data_1MA8 # _entry.id 1MA8 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.386 _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 1MA8 pdb_00001ma8 10.2210/pdb1ma8/pdb NDB AD0027 ? ? RCSB RCSB016790 ? ? WWPDB D_1000016790 ? ? # 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 2002-12-11 2 'Structure model' 1 1 2008-04-28 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2019-07-24 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' 'Data collection' 4 4 'Structure model' 'Derived calculations' 5 4 'Structure model' 'Refinement description' 6 5 'Structure model' 'Data collection' 7 5 'Structure model' 'Database references' # 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 4 'Structure model' struct_conn 3 5 'Structure model' chem_comp_atom 4 5 'Structure model' chem_comp_bond 5 5 'Structure model' database_2 # 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 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 4 5 'Structure model' '_database_2.pdbx_DOI' 5 5 'Structure model' '_database_2.pdbx_database_accession' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1MA8 _pdbx_database_status.recvd_initial_deposition_date 2002-08-01 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.SG_entry . _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_sf ? _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 'Teplova, M.' 1 'Wilds, C.J.' 2 'Wawrzak, Z.' 3 'Tereshko, V.' 4 'Du, Q.' 5 'Carrasco, N.' 6 'Huang, Z.' 7 'Egli, M.' 8 # _citation.id primary _citation.title 'Covalent incorporation of selenium into oligonucleotides for X-ray crystal structure determination via MAD: proof of principle' _citation.journal_abbrev BIOCHIMIE _citation.journal_volume 84 _citation.page_first 849 _citation.page_last 858 _citation.year 2002 _citation.journal_id_ASTM BICMBE _citation.country FR _citation.journal_id_ISSN 0300-9084 _citation.journal_id_CSD 0466 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 12458077 _citation.pdbx_database_id_DOI '10.1016/S0300-9084(02)01440-2' # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Teplova, M.' 1 ? primary 'Wilds, C.J.' 2 ? primary 'Wawrzak, Z.' 3 ? primary 'Tereshko, V.' 4 ? primary 'Du, Q.' 5 ? primary 'Carrasco, N.' 6 ? primary 'Huang, Z.' 7 ? primary 'Egli, M.' 8 ? # 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*UMSP*AP*CP*GP*C)-3'" 3123.965 2 ? ? ? 'U-Se-modified DNA duplex' 2 water nat water 18.015 141 ? ? ? ? # _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)(UMS)(DA)(DC)(DG)(DC)' _entity_poly.pdbx_seq_one_letter_code_can GCGTAUACGC _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 UMS 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 UMS 'DNA linking' n "2'-METHYLSELENYL-2'-DEOXYURIDINE-5'-PHOSPHATE" ? 'C10 H15 N2 O8 P Se' 401.168 # 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 UMS 6 6 6 UMS UMS 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 1 111 111 DG G B . n B 1 2 DC 2 112 112 DC C B . n B 1 3 DG 3 113 113 DG G B . n B 1 4 DT 4 114 114 DT T B . n B 1 5 DA 5 115 115 DA A B . n B 1 6 UMS 6 116 116 UMS UMS B . n B 1 7 DA 7 117 117 DA A B . n B 1 8 DC 8 118 118 DC C B . n B 1 9 DG 9 119 119 DG G B . n B 1 10 DC 10 120 120 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 1 702 702 HOH HOH A . C 2 HOH 2 703 703 HOH HOH A . C 2 HOH 3 704 704 HOH HOH A . C 2 HOH 4 705 705 HOH HOH A . C 2 HOH 5 706 706 HOH HOH A . C 2 HOH 6 707 707 HOH HOH A . C 2 HOH 7 709 709 HOH HOH A . C 2 HOH 8 710 710 HOH HOH A . C 2 HOH 9 711 711 HOH HOH A . C 2 HOH 10 712 712 HOH HOH A . C 2 HOH 11 713 713 HOH HOH A . C 2 HOH 12 714 714 HOH HOH A . C 2 HOH 13 715 715 HOH HOH A . C 2 HOH 14 717 717 HOH HOH A . C 2 HOH 15 719 719 HOH HOH A . C 2 HOH 16 720 720 HOH HOH A . C 2 HOH 17 722 722 HOH HOH A . C 2 HOH 18 723 723 HOH HOH A . C 2 HOH 19 725 725 HOH HOH A . C 2 HOH 20 726 726 HOH HOH A . C 2 HOH 21 729 729 HOH HOH A . C 2 HOH 22 731 731 HOH HOH A . C 2 HOH 23 732 732 HOH HOH A . C 2 HOH 24 734 734 HOH HOH A . C 2 HOH 25 735 735 HOH HOH A . C 2 HOH 26 740 740 HOH HOH A . C 2 HOH 27 743 743 HOH HOH A . C 2 HOH 28 745 745 HOH HOH A . C 2 HOH 29 750 750 HOH HOH A . C 2 HOH 30 751 751 HOH HOH A . C 2 HOH 31 752 752 HOH HOH A . C 2 HOH 32 757 757 HOH HOH A . C 2 HOH 33 758 758 HOH HOH A . C 2 HOH 34 759 759 HOH HOH A . C 2 HOH 35 761 761 HOH HOH A . C 2 HOH 36 762 762 HOH HOH A . C 2 HOH 37 768 768 HOH HOH A . C 2 HOH 38 769 769 HOH HOH A . C 2 HOH 39 771 771 HOH HOH A . C 2 HOH 40 781 781 HOH HOH A . C 2 HOH 41 783 783 HOH HOH A . C 2 HOH 42 784 784 HOH HOH A . C 2 HOH 43 785 785 HOH HOH A . C 2 HOH 44 786 786 HOH HOH A . C 2 HOH 45 789 789 HOH HOH A . C 2 HOH 46 792 792 HOH HOH A . C 2 HOH 47 793 793 HOH HOH A . C 2 HOH 48 795 795 HOH HOH A . C 2 HOH 49 797 797 HOH HOH A . C 2 HOH 50 798 798 HOH HOH A . C 2 HOH 51 800 800 HOH HOH A . C 2 HOH 52 805 805 HOH HOH A . C 2 HOH 53 806 806 HOH HOH A . C 2 HOH 54 808 808 HOH HOH A . C 2 HOH 55 811 811 HOH HOH A . C 2 HOH 56 814 814 HOH HOH A . C 2 HOH 57 815 815 HOH HOH A . C 2 HOH 58 818 818 HOH HOH A . C 2 HOH 59 822 822 HOH HOH A . C 2 HOH 60 824 824 HOH HOH A . C 2 HOH 61 825 825 HOH HOH A . C 2 HOH 62 828 828 HOH HOH A . C 2 HOH 63 829 829 HOH HOH A . C 2 HOH 64 830 830 HOH HOH A . C 2 HOH 65 831 831 HOH HOH A . C 2 HOH 66 835 835 HOH HOH A . C 2 HOH 67 836 836 HOH HOH A . C 2 HOH 68 837 837 HOH HOH A . C 2 HOH 69 838 838 HOH HOH A . C 2 HOH 70 839 839 HOH HOH A . C 2 HOH 71 840 840 HOH HOH A . C 2 HOH 72 846 846 HOH HOH A . D 2 HOH 1 701 701 HOH HOH B . D 2 HOH 2 708 708 HOH HOH B . D 2 HOH 3 716 716 HOH HOH B . D 2 HOH 4 718 718 HOH HOH B . D 2 HOH 5 721 721 HOH HOH B . D 2 HOH 6 724 724 HOH HOH B . D 2 HOH 7 727 727 HOH HOH B . D 2 HOH 8 728 728 HOH HOH B . D 2 HOH 9 730 730 HOH HOH B . D 2 HOH 10 733 733 HOH HOH B . D 2 HOH 11 736 736 HOH HOH B . D 2 HOH 12 737 737 HOH HOH B . D 2 HOH 13 738 738 HOH HOH B . D 2 HOH 14 739 739 HOH HOH B . D 2 HOH 15 741 741 HOH HOH B . D 2 HOH 16 742 742 HOH HOH B . D 2 HOH 17 744 744 HOH HOH B . D 2 HOH 18 746 746 HOH HOH B . D 2 HOH 19 747 747 HOH HOH B . D 2 HOH 20 748 748 HOH HOH B . D 2 HOH 21 749 749 HOH HOH B . D 2 HOH 22 753 753 HOH HOH B . D 2 HOH 23 754 754 HOH HOH B . D 2 HOH 24 755 755 HOH HOH B . D 2 HOH 25 756 756 HOH HOH B . D 2 HOH 26 760 760 HOH HOH B . D 2 HOH 27 763 763 HOH HOH B . D 2 HOH 28 764 764 HOH HOH B . D 2 HOH 29 765 765 HOH HOH B . D 2 HOH 30 766 766 HOH HOH B . D 2 HOH 31 767 767 HOH HOH B . D 2 HOH 32 770 770 HOH HOH B . D 2 HOH 33 772 772 HOH HOH B . D 2 HOH 34 773 773 HOH HOH B . D 2 HOH 35 774 774 HOH HOH B . D 2 HOH 36 775 775 HOH HOH B . D 2 HOH 37 776 776 HOH HOH B . D 2 HOH 38 777 777 HOH HOH B . D 2 HOH 39 779 779 HOH HOH B . D 2 HOH 40 780 780 HOH HOH B . D 2 HOH 41 787 787 HOH HOH B . D 2 HOH 42 788 788 HOH HOH B . D 2 HOH 43 790 790 HOH HOH B . D 2 HOH 44 791 791 HOH HOH B . D 2 HOH 45 796 796 HOH HOH B . D 2 HOH 46 799 799 HOH HOH B . D 2 HOH 47 801 801 HOH HOH B . D 2 HOH 48 802 802 HOH HOH B . D 2 HOH 49 804 804 HOH HOH B . D 2 HOH 50 807 807 HOH HOH B . D 2 HOH 51 810 810 HOH HOH B . D 2 HOH 52 812 812 HOH HOH B . D 2 HOH 53 813 813 HOH HOH B . D 2 HOH 54 816 816 HOH HOH B . D 2 HOH 55 817 817 HOH HOH B . D 2 HOH 56 819 819 HOH HOH B . D 2 HOH 57 820 820 HOH HOH B . D 2 HOH 58 821 821 HOH HOH B . D 2 HOH 59 823 823 HOH HOH B . D 2 HOH 60 826 826 HOH HOH B . D 2 HOH 61 827 827 HOH HOH B . D 2 HOH 62 832 832 HOH HOH B . D 2 HOH 63 833 833 HOH HOH B . D 2 HOH 64 834 834 HOH HOH B . D 2 HOH 65 841 841 HOH HOH B . D 2 HOH 66 842 842 HOH HOH B . D 2 HOH 67 843 843 HOH HOH B . D 2 HOH 68 844 844 HOH HOH B . D 2 HOH 69 845 845 HOH HOH B . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal SHELXL-97 refinement . ? 1 SCALEPACK 'data scaling' . ? 2 CNS refinement . ? 3 DENZO 'data reduction' . ? 4 CNS phasing . ? 5 # _cell.entry_id 1MA8 _cell.length_a 24.555 _cell.length_b 43.967 _cell.length_c 45.340 _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 1MA8 _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 # _exptl.entry_id 1MA8 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 34.63 _exptl_crystal.density_Matthews 1.88 _exptl_crystal.description ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 298 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.0 _exptl_crystal_grow.pdbx_details ;MPD, spermine tetrahydrochloride, potassium chloride, sodium chloride, sodium cacodylate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K ; _exptl_crystal_grow.pdbx_pH_range . # loop_ _exptl_crystal_grow_comp.crystal_id _exptl_crystal_grow_comp.id _exptl_crystal_grow_comp.sol_id _exptl_crystal_grow_comp.name _exptl_crystal_grow_comp.conc _exptl_crystal_grow_comp.volume _exptl_crystal_grow_comp.details 1 1 1 MPD ? ? ? 1 2 1 'spermine tetrahydrochloride' ? ? ? 1 3 1 KCl ? ? ? 1 4 1 NaCl ? ? ? 1 5 1 'sodium cacodylate' ? ? ? 1 6 2 MPD ? ? ? 1 7 2 NaCl ? ? ? # _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 MARRESEARCH _diffrn_detector.pdbx_collection_date 2001-05-30 _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 MAD _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 '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 ? # _reflns.entry_id 1MA8 _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.d_resolution_high 1.3 _reflns.d_resolution_low 20 _reflns.number_all ? _reflns.number_obs 23332 _reflns.percent_possible_obs 99.8 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value 0.049 _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 6.9 _reflns.R_free_details ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 1.3 _reflns_shell.d_res_low 1.35 _reflns_shell.percent_possible_all 100 _reflns_shell.Rmerge_I_obs ? _reflns_shell.pdbx_Rsym_value 0.263 _reflns_shell.meanI_over_sigI_obs ? _reflns_shell.pdbx_redundancy ? _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all ? _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 1MA8 _refine.ls_d_res_high 1.3 _refine.ls_d_res_low 10 _refine.pdbx_ls_sigma_F ? _refine.pdbx_ls_sigma_I 4 _refine.ls_number_reflns_all ? _refine.ls_number_reflns_obs 21189 _refine.ls_number_reflns_R_free 1048 _refine.ls_percent_reflns_obs ? _refine.ls_R_factor_all ? _refine.ls_R_factor_obs ? _refine.ls_R_factor_R_work 0.149 _refine.ls_R_factor_R_free 0.173 _refine.ls_redundancy_reflns_obs ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_R_free ? _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_method_to_determine_struct MAD _refine.pdbx_starting_model ? _refine.pdbx_ls_cross_valid_method ? _refine.pdbx_R_Free_selection_details random _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_stereochemistry_target_values ? _refine.solvent_model_details ? _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.pdbx_isotropic_thermal_model ? _refine.B_iso_mean ? _refine.aniso_B[1][1] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][2] ? _refine.aniso_B[2][3] ? _refine.aniso_B[3][3] ? _refine.details ? _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.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_SU_B ? _refine.overall_SU_ML ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_data_cutoff_high_rms_absF ? _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 628 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 141 _refine_hist.number_atoms_total 769 _refine_hist.d_res_high 1.3 _refine_hist.d_res_low 10 # 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_angle_d 0.023 ? ? ? 'X-RAY DIFFRACTION' ? s_bond_d 0.015 ? ? ? 'X-RAY DIFFRACTION' ? # _database_PDB_matrix.entry_id 1MA8 _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 1MA8 _struct.title ;A-DNA decamer GCGTA(UMS)ACGC with incorporated 2'-methylseleno-uridine ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1MA8 _struct_keywords.pdbx_keywords DNA _struct_keywords.text ;2'-methylseleno-uridine, 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 1MA8 _struct_ref.pdbx_db_accession 1MA8 _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 1MA8 A 1 ? 10 ? 1MA8 1 ? 10 ? 1 10 2 1 1MA8 B 1 ? 10 ? 1MA8 111 ? 120 ? 111 120 # _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 UMS 6 P ? ? A DA 5 A UMS 6 1_555 ? ? ? ? ? ? ? 1.595 ? ? covale2 covale both ? A UMS 6 "O3'" ? ? ? 1_555 A DA 7 P ? ? A UMS 6 A DA 7 1_555 ? ? ? ? ? ? ? 1.576 ? ? covale3 covale both ? B DA 5 "O3'" ? ? ? 1_555 B UMS 6 P ? ? B DA 115 B UMS 116 1_555 ? ? ? ? ? ? ? 1.621 ? ? covale4 covale both ? B UMS 6 "O3'" ? ? ? 1_555 B DA 7 P ? ? B UMS 116 B DA 117 1_555 ? ? ? ? ? ? ? 1.620 ? ? hydrog1 hydrog ? ? A DG 1 N1 ? ? ? 1_555 B DC 10 N3 ? ? A DG 1 B DC 120 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DG 1 N2 ? ? ? 1_555 B DC 10 O2 ? ? A DG 1 B DC 120 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DG 1 O6 ? ? ? 1_555 B DC 10 N4 ? ? A DG 1 B DC 120 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DC 2 N3 ? ? ? 1_555 B DG 9 N1 ? ? A DC 2 B DG 119 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DC 2 N4 ? ? ? 1_555 B DG 9 O6 ? ? A DC 2 B DG 119 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DC 2 O2 ? ? ? 1_555 B DG 9 N2 ? ? A DC 2 B DG 119 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DG 3 N1 ? ? ? 1_555 B DC 8 N3 ? ? A DG 3 B DC 118 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DG 3 N2 ? ? ? 1_555 B DC 8 O2 ? ? A DG 3 B DC 118 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DG 3 O6 ? ? ? 1_555 B DC 8 N4 ? ? A DG 3 B DC 118 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DT 4 N3 ? ? ? 1_555 B DA 7 N1 ? ? A DT 4 B DA 117 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DT 4 O4 ? ? ? 1_555 B DA 7 N6 ? ? A DT 4 B DA 117 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DA 5 N1 ? ? ? 1_555 B UMS 6 N3 ? ? A DA 5 B UMS 116 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DA 5 N6 ? ? ? 1_555 B UMS 6 O4 ? ? A DA 5 B UMS 116 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A UMS 6 N3 ? ? ? 1_555 B DA 5 N1 ? ? A UMS 6 B DA 115 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A UMS 6 O4 ? ? ? 1_555 B DA 5 N6 ? ? A UMS 6 B DA 115 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DA 7 N1 ? ? ? 1_555 B DT 4 N3 ? ? A DA 7 B DT 114 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DA 7 N6 ? ? ? 1_555 B DT 4 O4 ? ? A DA 7 B DT 114 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DC 8 N3 ? ? ? 1_555 B DG 3 N1 ? ? A DC 8 B DG 113 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DC 8 N4 ? ? ? 1_555 B DG 3 O6 ? ? A DC 8 B DG 113 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DC 8 O2 ? ? ? 1_555 B DG 3 N2 ? ? A DC 8 B DG 113 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DG 9 N1 ? ? ? 1_555 B DC 2 N3 ? ? A DG 9 B DC 112 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DG 9 N2 ? ? ? 1_555 B DC 2 O2 ? ? A DG 9 B DC 112 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DG 9 O6 ? ? ? 1_555 B DC 2 N4 ? ? A DG 9 B DC 112 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DC 10 N3 ? ? ? 1_555 B DG 1 N1 ? ? A DC 10 B DG 111 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DC 10 N4 ? ? ? 1_555 B DG 1 O6 ? ? A DC 10 B DG 111 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DC 10 O2 ? ? ? 1_555 B DG 1 N2 ? ? A DC 10 B DG 111 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _pdbx_validate_close_contact.id 1 _pdbx_validate_close_contact.PDB_model_num 1 _pdbx_validate_close_contact.auth_atom_id_1 O _pdbx_validate_close_contact.auth_asym_id_1 B _pdbx_validate_close_contact.auth_comp_id_1 HOH _pdbx_validate_close_contact.auth_seq_id_1 791 _pdbx_validate_close_contact.PDB_ins_code_1 ? _pdbx_validate_close_contact.label_alt_id_1 ? _pdbx_validate_close_contact.auth_atom_id_2 O _pdbx_validate_close_contact.auth_asym_id_2 B _pdbx_validate_close_contact.auth_comp_id_2 HOH _pdbx_validate_close_contact.auth_seq_id_2 820 _pdbx_validate_close_contact.PDB_ins_code_2 ? _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 0.91 # loop_ _pdbx_validate_symm_contact.id _pdbx_validate_symm_contact.PDB_model_num _pdbx_validate_symm_contact.auth_atom_id_1 _pdbx_validate_symm_contact.auth_asym_id_1 _pdbx_validate_symm_contact.auth_comp_id_1 _pdbx_validate_symm_contact.auth_seq_id_1 _pdbx_validate_symm_contact.PDB_ins_code_1 _pdbx_validate_symm_contact.label_alt_id_1 _pdbx_validate_symm_contact.site_symmetry_1 _pdbx_validate_symm_contact.auth_atom_id_2 _pdbx_validate_symm_contact.auth_asym_id_2 _pdbx_validate_symm_contact.auth_comp_id_2 _pdbx_validate_symm_contact.auth_seq_id_2 _pdbx_validate_symm_contact.PDB_ins_code_2 _pdbx_validate_symm_contact.label_alt_id_2 _pdbx_validate_symm_contact.site_symmetry_2 _pdbx_validate_symm_contact.dist 1 1 O A HOH 846 ? ? 1_555 O B HOH 842 ? ? 1_455 1.95 2 1 O A HOH 752 ? ? 1_555 O A HOH 808 ? ? 3_655 2.02 # loop_ _pdbx_validate_rmsd_bond.id _pdbx_validate_rmsd_bond.PDB_model_num _pdbx_validate_rmsd_bond.auth_atom_id_1 _pdbx_validate_rmsd_bond.auth_asym_id_1 _pdbx_validate_rmsd_bond.auth_comp_id_1 _pdbx_validate_rmsd_bond.auth_seq_id_1 _pdbx_validate_rmsd_bond.PDB_ins_code_1 _pdbx_validate_rmsd_bond.label_alt_id_1 _pdbx_validate_rmsd_bond.auth_atom_id_2 _pdbx_validate_rmsd_bond.auth_asym_id_2 _pdbx_validate_rmsd_bond.auth_comp_id_2 _pdbx_validate_rmsd_bond.auth_seq_id_2 _pdbx_validate_rmsd_bond.PDB_ins_code_2 _pdbx_validate_rmsd_bond.label_alt_id_2 _pdbx_validate_rmsd_bond.bond_value _pdbx_validate_rmsd_bond.bond_target_value _pdbx_validate_rmsd_bond.bond_deviation _pdbx_validate_rmsd_bond.bond_standard_deviation _pdbx_validate_rmsd_bond.linker_flag 1 1 N7 A DG 1 ? ? C8 A DG 1 ? ? 1.345 1.305 0.040 0.006 N 2 1 "C2'" A DC 2 ? ? "C1'" A DC 2 ? ? 1.448 1.518 -0.070 0.010 N 3 1 N1 A DC 2 ? ? C6 A DC 2 ? ? 1.321 1.367 -0.046 0.006 N 4 1 "C2'" A DG 3 ? ? "C1'" A DG 3 ? ? 1.444 1.518 -0.074 0.010 N 5 1 "C2'" A DT 4 ? ? "C1'" A DT 4 ? ? 1.436 1.518 -0.082 0.010 N 6 1 N3 A DA 5 ? ? C4 A DA 5 ? ? 1.307 1.344 -0.037 0.006 N 7 1 N1 A DC 8 ? ? C6 A DC 8 ? ? 1.328 1.367 -0.039 0.006 N 8 1 "C2'" A DG 9 ? ? "C1'" A DG 9 ? ? 1.456 1.518 -0.062 0.010 N 9 1 "C2'" B DG 111 ? ? "C1'" B DG 111 ? ? 1.445 1.518 -0.073 0.010 N 10 1 "C5'" B DC 112 ? ? "C4'" B DC 112 ? ? 1.557 1.512 0.045 0.007 N 11 1 "C2'" B DC 112 ? ? "C1'" B DC 112 ? ? 1.456 1.518 -0.062 0.010 N 12 1 "O4'" B DC 112 ? ? "C1'" B DC 112 ? ? 1.494 1.420 0.074 0.011 N 13 1 "O4'" B DC 112 ? ? "C4'" B DC 112 ? ? 1.514 1.449 0.065 0.009 N 14 1 "O3'" B DC 112 ? ? "C3'" B DC 112 ? ? 1.516 1.435 0.081 0.013 N 15 1 "O4'" B DG 113 ? ? "C4'" B DG 113 ? ? 1.505 1.449 0.056 0.009 N 16 1 "C2'" B DA 115 ? ? "C1'" B DA 115 ? ? 1.438 1.518 -0.080 0.010 N 17 1 "O4'" B DA 115 ? ? "C1'" B DA 115 ? ? 1.492 1.420 0.072 0.011 N 18 1 "C3'" B DG 119 ? ? "C2'" B DG 119 ? ? 1.456 1.516 -0.060 0.008 N 19 1 "C2'" B DG 119 ? ? "C1'" B DG 119 ? ? 1.418 1.518 -0.100 0.010 N 20 1 "O4'" B DG 119 ? ? "C1'" B DG 119 ? ? 1.506 1.420 0.086 0.011 N 21 1 "C2'" B DC 120 ? ? "C1'" B DC 120 ? ? 1.435 1.518 -0.083 0.010 N 22 1 "O4'" B DC 120 ? ? "C1'" B DC 120 ? ? 1.504 1.420 0.084 0.011 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 DG 1 ? ? "C1'" A DG 1 ? ? N9 A DG 1 ? ? 102.70 108.00 -5.30 0.70 N 2 1 C4 A DC 2 ? ? C5 A DC 2 ? ? C6 A DC 2 ? ? 114.28 117.40 -3.12 0.50 N 3 1 C5 A DC 2 ? ? C6 A DC 2 ? ? N1 A DC 2 ? ? 124.65 121.00 3.65 0.50 N 4 1 "O4'" A DG 3 ? ? "C1'" A DG 3 ? ? N9 A DG 3 ? ? 101.48 108.00 -6.52 0.70 N 5 1 "O4'" A DT 4 ? ? "C1'" A DT 4 ? ? N1 A DT 4 ? ? 103.65 108.00 -4.35 0.70 N 6 1 "O4'" A DA 7 ? ? "C4'" A DA 7 ? ? "C3'" A DA 7 ? ? 101.70 104.50 -2.80 0.40 N 7 1 "O4'" A DC 8 ? ? "C4'" A DC 8 ? ? "C3'" A DC 8 ? ? 101.93 104.50 -2.57 0.40 N 8 1 "O4'" A DG 9 ? ? "C1'" A DG 9 ? ? N9 A DG 9 ? ? 102.62 108.00 -5.38 0.70 N 9 1 N1 A DG 9 ? ? C6 A DG 9 ? ? O6 A DG 9 ? ? 123.74 119.90 3.84 0.60 N 10 1 N3 A DC 10 ? ? C4 A DC 10 ? ? N4 A DC 10 ? ? 113.24 118.00 -4.76 0.70 N 11 1 "O4'" B DG 111 ? ? "C1'" B DG 111 ? ? N9 B DG 111 ? ? 102.90 108.00 -5.10 0.70 N 12 1 "C1'" B DC 112 ? ? "O4'" B DC 112 ? ? "C4'" B DC 112 ? ? 102.48 110.10 -7.62 1.00 N 13 1 C5 B DG 113 ? ? N7 B DG 113 ? ? C8 B DG 113 ? ? 101.05 104.30 -3.25 0.50 N 14 1 N7 B DG 113 ? ? C8 B DG 113 ? ? N9 B DG 113 ? ? 116.84 113.10 3.74 0.50 N 15 1 N1 B DG 113 ? ? C6 B DG 113 ? ? O6 B DG 113 ? ? 116.07 119.90 -3.83 0.60 N 16 1 C5 B DG 113 ? ? C6 B DG 113 ? ? O6 B DG 113 ? ? 132.54 128.60 3.94 0.60 N 17 1 C5 B DT 114 ? ? C6 B DT 114 ? ? N1 B DT 114 ? ? 127.41 123.70 3.71 0.60 N 18 1 C4 B DT 114 ? ? C5 B DT 114 ? ? C7 B DT 114 ? ? 122.81 119.00 3.81 0.60 N 19 1 "O4'" B DA 115 ? ? "C1'" B DA 115 ? ? N9 B DA 115 ? ? 102.31 108.00 -5.69 0.70 N 20 1 C8 B DA 115 ? ? N9 B DA 115 ? ? C4 B DA 115 ? ? 108.25 105.80 2.45 0.40 N 21 1 P B DA 117 ? ? "O5'" B DA 117 ? ? "C5'" B DA 117 ? ? 110.80 120.90 -10.10 1.60 N 22 1 "O4'" B DG 119 ? ? "C1'" B DG 119 ? ? N9 B DG 119 ? ? 102.82 108.00 -5.18 0.70 N 23 1 "O4'" B DC 120 ? ? "C1'" B DC 120 ? ? N1 B DC 120 ? ? 102.12 108.00 -5.88 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 UMS 6 A UMS 6 ? DU ? 2 B UMS 6 B UMS 116 ? DU ? # 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 UMS OP3 O N N 147 UMS P P N N 148 UMS OP1 O N N 149 UMS OP2 O N N 150 UMS "O5'" O N N 151 UMS "C5'" C N N 152 UMS "C4'" C N R 153 UMS "O4'" O N N 154 UMS "C3'" C N R 155 UMS "O3'" O N N 156 UMS "C2'" C N R 157 UMS "SE2'" SE N N 158 UMS "C1'" C N R 159 UMS "CA'" C N N 160 UMS N1 N N N 161 UMS C2 C N N 162 UMS O2 O N N 163 UMS N3 N N N 164 UMS C4 C N N 165 UMS O4 O N N 166 UMS C5 C N N 167 UMS C6 C N N 168 UMS HOP3 H N N 169 UMS HOP2 H N N 170 UMS "H5'" H N N 171 UMS "H5'2" H N N 172 UMS "H4'" H N N 173 UMS "H3'" H N N 174 UMS "HO3'" H N N 175 UMS "H2'" H N N 176 UMS "H1'" H N N 177 UMS "HA'" H N N 178 UMS "HA'2" H N N 179 UMS "HA'3" H N N 180 UMS H3 H N N 181 UMS H5 H N N 182 UMS H6 H N N 183 # 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 UMS OP3 P sing N N 152 UMS OP3 HOP3 sing N N 153 UMS P OP1 doub N N 154 UMS P OP2 sing N N 155 UMS P "O5'" sing N N 156 UMS OP2 HOP2 sing N N 157 UMS "O5'" "C5'" sing N N 158 UMS "C5'" "C4'" sing N N 159 UMS "C5'" "H5'" sing N N 160 UMS "C5'" "H5'2" sing N N 161 UMS "C4'" "O4'" sing N N 162 UMS "C4'" "C3'" sing N N 163 UMS "C4'" "H4'" sing N N 164 UMS "O4'" "C1'" sing N N 165 UMS "C3'" "O3'" sing N N 166 UMS "C3'" "C2'" sing N N 167 UMS "C3'" "H3'" sing N N 168 UMS "O3'" "HO3'" sing N N 169 UMS "C2'" "SE2'" sing N N 170 UMS "C2'" "C1'" sing N N 171 UMS "C2'" "H2'" sing N N 172 UMS "SE2'" "CA'" sing N N 173 UMS "C1'" N1 sing N N 174 UMS "C1'" "H1'" sing N N 175 UMS "CA'" "HA'" sing N N 176 UMS "CA'" "HA'2" sing N N 177 UMS "CA'" "HA'3" sing N N 178 UMS N1 C2 sing N N 179 UMS N1 C6 sing N N 180 UMS C2 O2 doub N N 181 UMS C2 N3 sing N N 182 UMS N3 C4 sing N N 183 UMS N3 H3 sing N N 184 UMS C4 O4 doub N N 185 UMS C4 C5 sing N N 186 UMS C5 C6 doub N N 187 UMS C5 H5 sing N N 188 UMS C6 H6 sing N N 189 # _ndb_struct_conf_na.entry_id 1MA8 _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 -0.312 -0.124 0.145 3.387 -6.230 -1.566 1 A_DG1:DC120_B A 1 ? B 120 ? 19 1 1 A DC 2 1_555 B DG 9 1_555 0.118 -0.125 0.106 4.924 -12.955 0.824 2 A_DC2:DG119_B A 2 ? B 119 ? 19 1 1 A DG 3 1_555 B DC 8 1_555 -0.253 -0.160 0.103 -7.828 -18.099 0.494 3 A_DG3:DC118_B A 3 ? B 118 ? 19 1 1 A DT 4 1_555 B DA 7 1_555 -0.158 -0.102 0.046 -5.497 -16.266 -2.915 4 A_DT4:DA117_B A 4 ? B 117 ? 20 1 1 A DA 5 1_555 B UMS 6 1_555 0.097 -0.051 0.061 -0.740 -13.683 -2.933 5 A_DA5:UMS116_B A 5 ? B 116 ? 20 1 1 A UMS 6 1_555 B DA 5 1_555 -0.036 -0.084 0.165 4.419 -15.221 6.906 6 A_UMS6:DA115_B A 6 ? B 115 ? 20 1 1 A DA 7 1_555 B DT 4 1_555 -0.029 -0.141 0.009 2.419 -11.309 3.962 7 A_DA7:DT114_B A 7 ? B 114 ? 20 1 1 A DC 8 1_555 B DG 3 1_555 0.181 -0.164 -0.059 8.394 -12.185 0.236 8 A_DC8:DG113_B A 8 ? B 113 ? 19 1 1 A DG 9 1_555 B DC 2 1_555 -0.167 -0.181 -0.038 -6.112 -10.193 -1.140 9 A_DG9:DC112_B A 9 ? B 112 ? 19 1 1 A DC 10 1_555 B DG 1 1_555 0.204 -0.123 0.196 -4.268 4.821 -0.148 10 A_DC10:DG111_B A 10 ? B 111 ? 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 0.307 -1.443 3.262 1.029 0.153 39.253 -2.166 -0.335 3.263 0.228 -1.532 39.266 1 AA_DG1DC2:DG119DC120_BB A 1 ? B 120 ? A 2 ? B 119 ? 1 A DC 2 1_555 B DG 9 1_555 A DG 3 1_555 B DC 8 1_555 0.058 -2.077 3.380 0.717 11.464 26.796 -6.411 0.026 2.315 23.418 -1.464 29.113 2 AA_DC2DG3:DC118DG119_BB A 2 ? B 119 ? A 3 ? B 118 ? 1 A DG 3 1_555 B DC 8 1_555 A DT 4 1_555 B DA 7 1_555 -1.112 -1.392 3.114 -2.572 4.874 38.151 -2.676 1.386 2.986 7.410 3.910 38.532 3 AA_DG3DT4:DA117DC118_BB A 3 ? B 118 ? A 4 ? B 117 ? 1 A DT 4 1_555 B DA 7 1_555 A DA 5 1_555 B UMS 6 1_555 0.544 -1.521 3.121 1.889 17.350 23.935 -5.994 -0.738 1.692 36.296 -3.953 29.547 4 AA_DT4DA5:UMS116DA117_BB A 4 ? B 117 ? A 5 ? B 116 ? 1 A DA 5 1_555 B UMS 6 1_555 A UMS 6 1_555 B DA 5 1_555 0.802 -1.080 3.105 0.906 10.463 32.743 -3.310 -1.229 2.665 17.992 -1.558 34.342 5 AA_DA5UMS6:DA115UMS116_BB A 5 ? B 116 ? A 6 ? B 115 ? 1 A UMS 6 1_555 B DA 5 1_555 A DA 7 1_555 B DT 4 1_555 -0.155 -1.366 3.116 -0.324 15.361 31.182 -4.326 0.217 2.221 26.646 0.563 34.677 6 AA_UMS6DA7:DT114DA115_BB A 6 ? B 115 ? A 7 ? B 114 ? 1 A DA 7 1_555 B DT 4 1_555 A DC 8 1_555 B DG 3 1_555 -0.108 -1.872 3.249 -0.350 2.716 29.258 -4.255 0.141 3.068 5.362 0.691 29.383 7 AA_DA7DC8:DG113DT114_BB A 7 ? B 114 ? A 8 ? B 113 ? 1 A DC 8 1_555 B DG 3 1_555 A DG 9 1_555 B DC 2 1_555 -0.382 -1.964 3.509 -0.550 12.008 29.786 -5.636 0.596 2.553 22.253 1.019 32.069 8 AA_DC8DG9:DC112DG113_BB A 8 ? B 113 ? A 9 ? B 112 ? 1 A DG 9 1_555 B DC 2 1_555 A DC 10 1_555 B DG 1 1_555 0.244 -1.675 3.357 -0.404 1.710 35.278 -3.016 -0.463 3.272 2.820 0.667 35.320 9 AA_DG9DC10:DG111DC112_BB A 9 ? B 112 ? A 10 ? B 111 ? # _atom_sites.entry_id 1MA8 _atom_sites.fract_transf_matrix[1][1] 0.040725 _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] 0.022744 _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] 0.022056 _atom_sites.fract_transf_vector[1] 0.000000 _atom_sites.fract_transf_vector[2] 0.000000 _atom_sites.fract_transf_vector[3] 0.000000 # loop_ _atom_type.symbol C H N O P SE # loop_