'Data collection' 4 3 'Structure model' 'Derived calculations' 5 3 'Structure model' 'Source and taxonomy' 6 4 'Structure model' 'Data collection' 7 4 'Structure model' 'Database references' 8 4 'Structure model' 'Derived calculations' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 3 'Structure model' ndb_struct_conf_na 2 3 'Structure model' ndb_struct_na_base_pair 3 3 'Structure model' ndb_struct_na_base_pair_step 4 3 'Structure model' pdbx_distant_solvent_atoms 5 3 'Structure model' pdbx_entity_src_syn 6 3 'Structure model' pdbx_struct_assembly 7 3 'Structure model' pdbx_struct_assembly_gen 8 3 'Structure model' pdbx_struct_assembly_prop 9 3 'Structure model' pdbx_struct_oper_list 10 3 'Structure model' struct_conn 11 4 'Structure model' chem_comp_atom 12 4 'Structure model' chem_comp_bond 13 4 'Structure model' database_2 14 4 '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' '_ndb_struct_na_base_pair.buckle' 2 3 'Structure model' '_ndb_struct_na_base_pair_step.inclination' 3 3 'Structure model' '_pdbx_entity_src_syn.ncbi_taxonomy_id' 4 3 'Structure model' '_pdbx_entity_src_syn.organism_scientific' 5 3 'Structure model' '_struct_conn.ptnr2_label_atom_id' 6 4 'Structure model' '_database_2.pdbx_DOI' 7 4 'Structure model' '_database_2.pdbx_database_accession' 8 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 9 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 10 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 4MCE _pdbx_database_status.recvd_initial_deposition_date 2013-08-21 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Hudson, W.H.' 1 'Ortlund, E.A.' 2 # _citation.id primary _citation.title 'Conserved sequence-specific lincRNA-steroid receptor interactions drive transcriptional repression and direct cell fate.' _citation.journal_abbrev 'Nat Commun' _citation.journal_volume 5 _citation.page_first 5395 _citation.page_last 5395 _citation.year 2014 _citation.journal_id_ASTM ? _citation.country UK _citation.journal_id_ISSN 2041-1723 _citation.journal_id_CSD ? _citation.book_publisher ? _citation.pdbx_database_id_PubMed 25377354 _citation.pdbx_database_id_DOI 10.1038/ncomms6395 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Hudson, W.H.' 1 ? primary 'Pickard, M.R.' 2 ? primary 'de Vera, I.M.' 3 ? primary 'Kuiper, E.G.' 4 ? primary 'Mourtada-Maarabouni, M.' 5 ? primary 'Conn, G.L.' 6 ? primary 'Kojetin, D.J.' 7 ? primary 'Williams, G.T.' 8 ? primary 'Ortlund, E.A.' 9 ? # 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 'Gas5 GREM Fwd' 3154.892 2 ? ? ? ? 2 polymer syn 'Gas5 GREM Rev' 3506.154 2 ? ? ? ? 3 non-polymer syn 'SULFATE ION' 96.063 3 ? ? ? ? 4 water nat water 18.015 53 ? ? ? ? # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 polyribonucleotide no no CAGUGGUCUU CAGUGGUCUU A,C ? 2 polyribonucleotide no no AAGACUGCCUG AAGACUGCCUG B,D ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 3 'SULFATE ION' SO4 4 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 A n 1 3 G n 1 4 U n 1 5 G n 1 6 G n 1 7 U n 1 8 C n 1 9 U n 1 10 U n 2 1 A n 2 2 A n 2 3 G n 2 4 A n 2 5 C n 2 6 U n 2 7 G n 2 8 C n 2 9 C n 2 10 U n 2 11 G n # loop_ _pdbx_entity_src_syn.entity_id _pdbx_entity_src_syn.pdbx_src_id _pdbx_entity_src_syn.pdbx_alt_source_flag _pdbx_entity_src_syn.pdbx_beg_seq_num _pdbx_entity_src_syn.pdbx_end_seq_num _pdbx_entity_src_syn.organism_scientific _pdbx_entity_src_syn.organism_common_name _pdbx_entity_src_syn.ncbi_taxonomy_id _pdbx_entity_src_syn.details 1 1 sample ? ? 'Homo sapiens' ? 9606 'RNA Synthesis' 2 1 sample ? ? 'Homo sapiens' ? 9606 'RNA Synthesis' # 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 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 A 2 2 2 A A A . n A 1 3 G 3 3 3 G G A . n A 1 4 U 4 4 4 U U A . n A 1 5 G 5 5 5 G G A . n A 1 6 G 6 6 6 G G A . n A 1 7 U 7 7 7 U U A . n A 1 8 C 8 8 8 C C A . n A 1 9 U 9 9 9 U U A . n A 1 10 U 10 10 10 U U A . n B 2 1 A 1 1 1 A A B . n B 2 2 A 2 2 2 A A B . n B 2 3 G 3 3 3 G G B . n B 2 4 A 4 4 4 A A B . n B 2 5 C 5 5 5 C C B . n B 2 6 U 6 6 6 U U B . n B 2 7 G 7 7 7 G G B . n B 2 8 C 8 8 8 C C B . n B 2 9 C 9 9 9 C C B . n B 2 10 U 10 10 10 U U B . n B 2 11 G 11 11 ? ? ? B . n C 1 1 C 1 1 1 C C C . n C 1 2 A 2 2 2 A A C . n C 1 3 G 3 3 3 G G C . n C 1 4 U 4 4 4 U U C . n C 1 5 G 5 5 5 G G C . n C 1 6 G 6 6 6 G G C . n C 1 7 U 7 7 7 U U C . n C 1 8 C 8 8 8 C C C . n C 1 9 U 9 9 9 U U C . n C 1 10 U 10 10 10 U U C . n D 2 1 A 1 1 1 A A D . n D 2 2 A 2 2 2 A A D . n D 2 3 G 3 3 3 G G D . n D 2 4 A 4 4 4 A A D . n D 2 5 C 5 5 5 C C D . n D 2 6 U 6 6 6 U U D . n D 2 7 G 7 7 7 G G D . n D 2 8 C 8 8 8 C C D . n D 2 9 C 9 9 9 C C D . n D 2 10 U 10 10 10 U U D . n D 2 11 G 11 11 11 G G D . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code E 3 SO4 1 101 2 SO4 SO4 B . F 3 SO4 1 102 3 SO4 SO4 B . G 3 SO4 1 101 1 SO4 SO4 D . H 4 HOH 1 101 4 HOH HOH A . H 4 HOH 2 102 5 HOH HOH A . H 4 HOH 3 103 9 HOH HOH A . H 4 HOH 4 104 15 HOH HOH A . H 4 HOH 5 105 16 HOH HOH A . H 4 HOH 6 106 17 HOH HOH A . H 4 HOH 7 107 18 HOH HOH A . H 4 HOH 8 108 20 HOH HOH A . H 4 HOH 9 109 22 HOH HOH A . H 4 HOH 10 110 24 HOH HOH A . H 4 HOH 11 111 31 HOH HOH A . H 4 HOH 12 112 37 HOH HOH A . H 4 HOH 13 113 42 HOH HOH A . H 4 HOH 14 114 48 HOH HOH A . H 4 HOH 15 115 54 HOH HOH A . H 4 HOH 16 116 57 HOH HOH A . H 4 HOH 17 117 65 HOH HOH A . H 4 HOH 18 118 66 HOH HOH A . H 4 HOH 19 119 69 HOH HOH A . H 4 HOH 20 120 71 HOH HOH A . H 4 HOH 21 121 72 HOH HOH A . H 4 HOH 22 122 73 HOH HOH A . H 4 HOH 23 123 82 HOH HOH A . H 4 HOH 24 124 84 HOH HOH A . I 4 HOH 1 201 2 HOH HOH B . I 4 HOH 2 202 3 HOH HOH B . I 4 HOH 3 203 7 HOH HOH B . I 4 HOH 4 204 11 HOH HOH B . I 4 HOH 5 205 13 HOH HOH B . I 4 HOH 6 206 14 HOH HOH B . I 4 HOH 7 207 21 HOH HOH B . I 4 HOH 8 208 23 HOH HOH B . I 4 HOH 9 209 25 HOH HOH B . I 4 HOH 10 210 26 HOH HOH B . I 4 HOH 11 211 30 HOH HOH B . I 4 HOH 12 212 36 HOH HOH B . I 4 HOH 13 213 40 HOH HOH B . I 4 HOH 14 214 41 HOH HOH B . I 4 HOH 15 215 44 HOH HOH B . I 4 HOH 16 216 45 HOH HOH B . I 4 HOH 17 217 47 HOH HOH B . I 4 HOH 18 218 55 HOH HOH B . I 4 HOH 19 219 59 HOH HOH B . I 4 HOH 20 220 75 HOH HOH B . I 4 HOH 21 221 79 HOH HOH B . I 4 HOH 22 222 85 HOH HOH B . J 4 HOH 1 101 29 HOH HOH C . J 4 HOH 2 102 58 HOH HOH C . J 4 HOH 3 103 62 HOH HOH C . J 4 HOH 4 104 64 HOH HOH C . K 4 HOH 1 201 27 HOH HOH D . K 4 HOH 2 202 34 HOH HOH D . K 4 HOH 3 203 38 HOH HOH D . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal JDirector 'data collection' . ? 1 PHASER phasing . ? 2 PHENIX refinement '(phenix.refine: 1.7.1_743)' ? 3 HKL-2000 'data reduction' . ? 4 HKL-2000 'data scaling' . ? 5 # _cell.entry_id 4MCE _cell.length_a 43.485 _cell.length_b 43.485 _cell.length_c 173.188 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 18 _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 4MCE _symmetry.space_group_name_H-M 'H 3' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 146 _symmetry.space_group_name_Hall ? # _exptl.entry_id 4MCE _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.37 _exptl_crystal.density_percent_sol 48.00 _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 5.5 _exptl_crystal_grow.pdbx_details ;0.05 M sodium succinate pH 5.5 0.5 mM spermine 0.02 M magnesium chloride 3 M ammonium sulfate , VAPOR DIFFUSION, HANGING DROP, temperature 298K ; _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'RIGAKU SATURN 944+' _diffrn_detector.pdbx_collection_date 2011-05-04 _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 1.54 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source 'ROTATING ANODE' _diffrn_source.type RIGAKU _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.54 # _reflns.entry_id 4MCE _reflns.observed_criterion_sigma_I 0 _reflns.observed_criterion_sigma_F 0 _reflns.d_resolution_low 50 _reflns.d_resolution_high 2.2 _reflns.number_obs 6216 _reflns.number_all 6292 _reflns.percent_possible_obs 98.8 _reflns.pdbx_Rmerge_I_obs 0.069 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 3.5 _reflns.R_free_details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # _reflns_shell.d_res_high 2.20 _reflns_shell.d_res_low 2.24 _reflns_shell.percent_possible_all 82.1 _reflns_shell.Rmerge_I_obs 0.256 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 5.5 _reflns_shell.pdbx_redundancy 2.5 _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 ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.entry_id 4MCE _refine.ls_number_reflns_obs 6140 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 1.97 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 21.743 _refine.ls_d_res_high 2.205 _refine.ls_percent_reflns_obs 99.50 _refine.ls_R_factor_obs 0.1900 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.1809 _refine.ls_R_factor_R_free 0.2584 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 9.97 _refine.ls_number_reflns_R_free 612 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean ? _refine.aniso_B[1][1] -0.1784 _refine.aniso_B[2][2] -0.1784 _refine.aniso_B[3][3] 0.3568 _refine.aniso_B[1][2] -0.0000 _refine.aniso_B[1][3] -0.0000 _refine.aniso_B[2][3] 0.0000 _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.solvent_model_param_ksol 0.474 _refine.solvent_model_param_bsol 54.068 _refine.pdbx_solvent_vdw_probe_radii 0.30 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.00 _refine.pdbx_ls_cross_valid_method ? _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values TWIN_LSQ_F _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML . _refine.pdbx_overall_phase_error 28.65 _refine.overall_SU_B ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _refine.overall_SU_R_free ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_diffrn_id 1 _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_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 857 _refine_hist.pdbx_number_atoms_ligand 15 _refine_hist.number_atoms_solvent 53 _refine_hist.number_atoms_total 925 _refine_hist.d_res_high 2.205 _refine_hist.d_res_low 21.743 # 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_restraint_function _refine_ls_restr.pdbx_refine_id f_bond_d 0.006 ? ? 966 ? 'X-RAY DIFFRACTION' f_angle_d 0.764 ? ? 1497 ? 'X-RAY DIFFRACTION' f_dihedral_angle_d 15.885 ? ? 476 ? 'X-RAY DIFFRACTION' f_chiral_restr 0.058 ? ? 201 ? 'X-RAY DIFFRACTION' f_plane_restr 0.006 ? ? 41 ? 'X-RAY DIFFRACTION' # loop_ _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.number_reflns_R_work _refine_ls_shell.R_factor_R_work _refine_ls_shell.percent_reflns_obs _refine_ls_shell.R_factor_R_free _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.number_reflns_R_free _refine_ls_shell.number_reflns_all _refine_ls_shell.R_factor_all _refine_ls_shell.number_reflns_obs _refine_ls_shell.redundancy_reflns_obs _refine_ls_shell.pdbx_refine_id . 2.2081 2.4299 1370 0.2411 89.00 0.3158 . . 158 . . . . 'X-RAY DIFFRACTION' . 2.4299 2.7808 1364 0.2295 90.00 0.3498 . . 152 . . . . 'X-RAY DIFFRACTION' . 2.7808 3.5008 1399 0.1764 90.00 0.2680 . . 147 . . . . 'X-RAY DIFFRACTION' . 3.5008 20.6788 1379 0.1529 89.00 0.2134 . . 154 . . . . 'X-RAY DIFFRACTION' # _database_PDB_matrix.entry_id 4MCE _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 4MCE _struct.title 'Crystal structure of the Gas5 GRE Mimic' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 4MCE _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'RNA Double Helix, 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 2 ? C N N 1 ? D N N 2 ? E N N 3 ? F N N 3 ? G N N 3 ? H N N 4 ? I N N 4 ? J N N 4 ? K N N 4 ? # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.entity_id _struct_ref.pdbx_align_begin _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_db_isoform 1 PDB 4MCE 4MCE 1 ? CAGUGGUCUU ? 2 PDB 4MCE 4MCE 2 ? AAGACUGCCUG ? # 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 4MCE A 1 ? 10 ? 4MCE 1 ? 10 ? 1 10 2 1 4MCE C 1 ? 10 ? 4MCE 1 ? 10 ? 1 10 3 2 4MCE B 1 ? 11 ? 4MCE 1 ? 11 ? 1 11 4 2 4MCE D 1 ? 11 ? 4MCE 1 ? 11 ? 1 11 # loop_ _pdbx_struct_assembly.id _pdbx_struct_assembly.details _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count 1 author_and_software_defined_assembly PISA dimeric 2 2 author_and_software_defined_assembly PISA dimeric 2 # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 1170 ? 1 MORE -22 ? 1 'SSA (A^2)' 3970 ? 2 'ABSA (A^2)' 1080 ? 2 MORE -14 ? 2 'SSA (A^2)' 4030 ? # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 1 A,B,E,F,H,I 2 1 C,D,G,J,K # _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 C 1 N4 ? ? ? 1_555 B U 10 O2 ? ? A C 1 B U 10 1_555 ? ? ? ? ? ? 'C-U MISPAIR' ? ? ? hydrog2 hydrog ? ? A A 2 N6 ? ? ? 1_555 B C 9 N3 ? ? A A 2 B C 9 1_555 ? ? ? ? ? ? 'A-C MISPAIR' ? ? ? hydrog3 hydrog ? ? A G 3 N1 ? ? ? 1_555 B C 8 N3 ? ? A G 3 B C 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 3 N2 ? ? ? 1_555 B C 8 O2 ? ? A G 3 B C 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A G 3 O6 ? ? ? 1_555 B C 8 N4 ? ? A G 3 B C 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A U 4 N3 ? ? ? 1_555 B G 7 O6 ? ? A U 4 B G 7 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog7 hydrog ? ? A U 4 O2 ? ? ? 1_555 B G 7 N1 ? ? A U 4 B G 7 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog8 hydrog ? ? A G 5 N1 ? ? ? 1_555 B U 6 O2 ? ? A G 5 B U 6 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog9 hydrog ? ? A G 5 O6 ? ? ? 1_555 B U 6 N3 ? ? A G 5 B U 6 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog10 hydrog ? ? A G 6 N1 ? ? ? 1_555 B C 5 N3 ? ? A G 6 B C 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A G 6 N2 ? ? ? 1_555 B C 5 O2 ? ? A G 6 B C 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A G 6 O6 ? ? ? 1_555 B C 5 N4 ? ? A G 6 B C 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A U 7 N3 ? ? ? 1_555 B A 4 N1 ? ? A U 7 B A 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A U 7 O4 ? ? ? 1_555 B A 4 N6 ? ? A U 7 B A 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A C 8 N3 ? ? ? 1_555 B G 3 N1 ? ? A C 8 B G 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A C 8 N4 ? ? ? 1_555 B G 3 O6 ? ? A C 8 B G 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A C 8 O2 ? ? ? 1_555 B G 3 N2 ? ? A C 8 B G 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A U 9 N3 ? ? ? 1_555 B A 2 N1 ? ? A U 9 B A 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A U 9 O4 ? ? ? 1_555 B A 2 N6 ? ? A U 9 B A 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A U 10 N3 ? ? ? 1_555 B A 1 N1 ? ? A U 10 B A 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A U 10 O4 ? ? ? 1_555 B A 1 N6 ? ? A U 10 B A 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? C A 2 N6 ? ? ? 1_555 D C 9 N3 ? ? C A 2 D C 9 1_555 ? ? ? ? ? ? 'A-C MISPAIR' ? ? ? hydrog23 hydrog ? ? C G 3 N1 ? ? ? 1_555 D C 8 N3 ? ? C G 3 D C 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? C G 3 N2 ? ? ? 1_555 D C 8 O2 ? ? C G 3 D C 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? C G 3 O6 ? ? ? 1_555 D C 8 N4 ? ? C G 3 D C 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? C U 4 O2 ? ? ? 1_555 D G 7 N2 ? ? C U 4 D G 7 1_555 ? ? ? ? ? ? 'U-G MISPAIR' ? ? ? hydrog27 hydrog ? ? C G 5 N1 ? ? ? 1_555 D U 6 O2 ? ? C G 5 D U 6 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog28 hydrog ? ? C G 5 O6 ? ? ? 1_555 D U 6 N3 ? ? C G 5 D U 6 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog29 hydrog ? ? C G 6 N1 ? ? ? 1_555 D C 5 N3 ? ? C G 6 D C 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? C G 6 N2 ? ? ? 1_555 D C 5 O2 ? ? C G 6 D C 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? C G 6 O6 ? ? ? 1_555 D C 5 N4 ? ? C G 6 D C 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? C U 7 N3 ? ? ? 1_555 D A 4 N1 ? ? C U 7 D A 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? C U 7 O4 ? ? ? 1_555 D A 4 N6 ? ? C U 7 D A 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? C C 8 N3 ? ? ? 1_555 D G 3 N1 ? ? C C 8 D G 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? C C 8 N4 ? ? ? 1_555 D G 3 O6 ? ? C C 8 D G 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? C C 8 O2 ? ? ? 1_555 D G 3 N2 ? ? C C 8 D G 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? C U 9 N3 ? ? ? 1_555 D A 2 N1 ? ? C U 9 D A 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? C U 9 O4 ? ? ? 1_555 D A 2 N6 ? ? C U 9 D A 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? C U 10 N3 ? ? ? 1_555 D A 1 N1 ? ? C U 10 D A 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? C U 10 O4 ? ? ? 1_555 D A 1 N6 ? ? C U 10 D A 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # 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 B SO4 101 ? 9 'BINDING SITE FOR RESIDUE SO4 B 101' AC2 Software B SO4 102 ? 8 'BINDING SITE FOR RESIDUE SO4 B 102' AC3 Software D SO4 101 ? 3 'BINDING SITE FOR RESIDUE SO4 D 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 G B 3 ? G B 3 . ? 3_655 ? 2 AC1 9 G B 3 ? G B 3 . ? 2_545 ? 3 AC1 9 G B 3 ? G B 3 . ? 1_555 ? 4 AC1 9 HOH I . ? HOH B 202 . ? 1_555 ? 5 AC1 9 HOH I . ? HOH B 202 . ? 2_545 ? 6 AC1 9 HOH I . ? HOH B 202 . ? 3_655 ? 7 AC1 9 HOH I . ? HOH B 219 . ? 2_545 ? 8 AC1 9 HOH I . ? HOH B 219 . ? 1_555 ? 9 AC1 9 HOH I . ? HOH B 219 . ? 3_655 ? 10 AC2 8 G B 7 ? G B 7 . ? 1_555 ? 11 AC2 8 G B 7 ? G B 7 . ? 3_555 ? 12 AC2 8 G B 7 ? G B 7 . ? 2_555 ? 13 AC2 8 C B 8 ? C B 8 . ? 3_555 ? 14 AC2 8 C B 8 ? C B 8 . ? 2_555 ? 15 AC2 8 C B 8 ? C B 8 . ? 1_555 ? 16 AC2 8 HOH I . ? HOH B 221 . ? 1_555 ? 17 AC2 8 HOH I . ? HOH B 221 . ? 2_555 ? 18 AC3 3 C D 8 ? C D 8 . ? 2_545 ? 19 AC3 3 C D 8 ? C D 8 . ? 1_555 ? 20 AC3 3 C D 8 ? C D 8 . ? 3_655 ? # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 1 N4 C C 8 ? ? O C HOH 103 ? ? 2.00 2 1 "O2'" A C 8 ? ? O A HOH 114 ? ? 2.10 3 1 OP1 A C 8 ? ? O A HOH 103 ? ? 2.17 4 1 N6 B A 2 ? ? O B HOH 203 ? ? 2.17 # 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 ? E SO4 . 2 1 B SO4 101 ? E SO4 . 3 1 B SO4 102 ? F SO4 . 4 1 B SO4 102 ? F SO4 . 5 1 D SO4 101 ? G SO4 . 6 1 D SO4 101 ? G SO4 . # _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 A _pdbx_distant_solvent_atoms.auth_comp_id HOH _pdbx_distant_solvent_atoms.auth_seq_id 124 _pdbx_distant_solvent_atoms.PDB_ins_code ? _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance 9.70 _pdbx_distant_solvent_atoms.neighbor_ligand_distance . # _pdbx_unobs_or_zero_occ_residues.id 1 _pdbx_unobs_or_zero_occ_residues.PDB_model_num 1 _pdbx_unobs_or_zero_occ_residues.polymer_flag Y _pdbx_unobs_or_zero_occ_residues.occupancy_flag 1 _pdbx_unobs_or_zero_occ_residues.auth_asym_id B _pdbx_unobs_or_zero_occ_residues.auth_comp_id G _pdbx_unobs_or_zero_occ_residues.auth_seq_id 11 _pdbx_unobs_or_zero_occ_residues.PDB_ins_code ? _pdbx_unobs_or_zero_occ_residues.label_asym_id B _pdbx_unobs_or_zero_occ_residues.label_comp_id G _pdbx_unobs_or_zero_occ_residues.label_seq_id 11 # 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 G OP3 O N N 73 G P P N N 74 G OP1 O N N 75 G OP2 O N N 76 G "O5'" O N N 77 G "C5'" C N N 78 G "C4'" C N R 79 G "O4'" O N N 80 G "C3'" C N S 81 G "O3'" O N N 82 G "C2'" C N R 83 G "O2'" O N N 84 G "C1'" C N R 85 G N9 N Y N 86 G C8 C Y N 87 G N7 N Y N 88 G C5 C Y N 89 G C6 C N N 90 G O6 O N N 91 G N1 N N N 92 G C2 C N N 93 G N2 N N N 94 G N3 N N N 95 G C4 C Y N 96 G HOP3 H N N 97 G HOP2 H N N 98 G "H5'" H N N 99 G "H5''" H N N 100 G "H4'" H N N 101 G "H3'" H N N 102 G "HO3'" H N N 103 G "H2'" H N N 104 G "HO2'" H N N 105 G "H1'" H N N 106 G H8 H N N 107 G H1 H N N 108 G H21 H N N 109 G H22 H N N 110 HOH O O N N 111 HOH H1 H N N 112 HOH H2 H N N 113 SO4 S S N N 114 SO4 O1 O N N 115 SO4 O2 O N N 116 SO4 O3 O N N 117 SO4 O4 O N N 118 U OP3 O N N 119 U P P N N 120 U OP1 O N N 121 U OP2 O N N 122 U "O5'" O N N 123 U "C5'" C N N 124 U "C4'" C N R 125 U "O4'" O N N 126 U "C3'" C N S 127 U "O3'" O N N 128 U "C2'" C N R 129 U "O2'" O N N 130 U "C1'" C N R 131 U N1 N N N 132 U C2 C N N 133 U O2 O N N 134 U N3 N N N 135 U C4 C N N 136 U O4 O N N 137 U C5 C N N 138 U C6 C N N 139 U HOP3 H N N 140 U HOP2 H N N 141 U "H5'" H N N 142 U "H5''" H N N 143 U "H4'" H N N 144 U "H3'" H N N 145 U "HO3'" H N N 146 U "H2'" H N N 147 U "HO2'" H N N 148 U "H1'" H N N 149 U H3 H N N 150 U H5 H N N 151 U H6 H N N 152 # 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 G OP3 P sing N N 76 G OP3 HOP3 sing N N 77 G P OP1 doub N N 78 G P OP2 sing N N 79 G P "O5'" sing N N 80 G OP2 HOP2 sing N N 81 G "O5'" "C5'" sing N N 82 G "C5'" "C4'" sing N N 83 G "C5'" "H5'" sing N N 84 G "C5'" "H5''" sing N N 85 G "C4'" "O4'" sing N N 86 G "C4'" "C3'" sing N N 87 G "C4'" "H4'" sing N N 88 G "O4'" "C1'" sing N N 89 G "C3'" "O3'" sing N N 90 G "C3'" "C2'" sing N N 91 G "C3'" "H3'" sing N N 92 G "O3'" "HO3'" sing N N 93 G "C2'" "O2'" sing N N 94 G "C2'" "C1'" sing N N 95 G "C2'" "H2'" sing N N 96 G "O2'" "HO2'" sing N N 97 G "C1'" N9 sing N N 98 G "C1'" "H1'" sing N N 99 G N9 C8 sing Y N 100 G N9 C4 sing Y N 101 G C8 N7 doub Y N 102 G C8 H8 sing N N 103 G N7 C5 sing Y N 104 G C5 C6 sing N N 105 G C5 C4 doub Y N 106 G C6 O6 doub N N 107 G C6 N1 sing N N 108 G N1 C2 sing N N 109 G N1 H1 sing N N 110 G C2 N2 sing N N 111 G C2 N3 doub N N 112 G N2 H21 sing N N 113 G N2 H22 sing N N 114 G N3 C4 sing N N 115 HOH O H1 sing N N 116 HOH O H2 sing N N 117 SO4 S O1 doub N N 118 SO4 S O2 doub N N 119 SO4 S O3 sing N N 120 SO4 S O4 sing N N 121 U OP3 P sing N N 122 U OP3 HOP3 sing N N 123 U P OP1 doub N N 124 U P OP2 sing N N 125 U P "O5'" sing N N 126 U OP2 HOP2 sing N N 127 U "O5'" "C5'" sing N N 128 U "C5'" "C4'" sing N N 129 U "C5'" "H5'" sing N N 130 U "C5'" "H5''" sing N N 131 U "C4'" "O4'" sing N N 132 U "C4'" "C3'" sing N N 133 U "C4'" "H4'" sing N N 134 U "O4'" "C1'" sing N N 135 U "C3'" "O3'" sing N N 136 U "C3'" "C2'" sing N N 137 U "C3'" "H3'" sing N N 138 U "O3'" "HO3'" sing N N 139 U "C2'" "O2'" sing N N 140 U "C2'" "C1'" sing N N 141 U "C2'" "H2'" sing N N 142 U "O2'" "HO2'" sing N N 143 U "C1'" N1 sing N N 144 U "C1'" "H1'" sing N N 145 U N1 C2 sing N N 146 U N1 C6 sing N N 147 U C2 O2 doub N N 148 U C2 N3 sing N N 149 U N3 C4 sing N N 150 U N3 H3 sing N N 151 U C4 O4 doub N N 152 U C4 C5 sing N N 153 U C5 C6 doub N N 154 U C5 H5 sing N N 155 U C6 H6 sing N N 156 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 4MCE 'double helix' 4MCE '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 C 1 1_555 B U 10 1_555 -3.545 -2.288 -0.178 1.662 -10.234 11.661 1 A_C1:U10_B A 1 ? B 10 ? ? ? 1 A A 2 1_555 B C 9 1_555 -1.780 -0.089 0.570 7.853 -19.351 12.487 2 A_A2:C9_B A 2 ? B 9 ? ? 1 1 A G 3 1_555 B C 8 1_555 -0.279 -0.063 -0.692 -13.947 -16.555 8.182 3 A_G3:C8_B A 3 ? B 8 ? 19 1 1 A U 4 1_555 B G 7 1_555 2.520 -0.486 0.310 -5.100 -11.963 3.943 4 A_U4:G7_B A 4 ? B 7 ? 28 1 1 A G 5 1_555 B U 6 1_555 -2.670 -1.009 -0.052 -6.169 -8.538 -4.562 5 A_G5:U6_B A 5 ? B 6 ? 28 1 1 A G 6 1_555 B C 5 1_555 -0.063 -0.575 -0.040 -4.068 -14.867 -5.246 6 A_G6:C5_B A 6 ? B 5 ? 19 1 1 A U 7 1_555 B A 4 1_555 0.315 -0.146 -0.190 3.500 -13.147 2.643 7 A_U7:A4_B A 7 ? B 4 ? 20 1 1 A C 8 1_555 B G 3 1_555 0.564 -0.024 -0.503 6.345 -9.596 0.286 8 A_C8:G3_B A 8 ? B 3 ? 19 1 1 A U 9 1_555 B A 2 1_555 0.582 0.221 -0.343 3.103 -18.184 5.938 9 A_U9:A2_B A 9 ? B 2 ? 20 1 1 A U 10 1_555 B A 1 1_555 0.250 -0.045 0.617 -7.758 -5.155 9.525 10 A_U10:A1_B A 10 ? B 1 ? 20 1 1 C A 2 1_555 D C 9 1_555 -3.426 -0.498 -0.629 1.500 -1.187 9.929 11 C_A2:C9_D C 2 ? D 9 ? ? 1 1 C G 3 1_555 D C 8 1_555 -0.222 0.098 -0.685 -18.362 -19.924 -3.708 12 C_G3:C8_D C 3 ? D 8 ? 19 1 1 C U 4 1_555 D G 7 1_555 2.200 1.378 0.207 1.403 -1.656 25.180 13 C_U4:G7_D C 4 ? D 7 ? ? ? 1 C G 5 1_555 D U 6 1_555 -2.084 -0.720 -0.219 -10.539 -15.271 -2.465 14 C_G5:U6_D C 5 ? D 6 ? 28 1 1 C G 6 1_555 D C 5 1_555 -0.427 -0.358 -0.500 -8.815 -12.534 5.937 15 C_G6:C5_D C 6 ? D 5 ? 19 1 1 C U 7 1_555 D A 4 1_555 -1.004 -0.199 0.197 -4.810 -19.702 12.761 16 C_U7:A4_D C 7 ? D 4 ? 20 1 1 C C 8 1_555 D G 3 1_555 0.860 0.049 0.056 6.676 -27.278 5.983 17 C_C8:G3_D C 8 ? D 3 ? 19 1 1 C U 9 1_555 D A 2 1_555 0.406 -0.313 -0.017 2.144 -22.076 4.278 18 C_U9:A2_D C 9 ? D 2 ? 20 1 1 C U 10 1_555 D A 1 1_555 0.196 -0.357 -0.627 13.249 -15.863 -6.339 19 C_U10:A1_D C 10 ? D 1 ? 20 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A C 1 1_555 B U 10 1_555 A A 2 1_555 B C 9 1_555 0.546 -0.892 3.210 -8.448 3.975 40.495 -1.662 -1.627 2.946 5.652 12.013 41.513 1 AA_C1A2:C9U10_BB A 1 ? B 10 ? A 2 ? B 9 ? 1 A A 2 1_555 B C 9 1_555 A G 3 1_555 B C 8 1_555 -0.592 -1.372 3.864 5.927 14.571 36.407 -3.902 1.637 2.993 22.097 -8.989 39.554 2 AA_A2G3:C8C9_BB A 2 ? B 9 ? A 3 ? B 8 ? 1 A G 3 1_555 B C 8 1_555 A U 4 1_555 B G 7 1_555 -0.087 -0.952 3.009 -5.492 9.500 38.791 -2.341 -0.427 2.699 13.966 8.074 40.256 3 AA_G3U4:G7C8_BB A 3 ? B 8 ? A 4 ? B 7 ? 1 A U 4 1_555 B G 7 1_555 A G 5 1_555 B U 6 1_555 0.050 -2.863 2.981 3.242 11.838 11.324 -14.208 1.018 0.011 45.777 -12.535 16.685 4 AA_U4G5:U6G7_BB A 4 ? B 7 ? A 5 ? B 6 ? 1 A G 5 1_555 B U 6 1_555 A G 6 1_555 B C 5 1_555 0.139 -1.361 3.332 0.147 6.645 39.223 -2.761 -0.187 3.070 9.813 -0.217 39.760 5 AA_G5G6:C5U6_BB A 5 ? B 6 ? A 6 ? B 5 ? 1 A G 6 1_555 B C 5 1_555 A U 7 1_555 B A 4 1_555 0.373 -1.837 3.052 0.646 2.040 36.513 -3.185 -0.513 2.955 3.252 -1.030 36.574 6 AA_G6U7:A4C5_BB A 6 ? B 5 ? A 7 ? B 4 ? 1 A U 7 1_555 B A 4 1_555 A C 8 1_555 B G 3 1_555 -0.644 -1.359 3.259 -0.297 6.473 30.400 -3.723 1.148 2.921 12.170 0.559 31.067 7 AA_U7C8:G3A4_BB A 7 ? B 4 ? A 8 ? B 3 ? 1 A C 8 1_555 B G 3 1_555 A U 9 1_555 B A 2 1_555 0.079 -1.688 3.443 1.431 13.019 26.443 -5.931 0.132 2.368 26.493 -2.911 29.457 8 AA_C8U9:A2G3_BB A 8 ? B 3 ? A 9 ? B 2 ? 1 A U 9 1_555 B A 2 1_555 A U 10 1_555 B A 1 1_555 0.888 -1.945 3.413 -5.818 12.611 29.609 -5.441 -2.493 2.214 23.142 10.676 32.638 9 AA_U9U10:A1A2_BB A 9 ? B 2 ? A 10 ? B 1 ? 1 C A 2 1_555 D C 9 1_555 C G 3 1_555 D C 8 1_555 -0.504 -1.574 4.092 -2.389 8.312 38.961 -3.469 0.406 3.716 12.279 3.528 39.873 10 CC_A2G3:C8C9_DD C 2 ? D 9 ? C 3 ? D 8 ? 1 C G 3 1_555 D C 8 1_555 C U 4 1_555 D G 7 1_555 1.498 -1.197 2.541 -5.743 9.248 35.845 -2.717 -2.864 1.930 14.616 9.077 37.409 11 CC_G3U4:G7C8_DD C 3 ? D 8 ? C 4 ? D 7 ? 1 C U 4 1_555 D G 7 1_555 C G 5 1_555 D U 6 1_555 -0.793 -2.514 3.041 5.721 15.313 17.643 -9.113 3.053 0.464 40.397 -15.092 24.008 12 CC_U4G5:U6G7_DD C 4 ? D 7 ? C 5 ? D 6 ? 1 C G 5 1_555 D U 6 1_555 C G 6 1_555 D C 5 1_555 0.090 -0.956 3.264 -0.849 11.208 39.562 -2.533 -0.217 2.897 16.167 1.224 41.066 13 CC_G5G6:C5U6_DD C 5 ? D 6 ? C 6 ? D 5 ? 1 C G 6 1_555 D C 5 1_555 C U 7 1_555 D A 4 1_555 0.071 -1.296 3.092 -4.283 3.737 26.643 -3.611 -1.134 2.840 7.993 9.161 27.232 14 CC_G6U7:A4C5_DD C 6 ? D 5 ? C 7 ? D 4 ? 1 C U 7 1_555 D A 4 1_555 C C 8 1_555 D G 3 1_555 0.123 -0.596 3.044 2.952 4.835 39.527 -1.386 0.134 2.955 7.105 -4.338 39.915 15 CC_U7C8:G3A4_DD C 7 ? D 4 ? C 8 ? D 3 ? 1 C C 8 1_555 D G 3 1_555 C U 9 1_555 D A 2 1_555 -0.393 -1.032 3.053 -0.177 11.943 32.791 -3.325 0.633 2.536 20.334 0.302 34.842 16 CC_C8U9:A2G3_DD C 8 ? D 3 ? C 9 ? D 2 ? 1 C U 9 1_555 D A 2 1_555 C U 10 1_555 D A 1 1_555 -0.097 -0.919 3.098 4.802 2.005 33.182 -1.898 0.904 2.996 3.484 -8.344 33.576 17 CC_U9U10:A1A2_DD C 9 ? D 2 ? C 10 ? D 1 ? # _atom_sites.entry_id 4MCE _atom_sites.fract_transf_matrix[1][1] 0.022996 _atom_sites.fract_transf_matrix[1][2] 0.013277 _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] 0.026554 _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] 0.005774 _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_