data_2AXB # _entry.id 2AXB # _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 2AXB pdb_00002axb 10.2210/pdb2axb/pdb NDB AD0057 ? ? RCSB RCSB034425 ? ? WWPDB D_1000034425 ? ? # 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 2005-11-01 2 'Structure model' 1 1 2008-05-01 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2017-10-11 5 'Structure model' 1 4 2024-02-14 # _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' 'Refinement description' 4 5 'Structure model' 'Data collection' 5 5 'Structure model' 'Database references' 6 5 '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 4 'Structure model' software 2 5 'Structure model' chem_comp_atom 3 5 'Structure model' chem_comp_bond 4 5 'Structure model' database_2 5 5 'Structure model' struct_conn # 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' '_software.classification' 2 4 'Structure model' '_software.name' 3 5 'Structure model' '_database_2.pdbx_DOI' 4 5 'Structure model' '_database_2.pdbx_database_accession' 5 5 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 2AXB _pdbx_database_status.recvd_initial_deposition_date 2005-09-04 _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.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Diop-Frimpong, B.' 1 'Prakash, T.P.' 2 'Rajeev, K.G.' 3 'Manoharan, M.' 4 'Egli, M.' 5 # _citation.id primary _citation.title ;Stabilizing contributions of sulfur-modified nucleotides: crystal structure of a DNA duplex with 2'-O-[2-(methoxy)ethyl]-2-thiothymidines. ; _citation.journal_abbrev 'Nucleic Acids Res.' _citation.journal_volume 33 _citation.page_first 5297 _citation.page_last 5307 _citation.year 2005 _citation.journal_id_ASTM NARHAD _citation.country UK _citation.journal_id_ISSN 0305-1048 _citation.journal_id_CSD 0389 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 16170156 _citation.pdbx_database_id_DOI 10.1093/nar/gki823 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Diop-Frimpong, B.' 1 ? primary 'Prakash, T.P.' 2 ? primary 'Rajeev, K.G.' 3 ? primary 'Manoharan, M.' 4 ? primary 'Egli, M.' 5 ? # 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 "5'-D(*GP*CP*GP*TP*AP*(S2M)P*AP*CP*GP*C)-3')" 3135.150 2 ? ? ? ? 2 water nat water 18.015 154 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code '(DG)(DC)(DG)(DT)(DA)(S2M)(DA)(DC)(DG)(DC)' _entity_poly.pdbx_seq_one_letter_code_can GCGTATACGC _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DG n 1 2 DC n 1 3 DG n 1 4 DT n 1 5 DA n 1 6 S2M n 1 7 DA n 1 8 DC n 1 9 DG n 1 10 DC n # 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 DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 HOH non-polymer . WATER ? 'H2 O' 18.015 S2M 'RNA linking' n "2'-O-[2-(METHOXY)ETHYL]-2-THIOTHYMIDINE-5'-MONOPHOSPHATE" ? 'C13 H21 N2 O9 P S' 412.353 # 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 DG 1 1 1 DG G A . n A 1 2 DC 2 2 2 DC C A . n A 1 3 DG 3 3 3 DG G A . n A 1 4 DT 4 4 4 DT T A . n A 1 5 DA 5 5 5 DA A A . n A 1 6 S2M 6 6 6 S2M S2M A . n A 1 7 DA 7 7 7 DA A A . n A 1 8 DC 8 8 8 DC C A . n A 1 9 DG 9 9 9 DG G A . n A 1 10 DC 10 10 10 DC C A . n B 1 1 DG 1 11 11 DG G B . n B 1 2 DC 2 12 12 DC C B . n B 1 3 DG 3 13 13 DG G B . n B 1 4 DT 4 14 14 DT T B . n B 1 5 DA 5 15 15 DA A B . n B 1 6 S2M 6 16 16 S2M S2M B . n B 1 7 DA 7 17 17 DA A B . n B 1 8 DC 8 18 18 DC C B . n B 1 9 DG 9 19 19 DG G B . n B 1 10 DC 10 20 20 DC C B . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code C 2 HOH 1 11 5 HOH HOH A . C 2 HOH 2 12 8 HOH HOH A . C 2 HOH 3 13 12 HOH HOH A . C 2 HOH 4 14 14 HOH HOH A . C 2 HOH 5 15 15 HOH HOH A . C 2 HOH 6 16 16 HOH HOH A . C 2 HOH 7 17 17 HOH HOH A . C 2 HOH 8 18 18 HOH HOH A . C 2 HOH 9 19 19 HOH HOH A . C 2 HOH 10 20 20 HOH HOH A . C 2 HOH 11 21 21 HOH HOH A . C 2 HOH 12 22 23 HOH HOH A . C 2 HOH 13 23 24 HOH HOH A . C 2 HOH 14 24 30 HOH HOH A . C 2 HOH 15 25 31 HOH HOH A . C 2 HOH 16 26 32 HOH HOH A . C 2 HOH 17 27 33 HOH HOH A . C 2 HOH 18 28 39 HOH HOH A . C 2 HOH 19 29 43 HOH HOH A . C 2 HOH 20 30 44 HOH HOH A . C 2 HOH 21 31 47 HOH HOH A . C 2 HOH 22 32 48 HOH HOH A . C 2 HOH 23 33 49 HOH HOH A . C 2 HOH 24 34 50 HOH HOH A . C 2 HOH 25 35 51 HOH HOH A . C 2 HOH 26 36 53 HOH HOH A . C 2 HOH 27 37 54 HOH HOH A . C 2 HOH 28 38 55 HOH HOH A . C 2 HOH 29 39 56 HOH HOH A . C 2 HOH 30 40 57 HOH HOH A . C 2 HOH 31 41 58 HOH HOH A . C 2 HOH 32 42 59 HOH HOH A . C 2 HOH 33 43 60 HOH HOH A . C 2 HOH 34 44 66 HOH HOH A . C 2 HOH 35 45 67 HOH HOH A . C 2 HOH 36 46 69 HOH HOH A . C 2 HOH 37 47 70 HOH HOH A . C 2 HOH 38 48 73 HOH HOH A . C 2 HOH 39 49 78 HOH HOH A . C 2 HOH 40 50 79 HOH HOH A . C 2 HOH 41 51 82 HOH HOH A . C 2 HOH 42 52 83 HOH HOH A . C 2 HOH 43 53 84 HOH HOH A . C 2 HOH 44 54 85 HOH HOH A . C 2 HOH 45 55 86 HOH HOH A . C 2 HOH 46 56 88 HOH HOH A . C 2 HOH 47 57 92 HOH HOH A . C 2 HOH 48 58 93 HOH HOH A . C 2 HOH 49 59 94 HOH HOH A . C 2 HOH 50 60 99 HOH HOH A . C 2 HOH 51 61 101 HOH HOH A . C 2 HOH 52 62 102 HOH HOH A . C 2 HOH 53 63 104 HOH HOH A . C 2 HOH 54 64 105 HOH HOH A . C 2 HOH 55 65 106 HOH HOH A . C 2 HOH 56 66 108 HOH HOH A . C 2 HOH 57 67 109 HOH HOH A . C 2 HOH 58 68 110 HOH HOH A . C 2 HOH 59 69 111 HOH HOH A . C 2 HOH 60 70 113 HOH HOH A . C 2 HOH 61 71 114 HOH HOH A . C 2 HOH 62 72 117 HOH HOH A . C 2 HOH 63 73 120 HOH HOH A . C 2 HOH 64 74 121 HOH HOH A . C 2 HOH 65 75 125 HOH HOH A . C 2 HOH 66 76 132 HOH HOH A . C 2 HOH 67 77 134 HOH HOH A . C 2 HOH 68 78 138 HOH HOH A . C 2 HOH 69 79 140 HOH HOH A . C 2 HOH 70 80 142 HOH HOH A . C 2 HOH 71 81 143 HOH HOH A . C 2 HOH 72 82 144 HOH HOH A . C 2 HOH 73 83 145 HOH HOH A . C 2 HOH 74 84 146 HOH HOH A . C 2 HOH 75 85 147 HOH HOH A . C 2 HOH 76 86 150 HOH HOH A . C 2 HOH 77 87 151 HOH HOH A . C 2 HOH 78 88 153 HOH HOH A . C 2 HOH 79 89 156 HOH HOH A . C 2 HOH 80 90 157 HOH HOH A . D 2 HOH 1 21 1 HOH HOH B . D 2 HOH 2 22 2 HOH HOH B . D 2 HOH 3 23 3 HOH HOH B . D 2 HOH 4 24 4 HOH HOH B . D 2 HOH 5 25 6 HOH HOH B . D 2 HOH 6 26 7 HOH HOH B . D 2 HOH 7 27 9 HOH HOH B . D 2 HOH 8 28 10 HOH HOH B . D 2 HOH 9 29 11 HOH HOH B . D 2 HOH 10 30 13 HOH HOH B . D 2 HOH 11 31 22 HOH HOH B . D 2 HOH 12 32 26 HOH HOH B . D 2 HOH 13 33 27 HOH HOH B . D 2 HOH 14 34 28 HOH HOH B . D 2 HOH 15 35 29 HOH HOH B . D 2 HOH 16 36 34 HOH HOH B . D 2 HOH 17 37 35 HOH HOH B . D 2 HOH 18 38 36 HOH HOH B . D 2 HOH 19 39 37 HOH HOH B . D 2 HOH 20 40 38 HOH HOH B . D 2 HOH 21 41 40 HOH HOH B . D 2 HOH 22 42 41 HOH HOH B . D 2 HOH 23 43 42 HOH HOH B . D 2 HOH 24 44 45 HOH HOH B . D 2 HOH 25 45 46 HOH HOH B . D 2 HOH 26 46 52 HOH HOH B . D 2 HOH 27 47 61 HOH HOH B . D 2 HOH 28 48 62 HOH HOH B . D 2 HOH 29 49 63 HOH HOH B . D 2 HOH 30 50 64 HOH HOH B . D 2 HOH 31 51 65 HOH HOH B . D 2 HOH 32 52 68 HOH HOH B . D 2 HOH 33 53 71 HOH HOH B . D 2 HOH 34 54 72 HOH HOH B . D 2 HOH 35 55 74 HOH HOH B . D 2 HOH 36 56 76 HOH HOH B . D 2 HOH 37 57 77 HOH HOH B . D 2 HOH 38 58 80 HOH HOH B . D 2 HOH 39 59 81 HOH HOH B . D 2 HOH 40 60 87 HOH HOH B . D 2 HOH 41 61 89 HOH HOH B . D 2 HOH 42 62 90 HOH HOH B . D 2 HOH 43 63 91 HOH HOH B . D 2 HOH 44 64 95 HOH HOH B . D 2 HOH 45 65 96 HOH HOH B . D 2 HOH 46 66 97 HOH HOH B . D 2 HOH 47 67 98 HOH HOH B . D 2 HOH 48 68 100 HOH HOH B . D 2 HOH 49 69 103 HOH HOH B . D 2 HOH 50 70 107 HOH HOH B . D 2 HOH 51 71 112 HOH HOH B . D 2 HOH 52 72 115 HOH HOH B . D 2 HOH 53 73 116 HOH HOH B . D 2 HOH 54 74 118 HOH HOH B . D 2 HOH 55 75 119 HOH HOH B . D 2 HOH 56 76 122 HOH HOH B . D 2 HOH 57 77 123 HOH HOH B . D 2 HOH 58 78 124 HOH HOH B . D 2 HOH 59 79 126 HOH HOH B . D 2 HOH 60 80 127 HOH HOH B . D 2 HOH 61 81 128 HOH HOH B . D 2 HOH 62 82 129 HOH HOH B . D 2 HOH 63 83 131 HOH HOH B . D 2 HOH 64 84 133 HOH HOH B . D 2 HOH 65 85 135 HOH HOH B . D 2 HOH 66 86 136 HOH HOH B . D 2 HOH 67 87 137 HOH HOH B . D 2 HOH 68 88 139 HOH HOH B . D 2 HOH 69 89 141 HOH HOH B . D 2 HOH 70 90 148 HOH HOH B . D 2 HOH 71 91 149 HOH HOH B . D 2 HOH 72 92 152 HOH HOH B . D 2 HOH 73 93 158 HOH HOH B . D 2 HOH 74 94 160 HOH HOH B . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal REFMAC refinement 5.1.24 ? 1 MAR345 'data collection' . ? 2 XDS 'data scaling' . ? 3 AMoRE phasing . ? 4 # _cell.entry_id 2AXB _cell.length_a 25.251 _cell.length_b 45.002 _cell.length_c 44.971 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2AXB _symmetry.space_group_name_H-M 'P 21 21 21' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? # _exptl.entry_id 2AXB _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number ? # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 1.96 _exptl_crystal.density_percent_sol 37.17 _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 287 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH ? _exptl_crystal_grow.pdbx_details 'Mini Screen, VAPOR DIFFUSION, HANGING DROP, temperature 287K' _exptl_crystal_grow.pdbx_pH_range . # _diffrn.id 1 _diffrn.ambient_temp 103 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector ? _diffrn_detector.type ? _diffrn_detector.pdbx_collection_date 2003-03-07 _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 .9873 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'APS BEAMLINE 5ID-B' _diffrn_source.pdbx_synchrotron_site APS _diffrn_source.pdbx_synchrotron_beamline 5ID-B _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list .9873 # _reflns.entry_id 2AXB _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.d_resolution_high 1.61 _reflns.d_resolution_low 12.9 _reflns.number_all ? _reflns.number_obs 6642 _reflns.percent_possible_obs ? _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.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _refine.entry_id 2AXB _refine.ls_number_reflns_obs 6304 _refine.ls_number_reflns_all 6627 _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 12.90 _refine.ls_d_res_high 1.61 _refine.ls_percent_reflns_obs 95.13 _refine.ls_R_factor_obs 0.19589 _refine.ls_R_factor_all 0.19589 _refine.ls_R_factor_R_work 0.19559 _refine.ls_R_factor_R_free 0.2017 _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 338 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.872 _refine.correlation_coeff_Fo_to_Fc_free 0.875 _refine.B_iso_mean 8.976 _refine.aniso_B[1][1] 0.07 _refine.aniso_B[2][2] 0.01 _refine.aniso_B[3][3] -0.08 _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 MASK _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.40 _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 ADDED IN THE RIDING POSITIONS' _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 0.232 _refine.pdbx_overall_ESU_R_Free 0.102 _refine.overall_SU_ML 0.046 _refine.overall_SU_B 1.209 _refine.ls_redundancy_reflns_obs ? _refine.overall_SU_R_Cruickshank_DPI ? _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_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_phase_error ? _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 414 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 154 _refine_hist.number_atoms_total 568 _refine_hist.d_res_high 1.61 _refine_hist.d_res_low 12.90 # 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 0.012 0.021 ? 463 'X-RAY DIFFRACTION' ? r_bond_other_d 0.002 0.020 ? 198 'X-RAY DIFFRACTION' ? r_angle_refined_deg 2.534 3.000 ? 694 'X-RAY DIFFRACTION' ? r_angle_other_deg 1.629 3.000 ? 498 'X-RAY DIFFRACTION' ? r_chiral_restr 0.130 0.200 ? 62 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.009 0.020 ? 218 'X-RAY DIFFRACTION' ? r_gen_planes_other 0.011 0.020 ? 2 'X-RAY DIFFRACTION' ? r_nbd_refined 0.331 0.300 ? 122 'X-RAY DIFFRACTION' ? r_nbd_other 0.373 0.300 ? 245 'X-RAY DIFFRACTION' ? r_nbtor_other 0.200 0.500 ? 91 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined 0.321 0.500 ? 138 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined 0.091 0.300 ? 1 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other 0.195 0.300 ? 33 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 0.343 0.500 ? 19 'X-RAY DIFFRACTION' ? r_scbond_it 3.703 2.000 ? 463 'X-RAY DIFFRACTION' ? r_scangle_it 4.235 3.000 ? 690 'X-RAY DIFFRACTION' ? r_rigid_bond_restr 2.856 1.000 ? 463 'X-RAY DIFFRACTION' ? r_sphericity_free 17.014 9.000 ? 160 'X-RAY DIFFRACTION' ? r_sphericity_bonded 4.893 9.000 ? 414 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 1.613 _refine_ls_shell.d_res_low 1.654 _refine_ls_shell.number_reflns_R_work 414 _refine_ls_shell.R_factor_R_work 0.117 _refine_ls_shell.percent_reflns_obs ? _refine_ls_shell.R_factor_R_free 0.138 _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.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? # _database_PDB_matrix.entry_id 2AXB _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 2AXB _struct.title 'Crystal Structure Analysis Of A 2-O-[2-(methoxy)ethyl]-2-thiothymidine Modified Oligodeoxynucleotide Duplex' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2AXB _struct_keywords.pdbx_keywords DNA _struct_keywords.text DNA # 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 ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 2AXB _struct_ref.pdbx_db_accession 2AXB _struct_ref.pdbx_db_isoform ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? # 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 2AXB A 1 ? 10 ? 2AXB 1 ? 10 ? 1 10 2 1 2AXB B 1 ? 10 ? 2AXB 11 ? 20 ? 11 20 # _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 # _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 _struct_biol.pdbx_parent_biol_id ? _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 covale1 covale both ? A DA 5 "O3'" ? ? ? 1_555 A S2M 6 P ? ? A DA 5 A S2M 6 1_555 ? ? ? ? ? ? ? 1.566 ? ? covale2 covale one ? A S2M 6 "C3'" ? ? ? 1_555 A DA 7 P ? ? A S2M 6 A DA 7 1_555 ? ? ? ? ? ? ? 1.778 ? ? covale3 covale both ? A S2M 6 "O3'" ? ? ? 1_555 A DA 7 P ? ? A S2M 6 A DA 7 1_555 ? ? ? ? ? ? ? 1.587 ? ? covale4 covale one ? A S2M 6 "O3'" ? ? ? 1_555 A DA 7 OP1 ? ? A S2M 6 A DA 7 1_555 ? ? ? ? ? ? ? 2.016 ? ? covale5 covale both ? B DA 5 "O3'" ? ? ? 1_555 B S2M 6 P ? ? B DA 15 B S2M 16 1_555 ? ? ? ? ? ? ? 1.610 ? ? covale6 covale both ? B S2M 6 "O3'" ? ? ? 1_555 B DA 7 P ? ? B S2M 16 B DA 17 1_555 ? ? ? ? ? ? ? 1.588 ? ? hydrog1 hydrog ? ? A DG 1 N1 ? ? ? 1_555 B DC 10 N3 ? ? A DG 1 B DC 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DG 1 N2 ? ? ? 1_555 B DC 10 O2 ? ? A DG 1 B DC 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DG 1 O6 ? ? ? 1_555 B DC 10 N4 ? ? A DG 1 B DC 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DC 2 N3 ? ? ? 1_555 B DG 9 N1 ? ? A DC 2 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DC 2 N4 ? ? ? 1_555 B DG 9 O6 ? ? A DC 2 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DC 2 O2 ? ? ? 1_555 B DG 9 N2 ? ? A DC 2 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DG 3 N1 ? ? ? 1_555 B DC 8 N3 ? ? A DG 3 B DC 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DG 3 N2 ? ? ? 1_555 B DC 8 O2 ? ? A DG 3 B DC 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DG 3 O6 ? ? ? 1_555 B DC 8 N4 ? ? A DG 3 B DC 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DT 4 N3 ? ? ? 1_555 B DA 7 N1 ? ? A DT 4 B DA 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DT 4 O4 ? ? ? 1_555 B DA 7 N6 ? ? A DT 4 B DA 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DA 5 N1 ? ? ? 1_555 B S2M 6 N3 ? ? A DA 5 B S2M 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DA 5 N6 ? ? ? 1_555 B S2M 6 O4 ? ? A DA 5 B S2M 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A S2M 6 N3 ? ? ? 1_555 B DA 5 N1 ? ? A S2M 6 B DA 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A S2M 6 O4 ? ? ? 1_555 B DA 5 N6 ? ? A S2M 6 B DA 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DA 7 N1 ? ? ? 1_555 B DT 4 N3 ? ? A DA 7 B DT 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DA 7 N6 ? ? ? 1_555 B DT 4 O4 ? ? A DA 7 B DT 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DC 8 N3 ? ? ? 1_555 B DG 3 N1 ? ? A DC 8 B DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DC 8 N4 ? ? ? 1_555 B DG 3 O6 ? ? A DC 8 B DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DC 8 O2 ? ? ? 1_555 B DG 3 N2 ? ? A DC 8 B DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DG 9 N1 ? ? ? 1_555 B DC 2 N3 ? ? A DG 9 B DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DG 9 N2 ? ? ? 1_555 B DC 2 O2 ? ? A DG 9 B DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DG 9 O6 ? ? ? 1_555 B DC 2 N4 ? ? A DG 9 B DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DC 10 N3 ? ? ? 1_555 B DG 1 N1 ? ? A DC 10 B DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DC 10 N4 ? ? ? 1_555 B DG 1 O6 ? ? A DC 10 B DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DC 10 O2 ? ? ? 1_555 B DG 1 N2 ? ? A DC 10 B DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _pdbx_validate_rmsd_bond.id 1 _pdbx_validate_rmsd_bond.PDB_model_num 1 _pdbx_validate_rmsd_bond.auth_atom_id_1 "O3'" _pdbx_validate_rmsd_bond.auth_asym_id_1 B _pdbx_validate_rmsd_bond.auth_comp_id_1 DA _pdbx_validate_rmsd_bond.auth_seq_id_1 17 _pdbx_validate_rmsd_bond.PDB_ins_code_1 ? _pdbx_validate_rmsd_bond.label_alt_id_1 ? _pdbx_validate_rmsd_bond.auth_atom_id_2 "C3'" _pdbx_validate_rmsd_bond.auth_asym_id_2 B _pdbx_validate_rmsd_bond.auth_comp_id_2 DA _pdbx_validate_rmsd_bond.auth_seq_id_2 17 _pdbx_validate_rmsd_bond.PDB_ins_code_2 ? _pdbx_validate_rmsd_bond.label_alt_id_2 ? _pdbx_validate_rmsd_bond.bond_value 1.377 _pdbx_validate_rmsd_bond.bond_target_value 1.419 _pdbx_validate_rmsd_bond.bond_deviation -0.042 _pdbx_validate_rmsd_bond.bond_standard_deviation 0.006 _pdbx_validate_rmsd_bond.linker_flag N # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "O4'" A DC 2 ? ? "C1'" A DC 2 ? ? N1 A DC 2 ? ? 103.32 108.00 -4.68 0.70 N 2 1 C6 A DC 2 ? ? N1 A DC 2 ? ? C2 A DC 2 ? ? 123.19 120.30 2.89 0.40 N 3 1 "O4'" A DG 3 ? ? "C1'" A DG 3 ? ? N9 A DG 3 ? ? 113.49 108.30 5.19 0.30 N 4 1 "O4'" A DA 5 ? ? "C4'" A DA 5 ? ? "C3'" A DA 5 ? ? 101.43 104.50 -3.07 0.40 N 5 1 "O3'" A DA 5 ? ? P A S2M 6 ? ? OP2 A S2M 6 ? ? 124.21 110.50 13.71 1.10 Y 6 1 "C3'" A S2M 6 ? ? "O3'" A S2M 6 ? ? P A DA 7 ? ? 72.15 119.70 -47.55 1.20 Y 7 1 "O3'" A S2M 6 ? ? P A DA 7 ? ? OP2 A DA 7 ? ? 155.02 110.50 44.52 1.10 Y 8 1 "O3'" A S2M 6 ? ? P A DA 7 ? ? OP1 A DA 7 ? ? 81.97 105.20 -23.23 2.20 Y 9 1 OP1 A DA 7 ? ? P A DA 7 ? ? OP2 A DA 7 ? ? 108.45 119.60 -11.15 1.50 N 10 1 "O4'" A DG 9 ? ? "C4'" A DG 9 ? ? "C3'" A DG 9 ? ? 100.14 104.50 -4.36 0.40 N 11 1 C5 A DG 9 ? ? C6 A DG 9 ? ? O6 A DG 9 ? ? 132.64 128.60 4.04 0.60 N 12 1 "O4'" A DC 10 ? ? "C1'" A DC 10 ? ? N1 A DC 10 ? ? 114.09 108.30 5.79 0.30 N 13 1 "O4'" B DC 12 ? ? "C4'" B DC 12 ? ? "C3'" B DC 12 ? ? 100.38 104.50 -4.12 0.40 N 14 1 "O4'" B DC 12 ? ? "C1'" B DC 12 ? ? N1 B DC 12 ? ? 112.52 108.30 4.22 0.30 N 15 1 N3 B DC 12 ? ? C4 B DC 12 ? ? N4 B DC 12 ? ? 113.17 118.00 -4.83 0.70 N 16 1 "O4'" B DT 14 ? ? "C1'" B DT 14 ? ? "C2'" B DT 14 ? ? 110.04 106.80 3.24 0.50 N 17 1 N3 B DT 14 ? ? C4 B DT 14 ? ? O4 B DT 14 ? ? 124.04 119.90 4.14 0.60 N 18 1 "O4'" B DA 15 ? ? "C1'" B DA 15 ? ? N9 B DA 15 ? ? 110.79 108.30 2.49 0.30 N 19 1 "C3'" B DA 15 ? ? "O3'" B DA 15 ? ? P B S2M 16 ? ? 111.49 119.70 -8.21 1.20 Y 20 1 "O3'" B DA 15 ? ? P B S2M 16 ? ? OP1 B S2M 16 ? ? 118.06 110.50 7.56 1.10 Y 21 1 "O4'" B DC 18 ? ? "C1'" B DC 18 ? ? N1 B DC 18 ? ? 112.96 108.30 4.66 0.30 N 22 1 "O4'" B DC 20 ? ? "C1'" B DC 20 ? ? N1 B DC 20 ? ? 111.08 108.30 2.78 0.30 N 23 1 C5 B DC 20 ? ? C4 B DC 20 ? ? N4 B DC 20 ? ? 115.28 120.20 -4.92 0.70 N # 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 S2M 6 A S2M 6 ? DT ? 2 B S2M 6 B S2M 16 ? DT ? # 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 DA OP3 O N N 1 DA P P N N 2 DA OP1 O N N 3 DA OP2 O N N 4 DA "O5'" O N N 5 DA "C5'" C N N 6 DA "C4'" C N R 7 DA "O4'" O N N 8 DA "C3'" C N S 9 DA "O3'" O N N 10 DA "C2'" C N N 11 DA "C1'" C N R 12 DA N9 N Y N 13 DA C8 C Y N 14 DA N7 N Y N 15 DA C5 C Y N 16 DA C6 C Y N 17 DA N6 N N N 18 DA N1 N Y N 19 DA C2 C Y N 20 DA N3 N Y N 21 DA C4 C Y N 22 DA HOP3 H N N 23 DA HOP2 H N N 24 DA "H5'" H N N 25 DA "H5''" H N N 26 DA "H4'" H N N 27 DA "H3'" H N N 28 DA "HO3'" H N N 29 DA "H2'" H N N 30 DA "H2''" H N N 31 DA "H1'" H N N 32 DA H8 H N N 33 DA H61 H N N 34 DA H62 H N N 35 DA H2 H N N 36 DC OP3 O N N 37 DC P P N N 38 DC OP1 O N N 39 DC OP2 O N N 40 DC "O5'" O N N 41 DC "C5'" C N N 42 DC "C4'" C N R 43 DC "O4'" O N N 44 DC "C3'" C N S 45 DC "O3'" O N N 46 DC "C2'" C N N 47 DC "C1'" C N R 48 DC N1 N N N 49 DC C2 C N N 50 DC O2 O N N 51 DC N3 N N N 52 DC C4 C N N 53 DC N4 N N N 54 DC C5 C N N 55 DC C6 C N N 56 DC HOP3 H N N 57 DC HOP2 H N N 58 DC "H5'" H N N 59 DC "H5''" H N N 60 DC "H4'" H N N 61 DC "H3'" H N N 62 DC "HO3'" H N N 63 DC "H2'" H N N 64 DC "H2''" H N N 65 DC "H1'" H N N 66 DC H41 H N N 67 DC H42 H N N 68 DC H5 H N N 69 DC H6 H N N 70 DG OP3 O N N 71 DG P P N N 72 DG OP1 O N N 73 DG OP2 O N N 74 DG "O5'" O N N 75 DG "C5'" C N N 76 DG "C4'" C N R 77 DG "O4'" O N N 78 DG "C3'" C N S 79 DG "O3'" O N N 80 DG "C2'" C N N 81 DG "C1'" C N R 82 DG N9 N Y N 83 DG C8 C Y N 84 DG N7 N Y N 85 DG C5 C Y N 86 DG C6 C N N 87 DG O6 O N N 88 DG N1 N N N 89 DG C2 C N N 90 DG N2 N N N 91 DG N3 N N N 92 DG C4 C Y N 93 DG HOP3 H N N 94 DG HOP2 H N N 95 DG "H5'" H N N 96 DG "H5''" H N N 97 DG "H4'" H N N 98 DG "H3'" H N N 99 DG "HO3'" H N N 100 DG "H2'" H N N 101 DG "H2''" H N N 102 DG "H1'" H N N 103 DG H8 H N N 104 DG H1 H N N 105 DG H21 H N N 106 DG H22 H N N 107 DT OP3 O N N 108 DT P P N N 109 DT OP1 O N N 110 DT OP2 O N N 111 DT "O5'" O N N 112 DT "C5'" C N N 113 DT "C4'" C N R 114 DT "O4'" O N N 115 DT "C3'" C N S 116 DT "O3'" O N N 117 DT "C2'" C N N 118 DT "C1'" C N R 119 DT N1 N N N 120 DT C2 C N N 121 DT O2 O N N 122 DT N3 N N N 123 DT C4 C N N 124 DT O4 O N N 125 DT C5 C N N 126 DT C7 C N N 127 DT C6 C N N 128 DT HOP3 H N N 129 DT HOP2 H N N 130 DT "H5'" H N N 131 DT "H5''" H N N 132 DT "H4'" H N N 133 DT "H3'" H N N 134 DT "HO3'" H N N 135 DT "H2'" H N N 136 DT "H2''" H N N 137 DT "H1'" H N N 138 DT H3 H N N 139 DT H71 H N N 140 DT H72 H N N 141 DT H73 H N N 142 DT H6 H N N 143 HOH O O N N 144 HOH H1 H N N 145 HOH H2 H N N 146 S2M O4 O N N 147 S2M C4 C N N 148 S2M C5 C N N 149 S2M C6 C N N 150 S2M C5M C N N 151 S2M N3 N N N 152 S2M S2 S N N 153 S2M C2 C N N 154 S2M "C5'" C N N 155 S2M "O5'" O N N 156 S2M P P N N 157 S2M OP2 O N N 158 S2M OP1 O N N 159 S2M "C4'" C N R 160 S2M "O4'" O N N 161 S2M "C1'" C N R 162 S2M N1 N N N 163 S2M "C2'" C N R 164 S2M "C3'" C N R 165 S2M "O3'" O N N 166 S2M "O2'" O N N 167 S2M "CA'" C N N 168 S2M "CB'" C N N 169 S2M "OC'" O N N 170 S2M "CD'" C N N 171 S2M OP3 O N N 172 S2M H6 H N N 173 S2M H71 H N N 174 S2M H72 H N N 175 S2M H73 H N N 176 S2M H3 H N N 177 S2M "H5'" H N N 178 S2M "H5''" H N N 179 S2M HOP2 H N N 180 S2M "H4'" H N N 181 S2M "H1'" H N N 182 S2M "H2'" H N N 183 S2M "H3'" H N N 184 S2M "HO3'" H N N 185 S2M "HA'1" H N N 186 S2M "HA'2" H N N 187 S2M "HB'1" H N N 188 S2M "HB'2" H N N 189 S2M "HD'1" H N N 190 S2M "HD'2" H N N 191 S2M "HD'3" H N N 192 S2M HOP3 H N N 193 # 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 DA OP3 P sing N N 1 DA OP3 HOP3 sing N N 2 DA P OP1 doub N N 3 DA P OP2 sing N N 4 DA P "O5'" sing N N 5 DA OP2 HOP2 sing N N 6 DA "O5'" "C5'" sing N N 7 DA "C5'" "C4'" sing N N 8 DA "C5'" "H5'" sing N N 9 DA "C5'" "H5''" sing N N 10 DA "C4'" "O4'" sing N N 11 DA "C4'" "C3'" sing N N 12 DA "C4'" "H4'" sing N N 13 DA "O4'" "C1'" sing N N 14 DA "C3'" "O3'" sing N N 15 DA "C3'" "C2'" sing N N 16 DA "C3'" "H3'" sing N N 17 DA "O3'" "HO3'" sing N N 18 DA "C2'" "C1'" sing N N 19 DA "C2'" "H2'" sing N N 20 DA "C2'" "H2''" sing N N 21 DA "C1'" N9 sing N N 22 DA "C1'" "H1'" sing N N 23 DA N9 C8 sing Y N 24 DA N9 C4 sing Y N 25 DA C8 N7 doub Y N 26 DA C8 H8 sing N N 27 DA N7 C5 sing Y N 28 DA C5 C6 sing Y N 29 DA C5 C4 doub Y N 30 DA C6 N6 sing N N 31 DA C6 N1 doub Y N 32 DA N6 H61 sing N N 33 DA N6 H62 sing N N 34 DA N1 C2 sing Y N 35 DA C2 N3 doub Y N 36 DA C2 H2 sing N N 37 DA N3 C4 sing Y N 38 DC OP3 P sing N N 39 DC OP3 HOP3 sing N N 40 DC P OP1 doub N N 41 DC P OP2 sing N N 42 DC P "O5'" sing N N 43 DC OP2 HOP2 sing N N 44 DC "O5'" "C5'" sing N N 45 DC "C5'" "C4'" sing N N 46 DC "C5'" "H5'" sing N N 47 DC "C5'" "H5''" sing N N 48 DC "C4'" "O4'" sing N N 49 DC "C4'" "C3'" sing N N 50 DC "C4'" "H4'" sing N N 51 DC "O4'" "C1'" sing N N 52 DC "C3'" "O3'" sing N N 53 DC "C3'" "C2'" sing N N 54 DC "C3'" "H3'" sing N N 55 DC "O3'" "HO3'" sing N N 56 DC "C2'" "C1'" sing N N 57 DC "C2'" "H2'" sing N N 58 DC "C2'" "H2''" sing N N 59 DC "C1'" N1 sing N N 60 DC "C1'" "H1'" sing N N 61 DC N1 C2 sing N N 62 DC N1 C6 sing N N 63 DC C2 O2 doub N N 64 DC C2 N3 sing N N 65 DC N3 C4 doub N N 66 DC C4 N4 sing N N 67 DC C4 C5 sing N N 68 DC N4 H41 sing N N 69 DC N4 H42 sing N N 70 DC C5 C6 doub N N 71 DC C5 H5 sing N N 72 DC C6 H6 sing N N 73 DG OP3 P sing N N 74 DG OP3 HOP3 sing N N 75 DG P OP1 doub N N 76 DG P OP2 sing N N 77 DG P "O5'" sing N N 78 DG OP2 HOP2 sing N N 79 DG "O5'" "C5'" sing N N 80 DG "C5'" "C4'" sing N N 81 DG "C5'" "H5'" sing N N 82 DG "C5'" "H5''" sing N N 83 DG "C4'" "O4'" sing N N 84 DG "C4'" "C3'" sing N N 85 DG "C4'" "H4'" sing N N 86 DG "O4'" "C1'" sing N N 87 DG "C3'" "O3'" sing N N 88 DG "C3'" "C2'" sing N N 89 DG "C3'" "H3'" sing N N 90 DG "O3'" "HO3'" sing N N 91 DG "C2'" "C1'" sing N N 92 DG "C2'" "H2'" sing N N 93 DG "C2'" "H2''" sing N N 94 DG "C1'" N9 sing N N 95 DG "C1'" "H1'" sing N N 96 DG N9 C8 sing Y N 97 DG N9 C4 sing Y N 98 DG C8 N7 doub Y N 99 DG C8 H8 sing N N 100 DG N7 C5 sing Y N 101 DG C5 C6 sing N N 102 DG C5 C4 doub Y N 103 DG C6 O6 doub N N 104 DG C6 N1 sing N N 105 DG N1 C2 sing N N 106 DG N1 H1 sing N N 107 DG C2 N2 sing N N 108 DG C2 N3 doub N N 109 DG N2 H21 sing N N 110 DG N2 H22 sing N N 111 DG N3 C4 sing N N 112 DT OP3 P sing N N 113 DT OP3 HOP3 sing N N 114 DT P OP1 doub N N 115 DT P OP2 sing N N 116 DT P "O5'" sing N N 117 DT OP2 HOP2 sing N N 118 DT "O5'" "C5'" sing N N 119 DT "C5'" "C4'" sing N N 120 DT "C5'" "H5'" sing N N 121 DT "C5'" "H5''" sing N N 122 DT "C4'" "O4'" sing N N 123 DT "C4'" "C3'" sing N N 124 DT "C4'" "H4'" sing N N 125 DT "O4'" "C1'" sing N N 126 DT "C3'" "O3'" sing N N 127 DT "C3'" "C2'" sing N N 128 DT "C3'" "H3'" sing N N 129 DT "O3'" "HO3'" sing N N 130 DT "C2'" "C1'" sing N N 131 DT "C2'" "H2'" sing N N 132 DT "C2'" "H2''" sing N N 133 DT "C1'" N1 sing N N 134 DT "C1'" "H1'" sing N N 135 DT N1 C2 sing N N 136 DT N1 C6 sing N N 137 DT C2 O2 doub N N 138 DT C2 N3 sing N N 139 DT N3 C4 sing N N 140 DT N3 H3 sing N N 141 DT C4 O4 doub N N 142 DT C4 C5 sing N N 143 DT C5 C7 sing N N 144 DT C5 C6 doub N N 145 DT C7 H71 sing N N 146 DT C7 H72 sing N N 147 DT C7 H73 sing N N 148 DT C6 H6 sing N N 149 HOH O H1 sing N N 150 HOH O H2 sing N N 151 S2M O4 C4 doub N N 152 S2M C4 C5 sing N N 153 S2M C4 N3 sing N N 154 S2M C5 C6 doub N N 155 S2M C5 C5M sing N N 156 S2M C6 N1 sing N N 157 S2M C6 H6 sing N N 158 S2M C5M H71 sing N N 159 S2M C5M H72 sing N N 160 S2M C5M H73 sing N N 161 S2M N3 C2 sing N N 162 S2M N3 H3 sing N N 163 S2M S2 C2 doub N N 164 S2M C2 N1 sing N N 165 S2M "C5'" "O5'" sing N N 166 S2M "C5'" "C4'" sing N N 167 S2M "C5'" "H5'" sing N N 168 S2M "C5'" "H5''" sing N N 169 S2M "O5'" P sing N N 170 S2M P OP2 sing N N 171 S2M P OP1 doub N N 172 S2M P OP3 sing N N 173 S2M OP2 HOP2 sing N N 174 S2M "C4'" "O4'" sing N N 175 S2M "C4'" "C3'" sing N N 176 S2M "C4'" "H4'" sing N N 177 S2M "O4'" "C1'" sing N N 178 S2M "C1'" N1 sing N N 179 S2M "C1'" "C2'" sing N N 180 S2M "C1'" "H1'" sing N N 181 S2M "C2'" "C3'" sing N N 182 S2M "C2'" "O2'" sing N N 183 S2M "C2'" "H2'" sing N N 184 S2M "C3'" "O3'" sing N N 185 S2M "C3'" "H3'" sing N N 186 S2M "O3'" "HO3'" sing N N 187 S2M "O2'" "CA'" sing N N 188 S2M "CA'" "CB'" sing N N 189 S2M "CA'" "HA'1" sing N N 190 S2M "CA'" "HA'2" sing N N 191 S2M "CB'" "OC'" sing N N 192 S2M "CB'" "HB'1" sing N N 193 S2M "CB'" "HB'2" sing N N 194 S2M "OC'" "CD'" sing N N 195 S2M "CD'" "HD'1" sing N N 196 S2M "CD'" "HD'2" sing N N 197 S2M "CD'" "HD'3" sing N N 198 S2M OP3 HOP3 sing N N 199 # _ndb_struct_conf_na.entry_id 2AXB _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 DG 1 1_555 B DC 10 1_555 -0.505 -0.157 0.084 2.729 -5.400 -4.280 1 A_DG1:DC20_B A 1 ? B 20 ? 19 1 1 A DC 2 1_555 B DG 9 1_555 0.086 -0.006 -0.324 6.277 -12.962 5.196 2 A_DC2:DG19_B A 2 ? B 19 ? 19 1 1 A DG 3 1_555 B DC 8 1_555 -0.498 -0.156 0.012 -10.483 -17.639 -0.978 3 A_DG3:DC18_B A 3 ? B 18 ? 19 1 1 A DT 4 1_555 B DA 7 1_555 -0.402 -0.132 -0.302 -4.107 -18.998 1.265 4 A_DT4:DA17_B A 4 ? B 17 ? 20 1 1 A DA 5 1_555 B S2M 6 1_555 0.239 -0.006 0.345 -1.698 -11.257 -0.077 5 A_DA5:S2M16_B A 5 ? B 16 ? 20 1 1 A S2M 6 1_555 B DA 5 1_555 -0.176 0.037 -0.229 7.723 -17.403 -0.285 6 A_S2M6:DA15_B A 6 ? B 15 ? 20 1 1 A DA 7 1_555 B DT 4 1_555 -0.078 -0.178 -0.007 -1.808 -12.913 0.094 7 A_DA7:DT14_B A 7 ? B 14 ? 20 1 1 A DC 8 1_555 B DG 3 1_555 0.032 -0.469 -0.214 6.209 -13.825 -3.363 8 A_DC8:DG13_B A 8 ? B 13 ? 19 1 1 A DG 9 1_555 B DC 2 1_555 -0.292 -0.015 -0.277 -12.369 -12.033 3.367 9 A_DG9:DC12_B A 9 ? B 12 ? 19 1 1 A DC 10 1_555 B DG 1 1_555 0.235 -0.429 -0.009 -7.280 5.905 -1.153 10 A_DC10:DG11_B A 10 ? B 11 ? 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 DG 1 1_555 B DC 10 1_555 A DC 2 1_555 B DG 9 1_555 0.457 -1.449 3.157 2.517 4.117 38.622 -2.648 -0.397 3.015 6.196 -3.788 38.911 1 AA_DG1DC2:DG19DC20_BB A 1 ? B 20 ? A 2 ? B 19 ? 1 A DC 2 1_555 B DG 9 1_555 A DG 3 1_555 B DC 8 1_555 -0.186 -2.187 3.684 -3.522 9.541 25.687 -6.944 -0.482 2.714 20.467 7.556 27.596 2 AA_DC2DG3:DC18DG19_BB A 2 ? B 19 ? A 3 ? B 18 ? 1 A DG 3 1_555 B DC 8 1_555 A DT 4 1_555 B DA 7 1_555 -0.955 -1.532 2.981 1.499 4.443 37.021 -2.911 1.667 2.746 6.962 -2.349 37.306 3 AA_DG3DT4:DA17DC18_BB A 3 ? B 18 ? A 4 ? B 17 ? 1 A DT 4 1_555 B DA 7 1_555 A DA 5 1_555 B S2M 6 1_555 0.685 -1.375 3.262 -3.266 19.744 25.799 -5.399 -1.709 1.712 37.806 6.253 32.547 4 AA_DT4DA5:S2M16DA17_BB A 4 ? B 17 ? A 5 ? B 16 ? 1 A DA 5 1_555 B S2M 6 1_555 A S2M 6 1_555 B DA 5 1_555 -0.002 -1.134 3.235 6.083 5.069 32.923 -2.738 0.949 2.984 8.787 -10.545 33.836 5 AA_DA5S2M6:DA15S2M16_BB A 5 ? B 16 ? A 6 ? B 15 ? 1 A S2M 6 1_555 B DA 5 1_555 A DA 7 1_555 B DT 4 1_555 0.110 -1.379 3.415 -2.114 17.425 27.023 -5.387 -0.551 2.142 33.213 4.029 32.134 6 AA_S2M6DA7:DT14DA15_BB A 6 ? B 15 ? A 7 ? B 14 ? 1 A DA 7 1_555 B DT 4 1_555 A DC 8 1_555 B DG 3 1_555 0.211 -1.733 3.166 -1.262 2.688 33.419 -3.420 -0.562 3.012 4.663 2.189 33.547 7 AA_DA7DC8:DG13DT14_BB A 7 ? B 14 ? A 8 ? B 13 ? 1 A DC 8 1_555 B DG 3 1_555 A DG 9 1_555 B DC 2 1_555 0.001 -1.880 3.714 1.320 9.215 29.270 -5.458 0.270 2.994 17.679 -2.532 30.684 8 AA_DC8DG9:DC12DG13_BB A 8 ? B 13 ? A 9 ? B 12 ? 1 A DG 9 1_555 B DC 2 1_555 A DC 10 1_555 B DG 1 1_555 0.172 -1.636 3.217 1.760 3.146 34.236 -3.237 -0.027 3.064 5.326 -2.979 34.419 9 AA_DG9DC10:DG11DC12_BB A 9 ? B 12 ? A 10 ? B 11 ? # _atom_sites.entry_id 2AXB _atom_sites.fract_transf_matrix[1][1] 0.039602 _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] 0.022221 _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] 0.022237 _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_