data_384D # _entry.id 384D # _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 384D pdb_0000384d 10.2210/pdb384d/pdb NDB ADJB111 ? ? RCSB RCSB001316 ? ? WWPDB D_1000001316 ? ? # 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 1998-03-10 2 'Structure model' 1 1 2008-04-26 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2017-10-04 5 'Structure model' 1 4 2023-12-27 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' 'Refinement description' 4 5 'Structure model' 'Data collection' 5 5 'Structure model' 'Database references' 6 5 'Structure model' 'Derived calculations' 7 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' 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' pdbx_struct_conn_angle 6 5 'Structure model' struct_conn 7 5 'Structure model' struct_conn_type 8 5 'Structure model' struct_site 9 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 5 'Structure model' '_database_2.pdbx_DOI' 2 5 'Structure model' '_database_2.pdbx_database_accession' 3 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 4 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 5 5 'Structure model' '_pdbx_struct_conn_angle.value' 6 5 'Structure model' '_struct_conn.conn_type_id' 7 5 'Structure model' '_struct_conn.id' 8 5 'Structure model' '_struct_conn.pdbx_dist_value' 9 5 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 10 5 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 11 5 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 12 5 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 13 5 'Structure model' '_struct_conn.ptnr1_label_asym_id' 14 5 'Structure model' '_struct_conn.ptnr1_label_atom_id' 15 5 'Structure model' '_struct_conn.ptnr1_label_comp_id' 16 5 'Structure model' '_struct_conn.ptnr1_label_seq_id' 17 5 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 18 5 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 19 5 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 20 5 'Structure model' '_struct_conn.ptnr2_label_asym_id' 21 5 'Structure model' '_struct_conn.ptnr2_label_atom_id' 22 5 'Structure model' '_struct_conn.ptnr2_label_comp_id' 23 5 'Structure model' '_struct_conn.ptnr2_label_seq_id' 24 5 'Structure model' '_struct_conn_type.id' 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 384D _pdbx_database_status.recvd_initial_deposition_date 1998-03-02 _pdbx_database_status.deposit_site NDB _pdbx_database_status.process_site NDB _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 'Mayer-Jung, C.' 1 'Moras, D.' 2 'Timsit, Y.' 3 # _citation.id primary _citation.title 'Hydration and Recognition of Methylated CpG Steps in DNA' _citation.journal_abbrev 'Embo J.' _citation.journal_volume 17 _citation.page_first 2709 _citation.page_last 2718 _citation.year 1998 _citation.journal_id_ASTM EMJODG _citation.country UK _citation.journal_id_ISSN 0261-4189 _citation.journal_id_CSD 0897 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 9564052 _citation.pdbx_database_id_DOI 10.1093/emboj/17.9.2709 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Mayer-Jung, C.' 1 ? primary 'Moras, D.' 2 ? primary 'Timsit, Y.' 3 ? # 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(*CP*(5CM)P*GP*CP*(5CM)P*GP*GP*(5CM)P*GP*G)-3'" 3089.062 2 ? ? ? ? 2 non-polymer syn 'MAGNESIUM ION' 24.305 1 ? ? ? ? 3 water nat water 18.015 88 ? ? ? ? # _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 '(DC)(5CM)(DG)(DC)(5CM)(DG)(DG)(5CM)(DG)(DG)' _entity_poly.pdbx_seq_one_letter_code_can CCGCCGGCGG _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 DC n 1 2 5CM n 1 3 DG n 1 4 DC n 1 5 5CM n 1 6 DG n 1 7 DG n 1 8 5CM n 1 9 DG n 1 10 DG 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 5CM 'DNA linking' n "5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE" ? 'C10 H16 N3 O7 P' 321.224 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 HOH non-polymer . WATER ? 'H2 O' 18.015 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 # 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 DC 1 1 1 DC C A . n A 1 2 5CM 2 2 2 5CM C A . n A 1 3 DG 3 3 3 DG G A . n A 1 4 DC 4 4 4 DC C A . n A 1 5 5CM 5 5 5 5CM C A . n A 1 6 DG 6 6 6 DG G A . n A 1 7 DG 7 7 7 DG G A . n A 1 8 5CM 8 8 8 5CM C A . n A 1 9 DG 9 9 9 DG G A . n A 1 10 DG 10 10 10 DG G A . n B 1 1 DC 1 11 11 DC C B . n B 1 2 5CM 2 12 12 5CM C B . n B 1 3 DG 3 13 13 DG G B . n B 1 4 DC 4 14 14 DC C B . n B 1 5 5CM 5 15 15 5CM C B . n B 1 6 DG 6 16 16 DG G B . n B 1 7 DG 7 17 17 DG G B . n B 1 8 5CM 8 18 18 5CM C B . n B 1 9 DG 9 19 19 DG G B . n B 1 10 DG 10 20 20 DG 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 21 21 MG MO6 B . D 3 HOH 1 24 24 HOH HOH A . D 3 HOH 2 25 25 HOH HOH A . D 3 HOH 3 26 26 HOH HOH A . D 3 HOH 4 27 27 HOH HOH A . D 3 HOH 5 44 44 HOH HOH A . D 3 HOH 6 45 45 HOH HOH A . D 3 HOH 7 46 46 HOH HOH A . D 3 HOH 8 47 47 HOH HOH A . D 3 HOH 9 48 48 HOH HOH A . D 3 HOH 10 49 49 HOH HOH A . D 3 HOH 11 50 50 HOH HOH A . D 3 HOH 12 51 51 HOH HOH A . D 3 HOH 13 52 52 HOH HOH A . D 3 HOH 14 53 53 HOH HOH A . D 3 HOH 15 54 54 HOH HOH A . D 3 HOH 16 55 55 HOH HOH A . D 3 HOH 17 56 56 HOH HOH A . D 3 HOH 18 57 57 HOH HOH A . D 3 HOH 19 58 58 HOH HOH A . D 3 HOH 20 59 59 HOH HOH A . D 3 HOH 21 60 60 HOH HOH A . D 3 HOH 22 61 61 HOH HOH A . D 3 HOH 23 68 68 HOH HOH A . D 3 HOH 24 69 69 HOH HOH A . D 3 HOH 25 70 70 HOH HOH A . D 3 HOH 26 71 71 HOH HOH A . D 3 HOH 27 72 72 HOH HOH A . D 3 HOH 28 73 73 HOH HOH A . D 3 HOH 29 74 74 HOH HOH A . D 3 HOH 30 75 75 HOH HOH A . D 3 HOH 31 76 76 HOH HOH A . D 3 HOH 32 77 77 HOH HOH A . D 3 HOH 33 78 78 HOH HOH A . D 3 HOH 34 79 79 HOH HOH A . D 3 HOH 35 86 86 HOH HOH A . D 3 HOH 36 87 87 HOH HOH A . D 3 HOH 37 88 88 HOH HOH A . D 3 HOH 38 89 89 HOH HOH A . D 3 HOH 39 90 90 HOH HOH A . D 3 HOH 40 91 91 HOH HOH A . D 3 HOH 41 92 92 HOH HOH A . D 3 HOH 42 93 93 HOH HOH A . D 3 HOH 43 94 94 HOH HOH A . D 3 HOH 44 100 100 HOH HOH A . D 3 HOH 45 101 101 HOH HOH A . D 3 HOH 46 102 102 HOH HOH A . D 3 HOH 47 103 103 HOH HOH A . E 3 HOH 1 22 22 HOH HOH B . E 3 HOH 2 23 23 HOH HOH B . E 3 HOH 3 28 28 HOH HOH B . E 3 HOH 4 29 29 HOH HOH B . E 3 HOH 5 30 30 HOH HOH B . E 3 HOH 6 31 31 HOH HOH B . E 3 HOH 7 32 32 HOH HOH B . E 3 HOH 8 33 33 HOH HOH B . E 3 HOH 9 34 34 HOH HOH B . E 3 HOH 10 35 35 HOH HOH B . E 3 HOH 11 36 36 HOH HOH B . E 3 HOH 12 37 37 HOH HOH B . E 3 HOH 13 38 38 HOH HOH B . E 3 HOH 14 39 39 HOH HOH B . E 3 HOH 15 40 40 HOH HOH B . E 3 HOH 16 41 41 HOH HOH B . E 3 HOH 17 42 42 HOH HOH B . E 3 HOH 18 43 43 HOH HOH B . E 3 HOH 19 62 62 HOH HOH B . E 3 HOH 20 63 63 HOH HOH B . E 3 HOH 21 64 64 HOH HOH B . E 3 HOH 22 65 65 HOH HOH B . E 3 HOH 23 66 66 HOH HOH B . E 3 HOH 24 67 67 HOH HOH B . E 3 HOH 25 80 80 HOH HOH B . E 3 HOH 26 81 81 HOH HOH B . E 3 HOH 27 82 82 HOH HOH B . E 3 HOH 28 83 83 HOH HOH B . E 3 HOH 29 84 84 HOH HOH B . E 3 HOH 30 85 85 HOH HOH B . E 3 HOH 31 95 95 HOH HOH B . E 3 HOH 32 96 96 HOH HOH B . E 3 HOH 33 97 97 HOH HOH B . E 3 HOH 34 98 98 HOH HOH B . E 3 HOH 35 99 99 HOH HOH B . E 3 HOH 36 104 21 HOH MO6 B . E 3 HOH 37 105 21 HOH MO6 B . E 3 HOH 38 106 21 HOH MO6 B . E 3 HOH 39 107 21 HOH MO6 B . E 3 HOH 40 108 21 HOH MO6 B . E 3 HOH 41 109 21 HOH MO6 B . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal XDS 'data scaling' . ? 1 AUTOMAR 'data reduction' . ? 2 AMoRE phasing . ? 3 X-PLOR refinement 3.851 ? 4 XDS 'data reduction' . ? 5 # _cell.entry_id 384D _cell.length_a 54.900 _cell.length_b 54.900 _cell.length_c 45.600 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 384D _symmetry.space_group_name_H-M 'P 61' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting hexagonal _symmetry.Int_Tables_number 169 # _exptl.entry_id 384D _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 60.23 _exptl_crystal.density_Matthews 3.09 _exptl_crystal.description ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method ? _exptl_crystal_grow.temp ? _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.00 _exptl_crystal_grow.pdbx_details 'pH 6.00' _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.volume _exptl_crystal_grow_comp.conc _exptl_crystal_grow_comp.details 1 1 1 WATER ? ? ? 1 2 1 MPD ? ? ? 1 3 1 SPERMINE ? ? ? 1 4 1 MGCL2 ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 269.00 _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 1995-04-15 _diffrn_detector.details 'DOUBLE MIRRORS' # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'MIRROR + CHANNEL 4' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _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 'LURE BEAMLINE DW32' _diffrn_source.pdbx_synchrotron_site LURE _diffrn_source.pdbx_synchrotron_beamline DW32 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list ? # _reflns.entry_id 384D _reflns.observed_criterion_sigma_I 1.000 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 20.000 _reflns.d_resolution_high 2.150 _reflns.number_obs 4238 _reflns.number_all ? _reflns.percent_possible_obs 97.200 _reflns.pdbx_Rmerge_I_obs 0.044 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 5.100 _reflns.R_free_details ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _refine.entry_id 384D _refine.ls_number_reflns_obs 3827 _refine.ls_number_reflns_all 4238 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 2.000 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 7.000 _refine.ls_d_res_high 2.150 _refine.ls_percent_reflns_obs ? _refine.ls_R_factor_obs 0.1661 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.166 _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 ? _refine.ls_number_restraints ? _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 ? _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_ls_cross_valid_method ? _refine.details ? _refine.pdbx_starting_model 'P61 OCTAMER' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values ? _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.ls_redundancy_reflns_obs ? _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.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 404 _refine_hist.pdbx_number_atoms_ligand 13 _refine_hist.number_atoms_solvent 82 _refine_hist.number_atoms_total 499 _refine_hist.d_res_high 2.150 _refine_hist.d_res_low 7.000 # 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 x_bond_d 0.011 ? ? ? 'X-RAY DIFFRACTION' ? x_bond_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? x_bond_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? x_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? x_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? x_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? x_angle_deg 1.40 ? ? ? 'X-RAY DIFFRACTION' ? x_angle_deg_na ? ? ? ? 'X-RAY DIFFRACTION' ? x_angle_deg_prot ? ? ? ? 'X-RAY DIFFRACTION' ? x_dihedral_angle_d 27.0 ? ? ? 'X-RAY DIFFRACTION' ? x_dihedral_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? x_dihedral_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? x_improper_angle_d 1.60 ? ? ? 'X-RAY DIFFRACTION' ? x_improper_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? x_improper_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? x_mcbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? x_mcangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? x_scbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? x_scangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? # _pdbx_xplor_file.serial_no 1 _pdbx_xplor_file.param_file DNA.PARAM _pdbx_xplor_file.topol_file DNA.TOP _pdbx_xplor_file.pdbx_refine_id 'X-RAY DIFFRACTION' # _database_PDB_matrix.entry_id 384D _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 384D _struct.title 'HYDRATION AND RECOGNITION OF METHYLATED CPG STEPS IN DNA' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 384D _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'A-DNA, DOUBLE HELIX, MODIFIED, 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 3 ? E N N 3 ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 384D _struct_ref.pdbx_db_accession 384D _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 384D A 1 ? 10 ? 384D 1 ? 10 ? 1 10 2 1 384D B 1 ? 10 ? 384D 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,E # _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 DC 1 "O3'" ? ? ? 1_555 A 5CM 2 P ? ? A DC 1 A 5CM 2 1_555 ? ? ? ? ? ? ? 1.600 ? ? covale2 covale both ? A 5CM 2 "O3'" ? ? ? 1_555 A DG 3 P ? ? A 5CM 2 A DG 3 1_555 ? ? ? ? ? ? ? 1.590 ? ? covale3 covale both ? A DC 4 "O3'" ? ? ? 1_555 A 5CM 5 P ? ? A DC 4 A 5CM 5 1_555 ? ? ? ? ? ? ? 1.596 ? ? covale4 covale both ? A 5CM 5 "O3'" ? ? ? 1_555 A DG 6 P ? ? A 5CM 5 A DG 6 1_555 ? ? ? ? ? ? ? 1.594 ? ? covale5 covale both ? A DG 7 "O3'" ? ? ? 1_555 A 5CM 8 P ? ? A DG 7 A 5CM 8 1_555 ? ? ? ? ? ? ? 1.588 ? ? covale6 covale both ? A 5CM 8 "O3'" ? ? ? 1_555 A DG 9 P ? ? A 5CM 8 A DG 9 1_555 ? ? ? ? ? ? ? 1.600 ? ? covale7 covale both ? B DC 1 "O3'" ? ? ? 1_555 B 5CM 2 P ? ? B DC 11 B 5CM 12 1_555 ? ? ? ? ? ? ? 1.588 ? ? covale8 covale both ? B 5CM 2 "O3'" ? ? ? 1_555 B DG 3 P ? ? B 5CM 12 B DG 13 1_555 ? ? ? ? ? ? ? 1.591 ? ? covale9 covale both ? B DC 4 "O3'" ? ? ? 1_555 B 5CM 5 P ? ? B DC 14 B 5CM 15 1_555 ? ? ? ? ? ? ? 1.607 ? ? covale10 covale both ? B 5CM 5 "O3'" ? ? ? 1_555 B DG 6 P ? ? B 5CM 15 B DG 16 1_555 ? ? ? ? ? ? ? 1.589 ? ? covale11 covale both ? B DG 7 "O3'" ? ? ? 1_555 B 5CM 8 P ? ? B DG 17 B 5CM 18 1_555 ? ? ? ? ? ? ? 1.590 ? ? covale12 covale both ? B 5CM 8 "O3'" ? ? ? 1_555 B DG 9 P ? ? B 5CM 18 B DG 19 1_555 ? ? ? ? ? ? ? 1.584 ? ? metalc1 metalc ? ? C MG . MG ? ? ? 1_555 E HOH . O ? ? B MG 21 B HOH 104 1_555 ? ? ? ? ? ? ? 2.237 ? ? metalc2 metalc ? ? C MG . MG ? ? ? 1_555 E HOH . O ? ? B MG 21 B HOH 105 1_555 ? ? ? ? ? ? ? 2.072 ? ? metalc3 metalc ? ? C MG . MG ? ? ? 1_555 E HOH . O ? ? B MG 21 B HOH 106 1_555 ? ? ? ? ? ? ? 2.312 ? ? metalc4 metalc ? ? C MG . MG ? ? ? 1_555 E HOH . O ? ? B MG 21 B HOH 107 1_555 ? ? ? ? ? ? ? 2.219 ? ? metalc5 metalc ? ? C MG . MG ? ? ? 1_555 E HOH . O ? ? B MG 21 B HOH 108 1_555 ? ? ? ? ? ? ? 2.303 ? ? metalc6 metalc ? ? C MG . MG ? ? ? 1_555 E HOH . O ? ? B MG 21 B HOH 109 1_555 ? ? ? ? ? ? ? 2.967 ? ? hydrog1 hydrog ? ? A DC 1 N3 ? ? ? 1_555 B DG 10 N1 ? ? A DC 1 B DG 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DC 1 N4 ? ? ? 1_555 B DG 10 O6 ? ? A DC 1 B DG 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 1 O2 ? ? ? 1_555 B DG 10 N2 ? ? A DC 1 B DG 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A 5CM 2 N3 ? ? ? 1_555 B DG 9 N1 ? ? A 5CM 2 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A 5CM 2 N4 ? ? ? 1_555 B DG 9 O6 ? ? A 5CM 2 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A 5CM 2 O2 ? ? ? 1_555 B DG 9 N2 ? ? A 5CM 2 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DG 3 N1 ? ? ? 1_555 B 5CM 8 N3 ? ? A DG 3 B 5CM 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DG 3 N2 ? ? ? 1_555 B 5CM 8 O2 ? ? A DG 3 B 5CM 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DG 3 O6 ? ? ? 1_555 B 5CM 8 N4 ? ? A DG 3 B 5CM 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DC 4 N3 ? ? ? 1_555 B DG 7 N1 ? ? A DC 4 B DG 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DC 4 N4 ? ? ? 1_555 B DG 7 O6 ? ? A DC 4 B DG 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DC 4 O2 ? ? ? 1_555 B DG 7 N2 ? ? A DC 4 B DG 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A 5CM 5 N3 ? ? ? 1_555 B DG 6 N1 ? ? A 5CM 5 B DG 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A 5CM 5 N4 ? ? ? 1_555 B DG 6 O6 ? ? A 5CM 5 B DG 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A 5CM 5 O2 ? ? ? 1_555 B DG 6 N2 ? ? A 5CM 5 B DG 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DG 6 N1 ? ? ? 1_555 B 5CM 5 N3 ? ? A DG 6 B 5CM 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DG 6 N2 ? ? ? 1_555 B 5CM 5 O2 ? ? A DG 6 B 5CM 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DG 6 O6 ? ? ? 1_555 B 5CM 5 N4 ? ? A DG 6 B 5CM 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DG 7 N1 ? ? ? 1_555 B DC 4 N3 ? ? A DG 7 B DC 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DG 7 N2 ? ? ? 1_555 B DC 4 O2 ? ? A DG 7 B DC 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DG 7 O6 ? ? ? 1_555 B DC 4 N4 ? ? A DG 7 B DC 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A 5CM 8 N3 ? ? ? 1_555 B DG 3 N1 ? ? A 5CM 8 B DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A 5CM 8 N4 ? ? ? 1_555 B DG 3 O6 ? ? A 5CM 8 B DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A 5CM 8 O2 ? ? ? 1_555 B DG 3 N2 ? ? A 5CM 8 B DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DG 9 N1 ? ? ? 1_555 B 5CM 2 N3 ? ? A DG 9 B 5CM 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DG 9 N2 ? ? ? 1_555 B 5CM 2 O2 ? ? A DG 9 B 5CM 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A DG 9 O6 ? ? ? 1_555 B 5CM 2 N4 ? ? A DG 9 B 5CM 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A DG 10 N1 ? ? ? 1_555 B DC 1 N3 ? ? A DG 10 B DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A DG 10 N2 ? ? ? 1_555 B DC 1 O2 ? ? A DG 10 B DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A DG 10 O6 ? ? ? 1_555 B DC 1 N4 ? ? A DG 10 B DC 11 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 O ? E HOH . ? B HOH 104 ? 1_555 MG ? C MG . ? B MG 21 ? 1_555 O ? E HOH . ? B HOH 105 ? 1_555 87.0 ? 2 O ? E HOH . ? B HOH 104 ? 1_555 MG ? C MG . ? B MG 21 ? 1_555 O ? E HOH . ? B HOH 106 ? 1_555 149.1 ? 3 O ? E HOH . ? B HOH 105 ? 1_555 MG ? C MG . ? B MG 21 ? 1_555 O ? E HOH . ? B HOH 106 ? 1_555 90.7 ? 4 O ? E HOH . ? B HOH 104 ? 1_555 MG ? C MG . ? B MG 21 ? 1_555 O ? E HOH . ? B HOH 107 ? 1_555 86.5 ? 5 O ? E HOH . ? B HOH 105 ? 1_555 MG ? C MG . ? B MG 21 ? 1_555 O ? E HOH . ? B HOH 107 ? 1_555 154.7 ? 6 O ? E HOH . ? B HOH 106 ? 1_555 MG ? C MG . ? B MG 21 ? 1_555 O ? E HOH . ? B HOH 107 ? 1_555 82.6 ? 7 O ? E HOH . ? B HOH 104 ? 1_555 MG ? C MG . ? B MG 21 ? 1_555 O ? E HOH . ? B HOH 108 ? 1_555 94.5 ? 8 O ? E HOH . ? B HOH 105 ? 1_555 MG ? C MG . ? B MG 21 ? 1_555 O ? E HOH . ? B HOH 108 ? 1_555 96.0 ? 9 O ? E HOH . ? B HOH 106 ? 1_555 MG ? C MG . ? B MG 21 ? 1_555 O ? E HOH . ? B HOH 108 ? 1_555 116.3 ? 10 O ? E HOH . ? B HOH 107 ? 1_555 MG ? C MG . ? B MG 21 ? 1_555 O ? E HOH . ? B HOH 108 ? 1_555 108.9 ? 11 O ? E HOH . ? B HOH 104 ? 1_555 MG ? C MG . ? B MG 21 ? 1_555 O ? E HOH . ? B HOH 109 ? 1_555 80.5 ? 12 O ? E HOH . ? B HOH 105 ? 1_555 MG ? C MG . ? B MG 21 ? 1_555 O ? E HOH . ? B HOH 109 ? 1_555 90.3 ? 13 O ? E HOH . ? B HOH 106 ? 1_555 MG ? C MG . ? B MG 21 ? 1_555 O ? E HOH . ? B HOH 109 ? 1_555 68.7 ? 14 O ? E HOH . ? B HOH 107 ? 1_555 MG ? C MG . ? B MG 21 ? 1_555 O ? E HOH . ? B HOH 109 ? 1_555 64.5 ? 15 O ? E HOH . ? B HOH 108 ? 1_555 MG ? C MG . ? B MG 21 ? 1_555 O ? E HOH . ? B HOH 109 ? 1_555 171.8 ? # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _struct_site.pdbx_auth_asym_id B _struct_site.pdbx_auth_comp_id MG _struct_site.pdbx_auth_seq_id 21 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 6 _struct_site.details 'BINDING SITE FOR RESIDUE MG B 21' # 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 HOH E . ? HOH B 104 . ? 1_555 ? 2 AC1 6 HOH E . ? HOH B 105 . ? 1_555 ? 3 AC1 6 HOH E . ? HOH B 106 . ? 1_555 ? 4 AC1 6 HOH E . ? HOH B 107 . ? 1_555 ? 5 AC1 6 HOH E . ? HOH B 108 . ? 1_555 ? 6 AC1 6 HOH E . ? HOH B 109 . ? 1_555 ? # _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 37 _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 38 _pdbx_validate_close_contact.PDB_ins_code_2 ? _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 2.09 # 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 54 ? ? 1_555 O A HOH 101 ? ? 2_665 1.98 2 1 O A HOH 69 ? ? 1_555 O B HOH 97 ? ? 4_664 2.09 # _pdbx_validate_rmsd_angle.id 1 _pdbx_validate_rmsd_angle.PDB_model_num 1 _pdbx_validate_rmsd_angle.auth_atom_id_1 "O5'" _pdbx_validate_rmsd_angle.auth_asym_id_1 B _pdbx_validate_rmsd_angle.auth_comp_id_1 DC _pdbx_validate_rmsd_angle.auth_seq_id_1 11 _pdbx_validate_rmsd_angle.PDB_ins_code_1 ? _pdbx_validate_rmsd_angle.label_alt_id_1 ? _pdbx_validate_rmsd_angle.auth_atom_id_2 "C5'" _pdbx_validate_rmsd_angle.auth_asym_id_2 B _pdbx_validate_rmsd_angle.auth_comp_id_2 DC _pdbx_validate_rmsd_angle.auth_seq_id_2 11 _pdbx_validate_rmsd_angle.PDB_ins_code_2 ? _pdbx_validate_rmsd_angle.label_alt_id_2 ? _pdbx_validate_rmsd_angle.auth_atom_id_3 "C4'" _pdbx_validate_rmsd_angle.auth_asym_id_3 B _pdbx_validate_rmsd_angle.auth_comp_id_3 DC _pdbx_validate_rmsd_angle.auth_seq_id_3 11 _pdbx_validate_rmsd_angle.PDB_ins_code_3 ? _pdbx_validate_rmsd_angle.label_alt_id_3 ? _pdbx_validate_rmsd_angle.angle_value 104.29 _pdbx_validate_rmsd_angle.angle_target_value 109.40 _pdbx_validate_rmsd_angle.angle_deviation -5.11 _pdbx_validate_rmsd_angle.angle_standard_deviation 0.80 _pdbx_validate_rmsd_angle.linker_flag 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 5CM 2 A 5CM 2 ? DC ? 2 A 5CM 5 A 5CM 5 ? DC ? 3 A 5CM 8 A 5CM 8 ? DC ? 4 B 5CM 2 B 5CM 12 ? DC ? 5 B 5CM 5 B 5CM 15 ? DC ? 6 B 5CM 8 B 5CM 18 ? DC ? # 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 5CM N1 N N N 1 5CM C2 C N N 2 5CM N3 N N N 3 5CM C4 C N N 4 5CM C5 C N N 5 5CM C5A C N N 6 5CM C6 C N N 7 5CM O2 O N N 8 5CM N4 N N N 9 5CM "C1'" C N R 10 5CM "C2'" C N N 11 5CM "C3'" C N S 12 5CM "C4'" C N R 13 5CM "O4'" O N N 14 5CM "O3'" O N N 15 5CM "C5'" C N N 16 5CM "O5'" O N N 17 5CM P P N N 18 5CM OP1 O N N 19 5CM OP2 O N N 20 5CM OP3 O N N 21 5CM H5A1 H N N 22 5CM H5A2 H N N 23 5CM H5A3 H N N 24 5CM H6 H N N 25 5CM HN41 H N N 26 5CM HN42 H N N 27 5CM "H1'" H N N 28 5CM "H2'" H N N 29 5CM "H2''" H N N 30 5CM "H3'" H N N 31 5CM "H4'" H N N 32 5CM "HO3'" H N N 33 5CM "H5'" H N N 34 5CM "H5''" H N N 35 5CM HOP2 H N N 36 5CM HOP3 H N N 37 DC OP3 O N N 38 DC P P N N 39 DC OP1 O N N 40 DC OP2 O N N 41 DC "O5'" O N N 42 DC "C5'" C N N 43 DC "C4'" C N R 44 DC "O4'" O N N 45 DC "C3'" C N S 46 DC "O3'" O N N 47 DC "C2'" C N N 48 DC "C1'" C N R 49 DC N1 N N N 50 DC C2 C N N 51 DC O2 O N N 52 DC N3 N N N 53 DC C4 C N N 54 DC N4 N N N 55 DC C5 C N N 56 DC C6 C N N 57 DC HOP3 H N N 58 DC HOP2 H N N 59 DC "H5'" H N N 60 DC "H5''" H N N 61 DC "H4'" H N N 62 DC "H3'" H N N 63 DC "HO3'" H N N 64 DC "H2'" H N N 65 DC "H2''" H N N 66 DC "H1'" H N N 67 DC H41 H N N 68 DC H42 H N N 69 DC H5 H N N 70 DC H6 H N N 71 DG OP3 O N N 72 DG P P N N 73 DG OP1 O N N 74 DG OP2 O N N 75 DG "O5'" O N N 76 DG "C5'" C N N 77 DG "C4'" C N R 78 DG "O4'" O N N 79 DG "C3'" C N S 80 DG "O3'" O N N 81 DG "C2'" C N N 82 DG "C1'" C N R 83 DG N9 N Y N 84 DG C8 C Y N 85 DG N7 N Y N 86 DG C5 C Y N 87 DG C6 C N N 88 DG O6 O N N 89 DG N1 N N N 90 DG C2 C N N 91 DG N2 N N N 92 DG N3 N N N 93 DG C4 C Y N 94 DG HOP3 H N N 95 DG HOP2 H N N 96 DG "H5'" H N N 97 DG "H5''" H N N 98 DG "H4'" H N N 99 DG "H3'" H N N 100 DG "HO3'" H N N 101 DG "H2'" H N N 102 DG "H2''" H N N 103 DG "H1'" H N N 104 DG H8 H N N 105 DG H1 H N N 106 DG H21 H N N 107 DG H22 H N N 108 HOH O O N N 109 HOH H1 H N N 110 HOH H2 H N N 111 MG MG MG N N 112 # 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 5CM N1 C2 sing N N 1 5CM N1 C6 sing N N 2 5CM N1 "C1'" sing N N 3 5CM C2 N3 sing N N 4 5CM C2 O2 doub N N 5 5CM N3 C4 doub N N 6 5CM C4 C5 sing N N 7 5CM C4 N4 sing N N 8 5CM C5 C5A sing N N 9 5CM C5 C6 doub N N 10 5CM C5A H5A1 sing N N 11 5CM C5A H5A2 sing N N 12 5CM C5A H5A3 sing N N 13 5CM C6 H6 sing N N 14 5CM N4 HN41 sing N N 15 5CM N4 HN42 sing N N 16 5CM "C1'" "C2'" sing N N 17 5CM "C1'" "O4'" sing N N 18 5CM "C1'" "H1'" sing N N 19 5CM "C2'" "C3'" sing N N 20 5CM "C2'" "H2'" sing N N 21 5CM "C2'" "H2''" sing N N 22 5CM "C3'" "C4'" sing N N 23 5CM "C3'" "O3'" sing N N 24 5CM "C3'" "H3'" sing N N 25 5CM "C4'" "O4'" sing N N 26 5CM "C4'" "C5'" sing N N 27 5CM "C4'" "H4'" sing N N 28 5CM "O3'" "HO3'" sing N N 29 5CM "C5'" "O5'" sing N N 30 5CM "C5'" "H5'" sing N N 31 5CM "C5'" "H5''" sing N N 32 5CM "O5'" P sing N N 33 5CM P OP1 doub N N 34 5CM P OP2 sing N N 35 5CM P OP3 sing N N 36 5CM OP2 HOP2 sing N N 37 5CM OP3 HOP3 sing N 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 HOH O H1 sing N N 113 HOH O H2 sing N N 114 # _ndb_struct_conf_na.entry_id 384D _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 DC 1 1_555 B DG 10 1_555 0.058 -0.047 0.037 -5.391 2.446 -1.571 1 A_DC1:DG20_B A 1 ? B 20 ? 19 1 1 A 5CM 2 1_555 B DG 9 1_555 0.500 -0.014 -0.064 6.252 -13.251 1.298 2 A_5CM2:DG19_B A 2 ? B 19 ? 19 1 1 A DG 3 1_555 B 5CM 8 1_555 -0.381 -0.096 0.086 -1.682 -12.917 0.047 3 A_DG3:5CM18_B A 3 ? B 18 ? 19 1 1 A DC 4 1_555 B DG 7 1_555 0.657 -0.250 0.128 0.007 -10.431 1.367 4 A_DC4:DG17_B A 4 ? B 17 ? 19 1 1 A 5CM 5 1_555 B DG 6 1_555 0.385 -0.217 0.104 -1.436 -16.781 -0.581 5 A_5CM5:DG16_B A 5 ? B 16 ? 19 1 1 A DG 6 1_555 B 5CM 5 1_555 -0.430 -0.026 -0.161 -8.320 -6.700 3.770 6 A_DG6:5CM15_B A 6 ? B 15 ? 19 1 1 A DG 7 1_555 B DC 4 1_555 -0.659 -0.136 0.002 -6.630 -9.343 3.768 7 A_DG7:DC14_B A 7 ? B 14 ? 19 1 1 A 5CM 8 1_555 B DG 3 1_555 0.092 -0.037 0.027 2.661 -11.853 1.425 8 A_5CM8:DG13_B A 8 ? B 13 ? 19 1 1 A DG 9 1_555 B 5CM 2 1_555 -0.397 -0.088 -0.103 1.153 -6.278 2.224 9 A_DG9:5CM12_B A 9 ? B 12 ? 19 1 1 A DG 10 1_555 B DC 1 1_555 -0.205 -0.166 0.055 -1.331 -1.565 -2.747 10 A_DG10:DC11_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 DC 1 1_555 B DG 10 1_555 A 5CM 2 1_555 B DG 9 1_555 -0.416 -1.895 3.072 -0.356 2.775 32.164 -3.859 0.690 2.907 4.996 0.640 32.282 1 AA_DC15CM2:DG19DG20_BB A 1 ? B 20 ? A 2 ? B 19 ? 1 A 5CM 2 1_555 B DG 9 1_555 A DG 3 1_555 B 5CM 8 1_555 0.058 -1.531 3.369 -0.669 8.764 28.805 -4.676 -0.244 2.791 17.120 1.307 30.089 2 AA_5CM2DG3:5CM18DG19_BB A 2 ? B 19 ? A 3 ? B 18 ? 1 A DG 3 1_555 B 5CM 8 1_555 A DC 4 1_555 B DG 7 1_555 0.585 -1.559 3.361 0.992 5.082 34.924 -3.322 -0.818 3.126 8.410 -1.642 35.294 3 AA_DG3DC4:DG175CM18_BB A 3 ? B 18 ? A 4 ? B 17 ? 1 A DC 4 1_555 B DG 7 1_555 A 5CM 5 1_555 B DG 6 1_555 -1.217 -1.790 3.381 -0.142 6.689 30.782 -4.521 2.216 2.942 12.417 0.263 31.484 4 AA_DC45CM5:DG16DG17_BB A 4 ? B 17 ? A 5 ? B 16 ? 1 A 5CM 5 1_555 B DG 6 1_555 A DG 6 1_555 B 5CM 5 1_555 1.542 -1.856 3.342 4.043 9.788 24.759 -6.389 -2.324 2.644 21.608 -8.926 26.896 5 AA_5CM5DG6:5CM15DG16_BB A 5 ? B 16 ? A 6 ? B 15 ? 1 A DG 6 1_555 B 5CM 5 1_555 A DG 7 1_555 B DC 4 1_555 0.204 -1.837 3.443 0.555 0.487 29.622 -3.700 -0.276 3.416 0.952 -1.085 29.631 6 AA_DG6DG7:DC145CM15_BB A 6 ? B 15 ? A 7 ? B 14 ? 1 A DG 7 1_555 B DC 4 1_555 A 5CM 8 1_555 B DG 3 1_555 -1.004 -1.348 3.147 -1.958 2.510 36.197 -2.496 1.348 3.098 4.031 3.144 36.332 7 AA_DG75CM8:DG13DC14_BB A 7 ? B 14 ? A 8 ? B 13 ? 1 A 5CM 8 1_555 B DG 3 1_555 A DG 9 1_555 B 5CM 2 1_555 1.251 -2.086 3.236 0.614 11.067 21.838 -7.835 -2.791 1.993 27.081 -1.502 24.459 8 AA_5CM8DG9:5CM12DG13_BB A 8 ? B 13 ? A 9 ? B 12 ? 1 A DG 9 1_555 B 5CM 2 1_555 A DG 10 1_555 B DC 1 1_555 0.612 -2.546 3.371 0.250 0.288 27.092 -5.510 -1.241 3.350 0.615 -0.534 27.095 9 AA_DG9DG10:DC115CM12_BB A 9 ? B 12 ? A 10 ? B 11 ? # _pdbx_initial_refinement_model.accession_code 1VJ4 _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 'P61 OCTAMER' # _atom_sites.entry_id 384D _atom_sites.fract_transf_matrix[1][1] 0.018215 _atom_sites.fract_transf_matrix[1][2] 0.010516 _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] 0.021033 _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] 0.021930 _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 MG N O P # loop_