data_310D # _entry.id 310D # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.389 _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 310D pdb_0000310d 10.2210/pdb310d/pdb RCSB ARFS26 ? ? WWPDB D_1000178778 ? ? # 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 1997-06-24 2 'Structure model' 1 1 2008-05-22 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2020-06-24 5 'Structure model' 1 4 2024-02-21 6 'Structure model' 1 5 2024-04-03 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' 3 4 'Structure model' 'Data collection' 4 4 'Structure model' 'Database references' 5 4 'Structure model' 'Derived calculations' 6 4 'Structure model' 'Source and taxonomy' 7 5 'Structure model' 'Data collection' 8 5 'Structure model' 'Database references' 9 5 'Structure model' 'Derived calculations' 10 6 '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 4 'Structure model' diffrn_source 2 4 'Structure model' entity_src_gen 3 4 'Structure model' struct_conn 4 4 'Structure model' struct_ref 5 4 'Structure model' struct_ref_seq 6 5 'Structure model' chem_comp_atom 7 5 'Structure model' chem_comp_bond 8 5 'Structure model' database_2 9 5 'Structure model' pdbx_struct_conn_angle 10 5 'Structure model' struct_conn 11 5 'Structure model' struct_site 12 6 '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 4 'Structure model' '_diffrn_source.pdbx_synchrotron_site' 2 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 3 5 'Structure model' '_database_2.pdbx_DOI' 4 5 'Structure model' '_database_2.pdbx_database_accession' 5 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 6 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_symmetry' 7 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 8 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_symmetry' 9 5 'Structure model' '_pdbx_struct_conn_angle.value' 10 5 'Structure model' '_struct_conn.pdbx_dist_value' 11 5 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 12 5 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 13 5 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 14 5 'Structure model' '_struct_conn.ptnr1_label_asym_id' 15 5 'Structure model' '_struct_conn.ptnr1_label_atom_id' 16 5 'Structure model' '_struct_conn.ptnr1_label_comp_id' 17 5 'Structure model' '_struct_conn.ptnr1_label_seq_id' 18 5 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 19 5 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 20 5 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 21 5 'Structure model' '_struct_conn.ptnr2_label_asym_id' 22 5 'Structure model' '_struct_conn.ptnr2_label_atom_id' 23 5 'Structure model' '_struct_conn.ptnr2_label_comp_id' 24 5 'Structure model' '_struct_conn.ptnr2_symmetry' 25 5 'Structure model' '_struct_site.pdbx_auth_asym_id' 26 5 'Structure model' '_struct_site.pdbx_auth_comp_id' 27 5 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 310D _pdbx_database_status.recvd_initial_deposition_date 1996-05-25 _pdbx_database_status.deposit_site NDB _pdbx_database_status.process_site NDB _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Adamiak, D.A.' 1 'Milecki, J.' 2 'Adamiak, R.W.' 3 'Dauter, Z.' 4 'Rypniewski, W.R.' 5 # loop_ _citation.id _citation.title _citation.journal_abbrev _citation.journal_volume _citation.page_first _citation.page_last _citation.year _citation.journal_id_ASTM _citation.country _citation.journal_id_ISSN _citation.journal_id_CSD _citation.book_publisher _citation.pdbx_database_id_PubMed _citation.pdbx_database_id_DOI primary ;Crystal structure of 2'-O-Me(CGCGCG)2, an RNA duplex at 1.30 A resolution. Hydration pattern of 2'-O-methylated RNA. ; 'Nucleic Acids Res.' 25 4599 4607 1997 NARHAD UK 0305-1048 0389 ? 9358171 10.1093/nar/25.22.4599 1 ;Low Salt NMR Study of R(CGCGCG) and 2'-O-Me(CGCGCG) Reveals Structure of RNA Duplexes Containing Consecutive CG Base Pairs ; 'To be Published' ? ? ? ? ? ? ? 0353 ? ? ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Adamiak, D.A.' 1 ? primary 'Milecki, J.' 2 ? primary 'Popenda, M.' 3 ? primary 'Adamiak, R.W.' 4 ? primary 'Dauter, Z.' 5 ? primary 'Rypniewski, W.R.' 6 ? 1 'Popenda, M.' 7 ? 1 'Biala, E.' 8 ? 1 'Milecki, J.' 9 ? 1 'Adamiak, R.W.' 10 ? # 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 man ;RNA (5'-R(*(OMC)P*(OMG)P*(OMC)P*(OMG)P*(OMC)P*(OMG))-3') ; 1990.361 2 ? ? ? ? 2 non-polymer syn 'MAGNESIUM ION' 24.305 2 ? ? ? ? 3 water nat water 18.015 44 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code '(OMC)(OMG)(OMC)(OMG)(OMC)(OMG)' _entity_poly.pdbx_seq_one_letter_code_can CGCGCG _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 'MAGNESIUM ION' MG 3 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 OMC n 1 2 OMG n 1 3 OMC n 1 4 OMG n 1 5 OMC n 1 6 OMG n # _entity_src_gen.entity_id 1 _entity_src_gen.pdbx_src_id 1 _entity_src_gen.pdbx_alt_source_flag sample _entity_src_gen.pdbx_seq_type 'Biological sequence' _entity_src_gen.pdbx_beg_seq_num 1 _entity_src_gen.pdbx_end_seq_num 6 _entity_src_gen.gene_src_common_name ? _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene ? _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain ? _entity_src_gen.gene_src_tissue ? _entity_src_gen.gene_src_tissue_fraction ? _entity_src_gen.gene_src_details ? _entity_src_gen.pdbx_gene_src_fragment ? _entity_src_gen.pdbx_gene_src_scientific_name 'synthetic construct' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 32630 _entity_src_gen.pdbx_gene_src_variant ? _entity_src_gen.pdbx_gene_src_cell_line ? _entity_src_gen.pdbx_gene_src_atcc ? _entity_src_gen.pdbx_gene_src_organ ? _entity_src_gen.pdbx_gene_src_organelle ? _entity_src_gen.pdbx_gene_src_cell ? _entity_src_gen.pdbx_gene_src_cellular_location ? _entity_src_gen.host_org_common_name ? _entity_src_gen.pdbx_host_org_scientific_name ? _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id ? _entity_src_gen.host_org_genus ? _entity_src_gen.pdbx_host_org_gene ? _entity_src_gen.pdbx_host_org_organ ? _entity_src_gen.host_org_species ? _entity_src_gen.pdbx_host_org_tissue ? _entity_src_gen.pdbx_host_org_tissue_fraction ? _entity_src_gen.pdbx_host_org_strain ? _entity_src_gen.pdbx_host_org_variant ? _entity_src_gen.pdbx_host_org_cell_line ? _entity_src_gen.pdbx_host_org_atcc ? _entity_src_gen.pdbx_host_org_culture_collection ? _entity_src_gen.pdbx_host_org_cell ? _entity_src_gen.pdbx_host_org_organelle ? _entity_src_gen.pdbx_host_org_cellular_location ? _entity_src_gen.pdbx_host_org_vector_type ? _entity_src_gen.pdbx_host_org_vector ? _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name ? _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # 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 HOH non-polymer . WATER ? 'H2 O' 18.015 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 OMC 'RNA linking' n "O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE" ? 'C10 H16 N3 O8 P' 337.223 OMG 'RNA linking' n "O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE" ? 'C11 H16 N5 O8 P' 377.247 # 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 OMC 1 1 1 OMC +C A . n A 1 2 OMG 2 2 2 OMG +G A . n A 1 3 OMC 3 3 3 OMC +C A . n A 1 4 OMG 4 4 4 OMG +G A . n A 1 5 OMC 5 5 5 OMC +C A . n A 1 6 OMG 6 6 6 OMG +G A . n B 1 1 OMC 1 7 7 OMC +C B . n B 1 2 OMG 2 8 8 OMG +G B . n B 1 3 OMC 3 9 9 OMC +C B . n B 1 4 OMG 4 10 10 OMG +G B . n B 1 5 OMC 5 11 11 OMC +C B . n B 1 6 OMG 6 12 12 OMG +G 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 MG 1 14 14 MG MG A . D 2 MG 1 13 13 MG MG B . E 3 HOH 1 21 21 HOH HOH A . E 3 HOH 2 22 22 HOH HOH A . E 3 HOH 3 24 24 HOH HOH A . E 3 HOH 4 25 25 HOH HOH A . E 3 HOH 5 26 26 HOH HOH A . E 3 HOH 6 27 27 HOH HOH A . E 3 HOH 7 32 32 HOH HOH A . E 3 HOH 8 33 33 HOH HOH A . E 3 HOH 9 34 34 HOH HOH A . E 3 HOH 10 35 35 HOH HOH A . E 3 HOH 11 36 36 HOH HOH A . E 3 HOH 12 39 39 HOH HOH A . E 3 HOH 13 43 43 HOH HOH A . E 3 HOH 14 46 46 HOH HOH A . E 3 HOH 15 47 47 HOH HOH A . E 3 HOH 16 48 48 HOH HOH A . E 3 HOH 17 49 49 HOH HOH A . E 3 HOH 18 50 50 HOH HOH A . E 3 HOH 19 51 51 HOH HOH A . E 3 HOH 20 52 52 HOH HOH A . E 3 HOH 21 53 53 HOH HOH A . E 3 HOH 22 54 54 HOH HOH A . E 3 HOH 23 55 55 HOH HOH A . E 3 HOH 24 56 56 HOH HOH A . E 3 HOH 25 57 57 HOH HOH A . F 3 HOH 1 15 15 HOH HOH B . F 3 HOH 2 16 16 HOH HOH B . F 3 HOH 3 17 17 HOH HOH B . F 3 HOH 4 18 18 HOH HOH B . F 3 HOH 5 19 19 HOH HOH B . F 3 HOH 6 20 20 HOH HOH B . F 3 HOH 7 23 23 HOH HOH B . F 3 HOH 8 28 28 HOH HOH B . F 3 HOH 9 29 29 HOH HOH B . F 3 HOH 10 30 30 HOH HOH B . F 3 HOH 11 31 31 HOH HOH B . F 3 HOH 12 37 37 HOH HOH B . F 3 HOH 13 38 38 HOH HOH B . F 3 HOH 14 40 40 HOH HOH B . F 3 HOH 15 41 41 HOH HOH B . F 3 HOH 16 42 42 HOH HOH B . F 3 HOH 17 44 44 HOH HOH B . F 3 HOH 18 45 45 HOH HOH B . F 3 HOH 19 58 58 HOH HOH B . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal AMoRE phasing . ? 1 SHELXL-96 refinement . ? 2 DENZO 'data reduction' . ? 3 SCALEPACK 'data scaling' . ? 4 # _cell.entry_id 310D _cell.length_a 26.270 _cell.length_b 26.270 _cell.length_c 160.900 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 310D _symmetry.space_group_name_H-M 'P 61 2 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 # _exptl.entry_id 310D _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.10 _exptl_crystal.density_percent_sol 41.48 _exptl_crystal.description ? # _diffrn.id 1 _diffrn.ambient_temp 277.00 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'IMAGE PLATE' _diffrn_detector.type MARRESEARCH _diffrn_detector.pdbx_collection_date 1995-05-14 _diffrn_detector.details 'SEGMENTED MIRROR' # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'TRIANGULAR GE CRYSTAL' _diffrn_radiation.pdbx_diffrn_protocol ? _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength . _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'EMBL/DESY, HAMBURG BEAMLINE BW7B' _diffrn_source.pdbx_synchrotron_site 'EMBL/DESY, HAMBURG' _diffrn_source.pdbx_synchrotron_beamline BW7B _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list ? # _reflns.entry_id 310D _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 8.000 _reflns.d_resolution_high 1.300 _reflns.number_obs 8165 _reflns.number_all ? _reflns.percent_possible_obs 95.300 _reflns.pdbx_Rmerge_I_obs 0.07 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 32.0000 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 11.00 _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 1.300 _reflns_shell.d_res_low 1.320 _reflns_shell.percent_possible_all 91.90 _reflns_shell.Rmerge_I_obs 0.444 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 3.200 _reflns_shell.pdbx_redundancy 3.700 _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 310D _refine.ls_number_reflns_obs 8165 _refine.ls_number_reflns_all 8165 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.000 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 8.000 _refine.ls_d_res_high 1.300 _refine.ls_percent_reflns_obs 95.300 _refine.ls_R_factor_obs 0.172 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work ? _refine.ls_R_factor_R_free ? _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free ? _refine.ls_number_reflns_R_free ? _refine.ls_number_parameters 2778 _refine.ls_number_restraints 3275 _refine.occupancy_min ? _refine.occupancy_max ? _refine.B_iso_mean ? _refine.aniso_B[1][1] ? _refine.aniso_B[2][2] ? _refine.aniso_B[3][3] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][3] ? _refine.solvent_model_details 'MOEWS, KRETSINGER, J.MOL.BIOL. 91(1973)201' _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_ls_cross_valid_method ? _refine.details ? _refine.pdbx_starting_model ARN035 _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'CCP4 DICTIONARY' _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.overall_SU_B ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_overall_phase_error ? _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_analyze.entry_id 310D _refine_analyze.Luzzati_coordinate_error_obs ? _refine_analyze.Luzzati_sigma_a_obs ? _refine_analyze.Luzzati_d_res_low_obs ? _refine_analyze.Luzzati_coordinate_error_free ? _refine_analyze.Luzzati_sigma_a_free ? _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues 0 _refine_analyze.occupancy_sum_hydrogen 295.00 _refine_analyze.occupancy_sum_non_hydrogen 154.00 _refine_analyze.pdbx_refine_id 'X-RAY DIFFRACTION' # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 370 _refine_hist.pdbx_number_atoms_ligand 50 _refine_hist.number_atoms_solvent 44 _refine_hist.number_atoms_total 464 _refine_hist.d_res_high 1.300 _refine_hist.d_res_low 8.000 # 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 s_bond_d 0.025 ? ? ? 'X-RAY DIFFRACTION' ? s_angle_d 0.000 ? ? ? 'X-RAY DIFFRACTION' ? s_similar_dist 0.000 ? ? ? 'X-RAY DIFFRACTION' ? s_from_restr_planes 0.098 ? ? ? 'X-RAY DIFFRACTION' ? s_zero_chiral_vol 0.000 ? ? ? 'X-RAY DIFFRACTION' ? s_non_zero_chiral_vol 0.000 ? ? ? 'X-RAY DIFFRACTION' ? s_anti_bump_dis_restr 0.009 ? ? ? 'X-RAY DIFFRACTION' ? s_rigid_bond_adp_cmpnt 0.004 ? ? ? 'X-RAY DIFFRACTION' ? s_similar_adp_cmpnt 0.032 ? ? ? 'X-RAY DIFFRACTION' ? s_approx_iso_adps 0.085 ? ? ? 'X-RAY DIFFRACTION' ? # _pdbx_refine.entry_id 310D _pdbx_refine.R_factor_all_no_cutoff ? _pdbx_refine.R_factor_obs_no_cutoff 0.172 _pdbx_refine.free_R_factor_no_cutoff ? _pdbx_refine.free_R_val_test_set_size_perc_no_cutoff ? _pdbx_refine.free_R_val_test_set_ct_no_cutoff ? _pdbx_refine.R_factor_all_4sig_cutoff ? _pdbx_refine.R_factor_obs_4sig_cutoff 0.163 _pdbx_refine.free_R_factor_4sig_cutoff ? _pdbx_refine.free_R_val_test_set_size_perc_4sig_cutoff ? _pdbx_refine.free_R_val_test_set_ct_4sig_cutoff ? _pdbx_refine.number_reflns_obs_4sig_cutoff 6979 _pdbx_refine.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine.free_R_error_no_cutoff ? # _database_PDB_matrix.entry_id 310D _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 310D _struct.title ;Crystal structure of 2'-O-Me(CGCGCG)2: an RNA duplex at 1.3 A resolution. Hydration pattern of 2'-O-methylated RNA ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 310D _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'A-RNA, DOUBLE HELIX, MODIFIED, RNA' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 1 ? C N N 2 ? D N N 2 ? E N N 3 ? F N N 3 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 310D _struct_ref.pdbx_db_accession 310D _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 310D A 1 ? 6 ? 310D 1 ? 6 ? 1 6 2 1 310D B 1 ? 6 ? 310D 7 ? 12 ? 7 12 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # _struct_biol.id 1 # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale both ? A OMC 1 "O3'" ? ? ? 1_555 A OMG 2 P ? ? A OMC 1 A OMG 2 1_555 ? ? ? ? ? ? ? 1.619 ? ? covale2 covale both ? A OMG 2 "O3'" ? ? ? 1_555 A OMC 3 P ? ? A OMG 2 A OMC 3 1_555 ? ? ? ? ? ? ? 1.601 ? ? covale3 covale both ? A OMC 3 "O3'" ? ? ? 1_555 A OMG 4 P ? ? A OMC 3 A OMG 4 1_555 ? ? ? ? ? ? ? 1.633 ? ? covale4 covale both ? A OMG 4 "O3'" ? ? ? 1_555 A OMC 5 P ? ? A OMG 4 A OMC 5 1_555 ? ? ? ? ? ? ? 1.623 ? ? covale5 covale both ? A OMC 5 "O3'" ? ? ? 1_555 A OMG 6 P ? ? A OMC 5 A OMG 6 1_555 ? ? ? ? ? ? ? 1.582 ? ? covale6 covale both ? B OMC 1 "O3'" ? ? ? 1_555 B OMG 2 P ? ? B OMC 7 B OMG 8 1_555 ? ? ? ? ? ? ? 1.612 ? ? covale7 covale both ? B OMG 2 "O3'" ? ? ? 1_555 B OMC 3 P ? ? B OMG 8 B OMC 9 1_555 ? ? ? ? ? ? ? 1.639 ? ? covale8 covale both ? B OMC 3 "O3'" ? ? ? 1_555 B OMG 4 P ? ? B OMC 9 B OMG 10 1_555 ? ? ? ? ? ? ? 1.624 ? ? covale9 covale both ? B OMG 4 "O3'" ? ? ? 1_555 B OMC 5 P ? ? B OMG 10 B OMC 11 1_555 ? ? ? ? ? ? ? 1.641 ? ? covale10 covale both ? B OMC 5 "O3'" ? ? ? 1_555 B OMG 6 P ? ? B OMC 11 B OMG 12 1_555 ? ? ? ? ? ? ? 1.593 ? ? metalc1 metalc ? ? A OMG 2 OP1 ? ? ? 1_555 C MG . MG ? ? A OMG 2 A MG 14 1_555 ? ? ? ? ? ? ? 2.170 ? ? metalc2 metalc ? ? C MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 14 A HOH 53 1_555 ? ? ? ? ? ? ? 2.217 ? ? metalc3 metalc ? ? C MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 14 A HOH 54 1_555 ? ? ? ? ? ? ? 2.319 ? ? metalc4 metalc ? ? C MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 14 A HOH 55 1_555 ? ? ? ? ? ? ? 2.136 ? ? metalc5 metalc ? ? C MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 14 A HOH 56 1_555 ? ? ? ? ? ? ? 2.134 ? ? metalc6 metalc ? ? C MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 14 A HOH 57 10_665 ? ? ? ? ? ? ? 1.923 ? ? metalc7 metalc ? ? B OMC 5 OP1 ? ? ? 1_555 D MG . MG ? ? B OMC 11 B MG 13 1_555 ? ? ? ? ? ? ? 2.176 ? ? metalc8 metalc ? ? D MG . MG ? ? ? 1_555 F HOH . O ? ? B MG 13 B HOH 15 1_555 ? ? ? ? ? ? ? 1.943 ? ? metalc9 metalc ? ? D MG . MG ? ? ? 1_555 F HOH . O ? ? B MG 13 B HOH 16 1_555 ? ? ? ? ? ? ? 2.144 ? ? hydrog1 hydrog ? ? A OMC 1 N3 ? ? ? 1_555 B OMG 6 N1 ? ? A OMC 1 B OMG 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A OMC 1 N4 ? ? ? 1_555 B OMG 6 O6 ? ? A OMC 1 B OMG 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A OMC 1 O2 ? ? ? 1_555 B OMG 6 N2 ? ? A OMC 1 B OMG 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A OMG 2 N1 ? ? ? 1_555 B OMC 5 N3 ? ? A OMG 2 B OMC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A OMG 2 N2 ? ? ? 1_555 B OMC 5 O2 ? ? A OMG 2 B OMC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A OMG 2 O6 ? ? ? 1_555 B OMC 5 N4 ? ? A OMG 2 B OMC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A OMC 3 N3 ? ? ? 1_555 B OMG 4 N1 ? ? A OMC 3 B OMG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A OMC 3 N4 ? ? ? 1_555 B OMG 4 O6 ? ? A OMC 3 B OMG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A OMC 3 O2 ? ? ? 1_555 B OMG 4 N2 ? ? A OMC 3 B OMG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A OMG 4 N1 ? ? ? 1_555 B OMC 3 N3 ? ? A OMG 4 B OMC 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A OMG 4 N2 ? ? ? 1_555 B OMC 3 O2 ? ? A OMG 4 B OMC 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A OMG 4 O6 ? ? ? 1_555 B OMC 3 N4 ? ? A OMG 4 B OMC 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A OMC 5 N3 ? ? ? 1_555 B OMG 2 N1 ? ? A OMC 5 B OMG 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A OMC 5 N4 ? ? ? 1_555 B OMG 2 O6 ? ? A OMC 5 B OMG 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A OMC 5 O2 ? ? ? 1_555 B OMG 2 N2 ? ? A OMC 5 B OMG 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A OMG 6 N1 ? ? ? 1_555 B OMC 1 N3 ? ? A OMG 6 B OMC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A OMG 6 N2 ? ? ? 1_555 B OMC 1 O2 ? ? A OMG 6 B OMC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A OMG 6 O6 ? ? ? 1_555 B OMC 1 N4 ? ? A OMG 6 B OMC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? 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 OP1 ? A OMG 2 ? A OMG 2 ? 1_555 MG ? C MG . ? A MG 14 ? 1_555 O ? E HOH . ? A HOH 53 ? 1_555 80.2 ? 2 OP1 ? A OMG 2 ? A OMG 2 ? 1_555 MG ? C MG . ? A MG 14 ? 1_555 O ? E HOH . ? A HOH 54 ? 1_555 92.9 ? 3 O ? E HOH . ? A HOH 53 ? 1_555 MG ? C MG . ? A MG 14 ? 1_555 O ? E HOH . ? A HOH 54 ? 1_555 148.4 ? 4 OP1 ? A OMG 2 ? A OMG 2 ? 1_555 MG ? C MG . ? A MG 14 ? 1_555 O ? E HOH . ? A HOH 55 ? 1_555 95.7 ? 5 O ? E HOH . ? A HOH 53 ? 1_555 MG ? C MG . ? A MG 14 ? 1_555 O ? E HOH . ? A HOH 55 ? 1_555 95.2 ? 6 O ? E HOH . ? A HOH 54 ? 1_555 MG ? C MG . ? A MG 14 ? 1_555 O ? E HOH . ? A HOH 55 ? 1_555 116.2 ? 7 OP1 ? A OMG 2 ? A OMG 2 ? 1_555 MG ? C MG . ? A MG 14 ? 1_555 O ? E HOH . ? A HOH 56 ? 1_555 78.1 ? 8 O ? E HOH . ? A HOH 53 ? 1_555 MG ? C MG . ? A MG 14 ? 1_555 O ? E HOH . ? A HOH 56 ? 1_555 91.2 ? 9 O ? E HOH . ? A HOH 54 ? 1_555 MG ? C MG . ? A MG 14 ? 1_555 O ? E HOH . ? A HOH 56 ? 1_555 57.2 ? 10 O ? E HOH . ? A HOH 55 ? 1_555 MG ? C MG . ? A MG 14 ? 1_555 O ? E HOH . ? A HOH 56 ? 1_555 170.2 ? 11 OP1 ? A OMG 2 ? A OMG 2 ? 1_555 MG ? C MG . ? A MG 14 ? 1_555 O ? E HOH . ? A HOH 57 ? 10_665 160.8 ? 12 O ? E HOH . ? A HOH 53 ? 1_555 MG ? C MG . ? A MG 14 ? 1_555 O ? E HOH . ? A HOH 57 ? 10_665 116.9 ? 13 O ? E HOH . ? A HOH 54 ? 1_555 MG ? C MG . ? A MG 14 ? 1_555 O ? E HOH . ? A HOH 57 ? 10_665 76.9 ? 14 O ? E HOH . ? A HOH 55 ? 1_555 MG ? C MG . ? A MG 14 ? 1_555 O ? E HOH . ? A HOH 57 ? 10_665 75.0 ? 15 O ? E HOH . ? A HOH 56 ? 1_555 MG ? C MG . ? A MG 14 ? 1_555 O ? E HOH . ? A HOH 57 ? 10_665 108.6 ? 16 OP1 ? B OMC 5 ? B OMC 11 ? 1_555 MG ? D MG . ? B MG 13 ? 1_555 O ? F HOH . ? B HOH 15 ? 1_555 90.8 ? 17 OP1 ? B OMC 5 ? B OMC 11 ? 1_555 MG ? D MG . ? B MG 13 ? 1_555 O ? F HOH . ? B HOH 16 ? 1_555 89.9 ? 18 O ? F HOH . ? B HOH 15 ? 1_555 MG ? D MG . ? B MG 13 ? 1_555 O ? F HOH . ? B HOH 16 ? 1_555 89.3 ? # 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 MG 13 ? 6 'BINDING SITE FOR RESIDUE MG B 13' AC2 Software A MG 14 ? 6 'BINDING SITE FOR RESIDUE MG A 14' # 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 6 OMC B 5 ? OMC B 11 . ? 1_555 ? 2 AC1 6 OMC B 5 ? OMC B 11 . ? 9_765 ? 3 AC1 6 HOH F . ? HOH B 15 . ? 9_765 ? 4 AC1 6 HOH F . ? HOH B 15 . ? 1_555 ? 5 AC1 6 HOH F . ? HOH B 16 . ? 9_765 ? 6 AC1 6 HOH F . ? HOH B 16 . ? 1_555 ? 7 AC2 6 OMG A 2 ? OMG A 2 . ? 1_555 ? 8 AC2 6 HOH E . ? HOH A 53 . ? 1_555 ? 9 AC2 6 HOH E . ? HOH A 54 . ? 1_555 ? 10 AC2 6 HOH E . ? HOH A 55 . ? 1_555 ? 11 AC2 6 HOH E . ? HOH A 56 . ? 1_555 ? 12 AC2 6 HOH E . ? HOH A 57 . ? 10_665 ? # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 A OMC 1 A OMC 1 ? C "O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE" 2 A OMG 2 A OMG 2 ? G "O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE" 3 A OMC 3 A OMC 3 ? C "O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE" 4 A OMG 4 A OMG 4 ? G "O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE" 5 A OMC 5 A OMC 5 ? C "O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE" 6 A OMG 6 A OMG 6 ? G "O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE" 7 B OMC 1 B OMC 7 ? C "O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE" 8 B OMG 2 B OMG 8 ? G "O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE" 9 B OMC 3 B OMC 9 ? C "O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE" 10 B OMG 4 B OMG 10 ? G "O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE" 11 B OMC 5 B OMC 11 ? C "O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE" 12 B OMG 6 B OMG 12 ? G "O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE" # 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 MG 13 ? D MG . 2 1 A HOH 22 ? E HOH . 3 1 A HOH 33 ? E HOH . 4 1 B HOH 23 ? F 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 HOH O O N N 1 HOH H1 H N N 2 HOH H2 H N N 3 MG MG MG N N 4 OMC N1 N N N 5 OMC C2 C N N 6 OMC N3 N N N 7 OMC C4 C N N 8 OMC C5 C N N 9 OMC C6 C N N 10 OMC O2 O N N 11 OMC N4 N N N 12 OMC "C1'" C N R 13 OMC "C2'" C N R 14 OMC "O2'" O N N 15 OMC CM2 C N N 16 OMC "C3'" C N R 17 OMC "C4'" C N R 18 OMC "O4'" O N N 19 OMC "O3'" O N N 20 OMC "C5'" C N N 21 OMC "O5'" O N N 22 OMC P P N N 23 OMC OP1 O N N 24 OMC OP2 O N N 25 OMC OP3 O N N 26 OMC H5 H N N 27 OMC H6 H N N 28 OMC HN41 H N N 29 OMC HN42 H N N 30 OMC "H1'" H N N 31 OMC "H2'" H N N 32 OMC HM21 H N N 33 OMC HM22 H N N 34 OMC HM23 H N N 35 OMC "H3'" H N N 36 OMC "H4'" H N N 37 OMC "HO3'" H N N 38 OMC "H5'" H N N 39 OMC "H5''" H N N 40 OMC HOP2 H N N 41 OMC HOP3 H N N 42 OMG P P N N 43 OMG OP1 O N N 44 OMG OP2 O N N 45 OMG OP3 O N N 46 OMG "O5'" O N N 47 OMG "C5'" C N N 48 OMG "C4'" C N R 49 OMG "O4'" O N N 50 OMG "C3'" C N R 51 OMG "O3'" O N N 52 OMG "C2'" C N R 53 OMG "O2'" O N N 54 OMG CM2 C N N 55 OMG "C1'" C N R 56 OMG N9 N Y N 57 OMG C8 C Y N 58 OMG N7 N Y N 59 OMG C5 C Y N 60 OMG C6 C N N 61 OMG O6 O N N 62 OMG N1 N N N 63 OMG C2 C N N 64 OMG N2 N N N 65 OMG N3 N N N 66 OMG C4 C Y N 67 OMG HOP2 H N N 68 OMG HOP3 H N N 69 OMG "H5'" H N N 70 OMG "H5''" H N N 71 OMG "H4'" H N N 72 OMG "H3'" H N N 73 OMG "HO3'" H N N 74 OMG "H2'" H N N 75 OMG HM21 H N N 76 OMG HM22 H N N 77 OMG HM23 H N N 78 OMG "H1'" H N N 79 OMG H8 H N N 80 OMG HN1 H N N 81 OMG HN21 H N N 82 OMG HN22 H N N 83 # 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 HOH O H1 sing N N 1 HOH O H2 sing N N 2 OMC N1 C2 sing N N 3 OMC N1 C6 sing N N 4 OMC N1 "C1'" sing N N 5 OMC C2 N3 sing N N 6 OMC C2 O2 doub N N 7 OMC N3 C4 doub N N 8 OMC C4 C5 sing N N 9 OMC C4 N4 sing N N 10 OMC C5 C6 doub N N 11 OMC C5 H5 sing N N 12 OMC C6 H6 sing N N 13 OMC N4 HN41 sing N N 14 OMC N4 HN42 sing N N 15 OMC "C1'" "C2'" sing N N 16 OMC "C1'" "O4'" sing N N 17 OMC "C1'" "H1'" sing N N 18 OMC "C2'" "O2'" sing N N 19 OMC "C2'" "C3'" sing N N 20 OMC "C2'" "H2'" sing N N 21 OMC "O2'" CM2 sing N N 22 OMC CM2 HM21 sing N N 23 OMC CM2 HM22 sing N N 24 OMC CM2 HM23 sing N N 25 OMC "C3'" "C4'" sing N N 26 OMC "C3'" "O3'" sing N N 27 OMC "C3'" "H3'" sing N N 28 OMC "C4'" "O4'" sing N N 29 OMC "C4'" "C5'" sing N N 30 OMC "C4'" "H4'" sing N N 31 OMC "O3'" "HO3'" sing N N 32 OMC "C5'" "O5'" sing N N 33 OMC "C5'" "H5'" sing N N 34 OMC "C5'" "H5''" sing N N 35 OMC "O5'" P sing N N 36 OMC P OP1 doub N N 37 OMC P OP2 sing N N 38 OMC P OP3 sing N N 39 OMC OP2 HOP2 sing N N 40 OMC OP3 HOP3 sing N N 41 OMG P OP1 doub N N 42 OMG P OP2 sing N N 43 OMG P OP3 sing N N 44 OMG P "O5'" sing N N 45 OMG OP2 HOP2 sing N N 46 OMG OP3 HOP3 sing N N 47 OMG "O5'" "C5'" sing N N 48 OMG "C5'" "C4'" sing N N 49 OMG "C5'" "H5'" sing N N 50 OMG "C5'" "H5''" sing N N 51 OMG "C4'" "O4'" sing N N 52 OMG "C4'" "C3'" sing N N 53 OMG "C4'" "H4'" sing N N 54 OMG "O4'" "C1'" sing N N 55 OMG "C3'" "O3'" sing N N 56 OMG "C3'" "C2'" sing N N 57 OMG "C3'" "H3'" sing N N 58 OMG "O3'" "HO3'" sing N N 59 OMG "C2'" "O2'" sing N N 60 OMG "C2'" "C1'" sing N N 61 OMG "C2'" "H2'" sing N N 62 OMG "O2'" CM2 sing N N 63 OMG CM2 HM21 sing N N 64 OMG CM2 HM22 sing N N 65 OMG CM2 HM23 sing N N 66 OMG "C1'" N9 sing N N 67 OMG "C1'" "H1'" sing N N 68 OMG N9 C8 sing Y N 69 OMG N9 C4 sing Y N 70 OMG C8 N7 doub Y N 71 OMG C8 H8 sing N N 72 OMG N7 C5 sing Y N 73 OMG C5 C6 sing N N 74 OMG C5 C4 doub Y N 75 OMG C6 O6 doub N N 76 OMG C6 N1 sing N N 77 OMG N1 C2 sing N N 78 OMG N1 HN1 sing N N 79 OMG C2 N2 sing N N 80 OMG C2 N3 doub N N 81 OMG N2 HN21 sing N N 82 OMG N2 HN22 sing N N 83 OMG N3 C4 sing N N 84 # _ndb_struct_conf_na.entry_id 310D _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 OMC 1 1_555 B OMG 6 1_555 0.213 0.077 -0.108 7.215 -14.139 -0.793 1 A_OMC1:OMG12_B A 1 ? B 12 ? 19 1 1 A OMG 2 1_555 B OMC 5 1_555 -0.133 0.039 0.032 3.190 -12.471 0.226 2 A_OMG2:OMC11_B A 2 ? B 11 ? 19 1 1 A OMC 3 1_555 B OMG 4 1_555 0.181 0.018 -0.087 2.477 -14.099 -1.666 3 A_OMC3:OMG10_B A 3 ? B 10 ? 19 1 1 A OMG 4 1_555 B OMC 3 1_555 -0.179 0.026 0.007 -1.099 -13.053 -1.701 4 A_OMG4:OMC9_B A 4 ? B 9 ? 19 1 1 A OMC 5 1_555 B OMG 2 1_555 0.285 0.050 0.031 -3.506 -12.617 0.271 5 A_OMC5:OMG8_B A 5 ? B 8 ? 19 1 1 A OMG 6 1_555 B OMC 1 1_555 0.055 0.081 -0.081 -6.861 -15.798 -1.783 6 A_OMG6:OMC7_B A 6 ? B 7 ? 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 OMC 1 1_555 B OMG 6 1_555 A OMG 2 1_555 B OMC 5 1_555 -0.543 -1.928 3.387 -4.335 15.449 30.531 -5.465 0.299 2.238 27.114 7.608 34.401 1 AA_OMC1OMG2:OMC11OMG12_BB A 1 ? B 12 ? A 2 ? B 11 ? 1 A OMG 2 1_555 B OMC 5 1_555 A OMC 3 1_555 B OMG 4 1_555 -0.410 -1.413 3.440 -0.849 10.269 33.554 -3.876 0.555 2.904 17.288 1.429 35.057 2 AA_OMG2OMC3:OMG10OMC11_BB A 2 ? B 11 ? A 3 ? B 10 ? 1 A OMC 3 1_555 B OMG 4 1_555 A OMG 4 1_555 B OMC 3 1_555 -0.045 -1.841 3.340 -1.011 18.062 29.291 -5.589 -0.062 1.915 32.146 1.800 34.323 3 AA_OMC3OMG4:OMC9OMG10_BB A 3 ? B 10 ? A 4 ? B 9 ? 1 A OMG 4 1_555 B OMC 3 1_555 A OMC 5 1_555 B OMG 2 1_555 0.431 -1.400 3.477 1.563 10.358 34.675 -3.725 -0.472 2.967 16.908 -2.552 36.176 4 AA_OMG4OMC5:OMG8OMC9_BB A 4 ? B 9 ? A 5 ? B 8 ? 1 A OMC 5 1_555 B OMG 2 1_555 A OMG 6 1_555 B OMC 1 1_555 0.418 -1.964 3.345 4.048 16.269 31.803 -5.280 -0.160 2.155 27.436 -6.827 35.850 5 AA_OMC5OMG6:OMC7OMG8_BB A 5 ? B 8 ? A 6 ? B 7 ? # _pdbx_initial_refinement_model.accession_code 1RNA _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.details ARN035 # _atom_sites.entry_id 310D _atom_sites.fract_transf_matrix[1][1] 0.038066 _atom_sites.fract_transf_matrix[1][2] 0.021978 _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] 0.043955 _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] 0.006215 _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 H MG N O P # loop_