data_3VXV # _entry.id 3VXV # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.281 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 3VXV NDB NA2048 RCSB RCSB095636 WWPDB D_1000095636 # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 3VXX . unspecified PDB 3VYB . unspecified PDB 3VYQ . unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3VXV _pdbx_database_status.recvd_initial_deposition_date 2012-09-21 _pdbx_database_status.deposit_site PDBJ _pdbx_database_status.process_site PDBJ _pdbx_database_status.methods_development_category ? _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.pdb_format_compatible Y # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Otani, J.' 1 'Arita, K.' 2 'Kato, T.' 3 'Kinoshita, M.' 4 'Ariyoshi, M.' 5 'Shirakawa, M.' 6 # _citation.id primary _citation.title 'Structural basis of the versatile DNA recognition ability of the methyl-CpG binding domain of methyl-CpG binding domain protein 4' _citation.journal_abbrev J.Biol.Chem. _citation.journal_volume 288 _citation.page_first 6351 _citation.page_last 6362 _citation.year 2013 _citation.journal_id_ASTM JBCHA3 _citation.country US _citation.journal_id_ISSN 0021-9258 _citation.journal_id_CSD 0071 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 23316048 _citation.pdbx_database_id_DOI 10.1074/jbc.M112.431098 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Otani, J.' 1 primary 'Arita, K.' 2 primary 'Kato, T.' 3 primary 'Kinoshita, M.' 4 primary 'Kimura, H.' 5 primary 'Suetake, I.' 6 primary 'Tajima, S.' 7 primary 'Ariyoshi, M.' 8 primary 'Shirakawa, M.' 9 # _cell.entry_id 3VXV _cell.length_a 89.074 _cell.length_b 94.989 _cell.length_c 54.738 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.entry_id 3VXV _symmetry.space_group_name_H-M 'C 2 2 21' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer man 'Methyl-CpG-binding domain protein 4' 7829.089 1 3.2.2.- ? 'methyl CpG binding domain, UNP residues 69-136' ? 2 polymer syn ;DNA (5'-D(*GP*TP*CP*AP*CP*TP*AP*CP*(5CM)P*GP*GP*AP*CP*A)-3') ; 4263.809 1 ? ? ? ? 3 polymer syn ;DNA (5'-D(*GP*TP*CP*TP*GP*GP*TP*AP*GP*TP*GP*AP*CP*T)-3') ; 4326.812 1 ? ? ? ? 4 non-polymer syn 'ACETATE ION' 59.044 3 ? ? ? ? 5 non-polymer syn 1,2-ETHANEDIOL 62.068 6 ? ? ? ? 6 water nat water 18.015 154 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name 'Methyl-CpG-binding protein MBD4, Mismatch-specific DNA N-glycosylase' # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 'polypeptide(L)' no no SGHKPVPCGWERVVKQRLSGKTAGKFDVYFISPQGLKFRSKRSLANYLLKNGETFLKPEDFNFTVLPKG SGHKPVPCGWERVVKQRLSGKTAGKFDVYFISPQGLKFRSKRSLANYLLKNGETFLKPEDFNFTVLPKG A ? 2 polydeoxyribonucleotide no yes '(DG)(DT)(DC)(DA)(DC)(DT)(DA)(DC)(5CM)(DG)(DG)(DA)(DC)(DA)' GTCACTACCGGACA B ? 3 polydeoxyribonucleotide no no '(DG)(DT)(DC)(DT)(DG)(DG)(DT)(DA)(DG)(DT)(DG)(DA)(DC)(DT)' GTCTGGTAGTGACT C ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 SER n 1 2 GLY n 1 3 HIS n 1 4 LYS n 1 5 PRO n 1 6 VAL n 1 7 PRO n 1 8 CYS n 1 9 GLY n 1 10 TRP n 1 11 GLU n 1 12 ARG n 1 13 VAL n 1 14 VAL n 1 15 LYS n 1 16 GLN n 1 17 ARG n 1 18 LEU n 1 19 SER n 1 20 GLY n 1 21 LYS n 1 22 THR n 1 23 ALA n 1 24 GLY n 1 25 LYS n 1 26 PHE n 1 27 ASP n 1 28 VAL n 1 29 TYR n 1 30 PHE n 1 31 ILE n 1 32 SER n 1 33 PRO n 1 34 GLN n 1 35 GLY n 1 36 LEU n 1 37 LYS n 1 38 PHE n 1 39 ARG n 1 40 SER n 1 41 LYS n 1 42 ARG n 1 43 SER n 1 44 LEU n 1 45 ALA n 1 46 ASN n 1 47 TYR n 1 48 LEU n 1 49 LEU n 1 50 LYS n 1 51 ASN n 1 52 GLY n 1 53 GLU n 1 54 THR n 1 55 PHE n 1 56 LEU n 1 57 LYS n 1 58 PRO n 1 59 GLU n 1 60 ASP n 1 61 PHE n 1 62 ASN n 1 63 PHE n 1 64 THR n 1 65 VAL n 1 66 LEU n 1 67 PRO n 1 68 LYS n 1 69 GLY n 2 1 DG n 2 2 DT n 2 3 DC n 2 4 DA n 2 5 DC n 2 6 DT n 2 7 DA n 2 8 DC n 2 9 5CM n 2 10 DG n 2 11 DG n 2 12 DA n 2 13 DC n 2 14 DA n 3 1 DG n 3 2 DT n 3 3 DC n 3 4 DT n 3 5 DG n 3 6 DG n 3 7 DT n 3 8 DA n 3 9 DG n 3 10 DT n 3 11 DG n 3 12 DA n 3 13 DC n 3 14 DT n # _entity_src_gen.entity_id 1 _entity_src_gen.pdbx_src_id 1 _entity_src_gen.pdbx_alt_source_flag sample _entity_src_gen.pdbx_seq_type ? _entity_src_gen.pdbx_beg_seq_num ? _entity_src_gen.pdbx_end_seq_num ? _entity_src_gen.gene_src_common_name mouse _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene Mbd4 _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain ? _entity_src_gen.gene_src_tissue ? _entity_src_gen.gene_src_tissue_fraction ? _entity_src_gen.gene_src_details ? _entity_src_gen.pdbx_gene_src_fragment ? _entity_src_gen.pdbx_gene_src_scientific_name 'Mus musculus' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 10090 _entity_src_gen.pdbx_gene_src_variant ? _entity_src_gen.pdbx_gene_src_cell_line ? _entity_src_gen.pdbx_gene_src_atcc ? _entity_src_gen.pdbx_gene_src_organ ? _entity_src_gen.pdbx_gene_src_organelle ? _entity_src_gen.pdbx_gene_src_cell ? _entity_src_gen.pdbx_gene_src_cellular_location ? _entity_src_gen.host_org_common_name ? _entity_src_gen.pdbx_host_org_scientific_name 'Escherichia coli' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 562 _entity_src_gen.host_org_genus ? _entity_src_gen.pdbx_host_org_gene ? _entity_src_gen.pdbx_host_org_organ ? _entity_src_gen.host_org_species ? _entity_src_gen.pdbx_host_org_tissue ? _entity_src_gen.pdbx_host_org_tissue_fraction ? _entity_src_gen.pdbx_host_org_strain 'BL21(DE3)' _entity_src_gen.pdbx_host_org_variant ? _entity_src_gen.pdbx_host_org_cell_line ? _entity_src_gen.pdbx_host_org_atcc ? _entity_src_gen.pdbx_host_org_culture_collection ? _entity_src_gen.pdbx_host_org_cell ? _entity_src_gen.pdbx_host_org_organelle ? _entity_src_gen.pdbx_host_org_cellular_location ? _entity_src_gen.pdbx_host_org_vector_type plasmid _entity_src_gen.pdbx_host_org_vector ? _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name ? _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.entity_id _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin _struct_ref.pdbx_db_isoform 1 UNP MBD4_MOUSE Q9Z2D7 1 GHKPVPCGWERVVKQRLSGKTAGKFDVYFISPQGLKFRSKRSLANYLLKNGETFLKPEDFNFTVLPKG 69 ? 2 PDB 3VXV 3VXV 2 ? ? ? 3 PDB 3VXV 3VXV 3 ? ? ? # 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 3VXV A 2 ? 69 ? Q9Z2D7 69 ? 136 ? 69 136 2 2 3VXV B 1 ? 14 ? 3VXV 1 ? 14 ? 1 14 3 3 3VXV C 1 ? 14 ? 3VXV 1 ? 14 ? 1 14 # _struct_ref_seq_dif.align_id 1 _struct_ref_seq_dif.pdbx_pdb_id_code 3VXV _struct_ref_seq_dif.mon_id SER _struct_ref_seq_dif.pdbx_pdb_strand_id A _struct_ref_seq_dif.seq_num 1 _struct_ref_seq_dif.pdbx_pdb_ins_code ? _struct_ref_seq_dif.pdbx_seq_db_name UNP _struct_ref_seq_dif.pdbx_seq_db_accession_code Q9Z2D7 _struct_ref_seq_dif.db_mon_id ? _struct_ref_seq_dif.pdbx_seq_db_seq_num ? _struct_ref_seq_dif.details 'EXPRESSION TAG' _struct_ref_seq_dif.pdbx_auth_seq_num 68 _struct_ref_seq_dif.pdbx_ordinal 1 # 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 ACT non-polymer . 'ACETATE ION' ? 'C2 H3 O2 -1' 59.044 ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 CYS 'L-peptide linking' y CYSTEINE ? 'C3 H7 N O2 S' 121.158 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 EDO non-polymer . 1,2-ETHANEDIOL 'ETHYLENE GLYCOL' 'C2 H6 O2' 62.068 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 HOH non-polymer . WATER ? 'H2 O' 18.015 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _exptl.entry_id 3VXV _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 2 # loop_ _exptl_crystal.id _exptl_crystal.density_meas _exptl_crystal.density_Matthews _exptl_crystal.density_percent_sol _exptl_crystal.description _exptl_crystal.F_000 _exptl_crystal.preparation 1 ? 3.53 65.11 ? ? ? 2 ? ? ? ? ? ? # loop_ _exptl_crystal_grow.crystal_id _exptl_crystal_grow.method _exptl_crystal_grow.temp _exptl_crystal_grow.temp_details _exptl_crystal_grow.pH _exptl_crystal_grow.pdbx_pH_range _exptl_crystal_grow.pdbx_details 1 'VAPOR DIFFUSION, HANGING DROP' 293 ? 4.4 ? 'pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K' 2 'VAPOR DIFFUSION, HANGING DROP' 293 ? 4.4 ? 'pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K' # loop_ _diffrn.id _diffrn.ambient_temp _diffrn.ambient_temp_details _diffrn.crystal_id 1 95 ? 1 2 95 ? 2 # loop_ _diffrn_detector.diffrn_id _diffrn_detector.detector _diffrn_detector.type _diffrn_detector.pdbx_collection_date _diffrn_detector.details 1 CCD 'ADSC QUANTUM 210r' 2010-01-27 ? 2 CCD 'ADSC QUANTUM 270' 2009-10-14 ? # loop_ _diffrn_radiation.diffrn_id _diffrn_radiation.wavelength_id _diffrn_radiation.pdbx_monochromatic_or_laue_m_l _diffrn_radiation.monochromator _diffrn_radiation.pdbx_diffrn_protocol _diffrn_radiation.pdbx_scattering_type 1 1 M ? 'SINGLE WAVELENGTH' x-ray 2 2 M ? 'SINGLE WAVELENGTH' x-ray # loop_ _diffrn_radiation_wavelength.id _diffrn_radiation_wavelength.wavelength _diffrn_radiation_wavelength.wt 1 1.000 1.0 2 . 1.0 # loop_ _diffrn_source.diffrn_id _diffrn_source.source _diffrn_source.type _diffrn_source.pdbx_synchrotron_site _diffrn_source.pdbx_synchrotron_beamline _diffrn_source.pdbx_wavelength _diffrn_source.pdbx_wavelength_list 1 SYNCHROTRON 'PHOTON FACTORY BEAMLINE BL-5A' 'Photon Factory' BL-5A ? 1.000 2 SYNCHROTRON 'PHOTON FACTORY BEAMLINE AR-NE3A' 'Photon Factory' AR-NE3A ? ? # _reflns.pdbx_diffrn_id 1,2 _reflns.pdbx_ordinal 1 _reflns.entry_id 3VXV _reflns.observed_criterion_sigma_I 1 _reflns.observed_criterion_sigma_F 1 _reflns.d_resolution_low 50 _reflns.d_resolution_high 2.0 _reflns.number_obs 16062 _reflns.number_all 16110 _reflns.percent_possible_obs 99.7 _reflns.pdbx_Rmerge_I_obs 0.031 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 18.2 _reflns.B_iso_Wilson_estimate 36.360 _reflns.pdbx_redundancy 7.2 _reflns.R_free_details ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? # _reflns_shell.pdbx_diffrn_id 1,2 _reflns_shell.pdbx_ordinal 1 _reflns_shell.d_res_high 2.00 _reflns_shell.d_res_low 2.07 _reflns_shell.percent_possible_all 100 _reflns_shell.Rmerge_I_obs 0.365 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 4.3 _reflns_shell.pdbx_redundancy 7.3 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all ? _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 3VXV _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.ls_number_reflns_obs 16002 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 1.34 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 23.747 _refine.ls_d_res_high 2.00 _refine.ls_percent_reflns_obs 99.44 _refine.ls_R_factor_obs 0.1892 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.1875 _refine.ls_R_factor_R_free 0.2235 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 5.01 _refine.ls_number_reflns_R_free 801 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean 40.4743 _refine.aniso_B[1][1] -12.9528 _refine.aniso_B[2][2] 10.7675 _refine.aniso_B[3][3] 2.1853 _refine.aniso_B[1][2] 0.0000 _refine.aniso_B[1][3] 0.0000 _refine.aniso_B[2][3] -0.0000 _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.solvent_model_param_ksol 0.342 _refine.solvent_model_param_bsol 54.253 _refine.pdbx_solvent_vdw_probe_radii 1.10 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.86 _refine.pdbx_ls_cross_valid_method ? _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct SAD _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values ML _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 0.30 _refine.B_iso_max 84.750 _refine.B_iso_min 22.070 _refine.pdbx_overall_phase_error 24.6200 _refine.occupancy_max 1.000 _refine.occupancy_min 0.500 _refine.ls_redundancy_reflns_obs ? _refine.overall_SU_B ? _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_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 525 _refine_hist.pdbx_number_atoms_nucleic_acid 570 _refine_hist.pdbx_number_atoms_ligand 36 _refine_hist.number_atoms_solvent 154 _refine_hist.number_atoms_total 1285 _refine_hist.d_res_high 2.00 _refine_hist.d_res_low 23.747 # 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 f_bond_d 0.018 ? ? 1205 'X-RAY DIFFRACTION' ? f_angle_d 2.071 ? ? 1728 'X-RAY DIFFRACTION' ? f_dihedral_angle_d 23.326 ? ? 479 'X-RAY DIFFRACTION' ? f_chiral_restr 0.119 ? ? 185 'X-RAY DIFFRACTION' ? f_plane_restr 0.010 ? ? 123 'X-RAY DIFFRACTION' ? # loop_ _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.percent_reflns_obs _refine_ls_shell.number_reflns_R_work _refine_ls_shell.R_factor_all _refine_ls_shell.R_factor_R_work _refine_ls_shell.R_factor_R_free _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.number_reflns_R_free _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.number_reflns_all _refine_ls_shell.number_reflns_obs _refine_ls_shell.pdbx_refine_id _refine_ls_shell.redundancy_reflns_obs 1.9989 2.1240 6 100.0000 2475 . 0.2332 0.2707 . 150 . 2625 . 'X-RAY DIFFRACTION' . 2.1240 2.2879 6 99.0000 2493 . 0.2553 0.3677 . 139 . 2632 . 'X-RAY DIFFRACTION' . 2.2879 2.5179 6 100.0000 2500 . 0.2338 0.2924 . 148 . 2648 . 'X-RAY DIFFRACTION' . 2.5179 2.8817 6 100.0000 2545 . 0.2178 0.2713 . 125 . 2670 . 'X-RAY DIFFRACTION' . 2.8817 3.6286 6 100.0000 2566 . 0.1711 0.2235 . 117 . 2683 . 'X-RAY DIFFRACTION' . 3.6286 23.7489 6 98.0000 2622 . 0.1626 0.1633 . 122 . 2744 . 'X-RAY DIFFRACTION' . # _struct.entry_id 3VXV _struct.title 'Crystal structure of methyl CpG Binding Domain of MBD4 in complex with the 5mCG/TG sequence' _struct.pdbx_descriptor 'Methyl-CpG-binding domain protein 4 (E.C.3.2.2.-)/DNA' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3VXV _struct_keywords.pdbx_keywords HYDROLASE/DNA _struct_keywords.text 'methyl CpG binding domain, protein-DNA complex, versatile base recognition, HYDROLASE-DNA complex' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? D N N 4 ? E N N 4 ? F N N 5 ? G N N 5 ? H N N 5 ? I N N 5 ? J N N 5 ? K N N 4 ? L N N 5 ? M N N 6 ? N N N 6 ? O N N 6 ? # _struct_biol.id 1 _struct_biol.details ? # loop_ _struct_conf.conf_type_id _struct_conf.id _struct_conf.pdbx_PDB_helix_id _struct_conf.beg_label_comp_id _struct_conf.beg_label_asym_id _struct_conf.beg_label_seq_id _struct_conf.pdbx_beg_PDB_ins_code _struct_conf.end_label_comp_id _struct_conf.end_label_asym_id _struct_conf.end_label_seq_id _struct_conf.pdbx_end_PDB_ins_code _struct_conf.beg_auth_comp_id _struct_conf.beg_auth_asym_id _struct_conf.beg_auth_seq_id _struct_conf.end_auth_comp_id _struct_conf.end_auth_asym_id _struct_conf.end_auth_seq_id _struct_conf.pdbx_PDB_helix_class _struct_conf.details _struct_conf.pdbx_PDB_helix_length HELX_P HELX_P1 1 SER A 40 ? GLY A 52 ? SER A 107 GLY A 119 1 ? 13 HELX_P HELX_P2 2 LYS A 57 ? PHE A 61 ? LYS A 124 PHE A 128 5 ? 5 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # 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 disulf1 disulf ? ? A CYS 8 SG ? ? ? 1_555 A CYS 8 SG ? ? A CYS 75 A CYS 75 3_555 ? ? ? ? ? ? ? 2.043 ? covale1 covale ? ? B DC 8 "O3'" ? ? ? 1_555 B 5CM 9 P ? ? B DC 8 B 5CM 9 1_555 ? ? ? ? ? ? ? 1.603 ? covale2 covale ? ? B 5CM 9 "O3'" ? ? ? 1_555 B DG 10 P ? ? B 5CM 9 B DG 10 1_555 ? ? ? ? ? ? ? 1.608 ? hydrog1 hydrog ? ? B DG 1 N1 ? ? ? 1_555 C DC 13 N3 ? ? B DG 1 C DC 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog2 hydrog ? ? B DG 1 N2 ? ? ? 1_555 C DC 13 O2 ? ? B DG 1 C DC 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog3 hydrog ? ? B DG 1 O6 ? ? ? 1_555 C DC 13 N4 ? ? B DG 1 C DC 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog4 hydrog ? ? B DT 2 N3 ? ? ? 1_555 C DA 12 N1 ? ? B DT 2 C DA 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog5 hydrog ? ? B DT 2 O4 ? ? ? 1_555 C DA 12 N6 ? ? B DT 2 C DA 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog6 hydrog ? ? B DC 3 N3 ? ? ? 1_555 C DG 11 N1 ? ? B DC 3 C DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog7 hydrog ? ? B DC 3 N4 ? ? ? 1_555 C DG 11 O6 ? ? B DC 3 C DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog8 hydrog ? ? B DC 3 O2 ? ? ? 1_555 C DG 11 N2 ? ? B DC 3 C DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog9 hydrog ? ? B DA 4 N1 ? ? ? 1_555 C DT 10 N3 ? ? B DA 4 C DT 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog10 hydrog ? ? B DA 4 N6 ? ? ? 1_555 C DT 10 O4 ? ? B DA 4 C DT 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog11 hydrog ? ? B DC 5 N3 ? ? ? 1_555 C DG 9 N1 ? ? B DC 5 C DG 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog12 hydrog ? ? B DC 5 N4 ? ? ? 1_555 C DG 9 O6 ? ? B DC 5 C DG 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog13 hydrog ? ? B DC 5 O2 ? ? ? 1_555 C DG 9 N2 ? ? B DC 5 C DG 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog14 hydrog ? ? B DT 6 N3 ? ? ? 1_555 C DA 8 N1 ? ? B DT 6 C DA 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog15 hydrog ? ? B DT 6 O4 ? ? ? 1_555 C DA 8 N6 ? ? B DT 6 C DA 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog16 hydrog ? ? B DA 7 N1 ? ? ? 1_555 C DT 7 N3 ? ? B DA 7 C DT 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog17 hydrog ? ? B DA 7 N6 ? ? ? 1_555 C DT 7 O4 ? ? B DA 7 C DT 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog18 hydrog ? ? B DC 8 N3 ? ? ? 1_555 C DG 6 N1 ? ? B DC 8 C DG 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog19 hydrog ? ? B DC 8 N4 ? ? ? 1_555 C DG 6 O6 ? ? B DC 8 C DG 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog20 hydrog ? ? B DC 8 O2 ? ? ? 1_555 C DG 6 N2 ? ? B DC 8 C DG 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog21 hydrog ? ? B 5CM 9 N3 ? ? ? 1_555 C DG 5 N1 ? ? B 5CM 9 C DG 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog22 hydrog ? ? B 5CM 9 N4 ? ? ? 1_555 C DG 5 O6 ? ? B 5CM 9 C DG 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog23 hydrog ? ? B 5CM 9 O2 ? ? ? 1_555 C DG 5 N2 ? ? B 5CM 9 C DG 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog24 hydrog ? ? B DG 10 N1 ? ? ? 1_555 C DT 4 O2 ? ? B DG 10 C DT 4 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? hydrog25 hydrog ? ? B DG 10 O6 ? ? ? 1_555 C DT 4 N3 ? ? B DG 10 C DT 4 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? hydrog26 hydrog ? ? B DG 11 N1 ? ? ? 1_555 C DC 3 N3 ? ? B DG 11 C DC 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog27 hydrog ? ? B DG 11 N2 ? ? ? 1_555 C DC 3 O2 ? ? B DG 11 C DC 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog28 hydrog ? ? B DG 11 O6 ? ? ? 1_555 C DC 3 N4 ? ? B DG 11 C DC 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog29 hydrog ? ? B DA 12 N1 ? ? ? 1_555 C DT 2 N3 ? ? B DA 12 C DT 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog30 hydrog ? ? B DA 12 N6 ? ? ? 1_555 C DT 2 O4 ? ? B DA 12 C DT 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog31 hydrog ? ? B DC 13 N3 ? ? ? 1_555 C DG 1 N1 ? ? B DC 13 C DG 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog32 hydrog ? ? B DC 13 N4 ? ? ? 1_555 C DG 1 O6 ? ? B DC 13 C DG 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog33 hydrog ? ? B DC 13 O2 ? ? ? 1_555 C DG 1 N2 ? ? B DC 13 C DG 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference disulf ? ? covale ? ? hydrog ? ? # _struct_sheet.id A _struct_sheet.type ? _struct_sheet.number_strands 3 _struct_sheet.details ? # loop_ _struct_sheet_order.sheet_id _struct_sheet_order.range_id_1 _struct_sheet_order.range_id_2 _struct_sheet_order.offset _struct_sheet_order.sense A 1 2 ? anti-parallel A 2 3 ? anti-parallel # loop_ _struct_sheet_range.sheet_id _struct_sheet_range.id _struct_sheet_range.beg_label_comp_id _struct_sheet_range.beg_label_asym_id _struct_sheet_range.beg_label_seq_id _struct_sheet_range.pdbx_beg_PDB_ins_code _struct_sheet_range.end_label_comp_id _struct_sheet_range.end_label_asym_id _struct_sheet_range.end_label_seq_id _struct_sheet_range.pdbx_end_PDB_ins_code _struct_sheet_range.beg_auth_comp_id _struct_sheet_range.beg_auth_asym_id _struct_sheet_range.beg_auth_seq_id _struct_sheet_range.end_auth_comp_id _struct_sheet_range.end_auth_asym_id _struct_sheet_range.end_auth_seq_id A 1 GLU A 11 ? GLN A 16 ? GLU A 78 GLN A 83 A 2 PHE A 26 ? ILE A 31 ? PHE A 93 ILE A 98 A 3 LYS A 37 ? PHE A 38 ? LYS A 104 PHE A 105 # loop_ _pdbx_struct_sheet_hbond.sheet_id _pdbx_struct_sheet_hbond.range_id_1 _pdbx_struct_sheet_hbond.range_id_2 _pdbx_struct_sheet_hbond.range_1_label_atom_id _pdbx_struct_sheet_hbond.range_1_label_comp_id _pdbx_struct_sheet_hbond.range_1_label_asym_id _pdbx_struct_sheet_hbond.range_1_label_seq_id _pdbx_struct_sheet_hbond.range_1_PDB_ins_code _pdbx_struct_sheet_hbond.range_1_auth_atom_id _pdbx_struct_sheet_hbond.range_1_auth_comp_id _pdbx_struct_sheet_hbond.range_1_auth_asym_id _pdbx_struct_sheet_hbond.range_1_auth_seq_id _pdbx_struct_sheet_hbond.range_2_label_atom_id _pdbx_struct_sheet_hbond.range_2_label_comp_id _pdbx_struct_sheet_hbond.range_2_label_asym_id _pdbx_struct_sheet_hbond.range_2_label_seq_id _pdbx_struct_sheet_hbond.range_2_PDB_ins_code _pdbx_struct_sheet_hbond.range_2_auth_atom_id _pdbx_struct_sheet_hbond.range_2_auth_comp_id _pdbx_struct_sheet_hbond.range_2_auth_asym_id _pdbx_struct_sheet_hbond.range_2_auth_seq_id A 1 2 N VAL A 13 ? N VAL A 80 O TYR A 29 ? O TYR A 96 A 2 3 N PHE A 30 ? N PHE A 97 O PHE A 38 ? O PHE A 105 # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software ? ? ? ? 4 'BINDING SITE FOR RESIDUE ACT A 201' AC2 Software ? ? ? ? 3 'BINDING SITE FOR RESIDUE ACT A 202' AC3 Software ? ? ? ? 5 'BINDING SITE FOR RESIDUE EDO A 203' AC4 Software ? ? ? ? 5 'BINDING SITE FOR RESIDUE EDO A 204' AC5 Software ? ? ? ? 4 'BINDING SITE FOR RESIDUE EDO A 205' AC6 Software ? ? ? ? 3 'BINDING SITE FOR RESIDUE EDO A 206' AC7 Software ? ? ? ? 3 'BINDING SITE FOR RESIDUE EDO A 207' AC8 Software ? ? ? ? 4 'BINDING SITE FOR RESIDUE ACT B 101' AC9 Software ? ? ? ? 3 'BINDING SITE FOR RESIDUE EDO C 101' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 4 GLU A 53 ? GLU A 120 . ? 1_555 ? 2 AC1 4 DC C 13 ? DC C 13 . ? 8_545 ? 3 AC1 4 DT C 14 ? DT C 14 . ? 6_445 ? 4 AC1 4 DT C 14 ? DT C 14 . ? 8_545 ? 5 AC2 3 GLN A 34 ? GLN A 101 . ? 1_555 ? 6 AC2 3 ASN A 51 ? ASN A 118 . ? 1_555 ? 7 AC2 3 GLU A 53 ? GLU A 120 . ? 1_555 ? 8 AC3 5 GLN A 16 ? GLN A 83 . ? 1_555 ? 9 AC3 5 ARG A 17 ? ARG A 84 . ? 1_555 ? 10 AC3 5 HOH M . ? HOH A 318 . ? 1_555 ? 11 AC3 5 DC C 3 ? DC C 3 . ? 1_555 ? 12 AC3 5 DT C 4 ? DT C 4 . ? 1_555 ? 13 AC4 5 GLY A 9 ? GLY A 76 . ? 1_555 ? 14 AC4 5 GLU A 11 ? GLU A 78 . ? 1_555 ? 15 AC4 5 ILE A 31 ? ILE A 98 . ? 1_555 ? 16 AC4 5 SER A 32 ? SER A 99 . ? 1_555 ? 17 AC4 5 DA B 14 ? DA B 14 . ? 2_555 ? 18 AC5 4 CYS A 8 ? CYS A 75 . ? 1_555 ? 19 AC5 4 CYS A 8 ? CYS A 75 . ? 3_555 ? 20 AC5 4 GLY A 9 ? GLY A 76 . ? 1_555 ? 21 AC5 4 TRP A 10 ? TRP A 77 . ? 1_555 ? 22 AC6 3 LYS A 37 ? LYS A 104 . ? 1_555 ? 23 AC6 3 PHE A 38 ? PHE A 105 . ? 1_555 ? 24 AC6 3 ACT K . ? ACT B 101 . ? 1_555 ? 25 AC7 3 VAL A 65 ? VAL A 132 . ? 1_555 ? 26 AC7 3 LEU A 66 ? LEU A 133 . ? 1_555 ? 27 AC7 3 PRO A 67 ? PRO A 134 . ? 1_555 ? 28 AC8 4 EDO I . ? EDO A 206 . ? 1_555 ? 29 AC8 4 5CM B 9 ? 5CM B 9 . ? 1_555 ? 30 AC8 4 DG B 10 ? DG B 10 . ? 1_555 ? 31 AC8 4 HOH N . ? HOH B 248 . ? 1_555 ? 32 AC9 3 DC B 13 ? DC B 13 . ? 1_555 ? 33 AC9 3 DT C 2 ? DT C 2 . ? 1_555 ? 34 AC9 3 DC C 3 ? DC C 3 . ? 1_555 ? # _database_PDB_matrix.entry_id 3VXV _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 # _atom_sites.entry_id 3VXV _atom_sites.fract_transf_matrix[1][1] 0.011227 _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] 0.010528 _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] 0.018269 _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_ _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 SER 1 68 ? ? ? A . n A 1 2 GLY 2 69 ? ? ? A . n A 1 3 HIS 3 70 ? ? ? A . n A 1 4 LYS 4 71 71 LYS LYS A . n A 1 5 PRO 5 72 72 PRO PRO A . n A 1 6 VAL 6 73 73 VAL VAL A . n A 1 7 PRO 7 74 74 PRO PRO A . n A 1 8 CYS 8 75 75 CYS CYS A . n A 1 9 GLY 9 76 76 GLY GLY A . n A 1 10 TRP 10 77 77 TRP TRP A . n A 1 11 GLU 11 78 78 GLU GLU A . n A 1 12 ARG 12 79 79 ARG ARG A . n A 1 13 VAL 13 80 80 VAL VAL A . n A 1 14 VAL 14 81 81 VAL VAL A . n A 1 15 LYS 15 82 82 LYS LYS A . n A 1 16 GLN 16 83 83 GLN GLN A . n A 1 17 ARG 17 84 84 ARG ARG A . n A 1 18 LEU 18 85 85 LEU LEU A . n A 1 19 SER 19 86 86 SER SER A . n A 1 20 GLY 20 87 87 GLY GLY A . n A 1 21 LYS 21 88 88 LYS LYS A . n A 1 22 THR 22 89 89 THR THR A . n A 1 23 ALA 23 90 90 ALA ALA A . n A 1 24 GLY 24 91 91 GLY GLY A . n A 1 25 LYS 25 92 92 LYS LYS A . n A 1 26 PHE 26 93 93 PHE PHE A . n A 1 27 ASP 27 94 94 ASP ASP A . n A 1 28 VAL 28 95 95 VAL VAL A . n A 1 29 TYR 29 96 96 TYR TYR A . n A 1 30 PHE 30 97 97 PHE PHE A . n A 1 31 ILE 31 98 98 ILE ILE A . n A 1 32 SER 32 99 99 SER SER A . n A 1 33 PRO 33 100 100 PRO PRO A . n A 1 34 GLN 34 101 101 GLN GLN A . n A 1 35 GLY 35 102 102 GLY GLY A . n A 1 36 LEU 36 103 103 LEU LEU A . n A 1 37 LYS 37 104 104 LYS LYS A . n A 1 38 PHE 38 105 105 PHE PHE A . n A 1 39 ARG 39 106 106 ARG ARG A . n A 1 40 SER 40 107 107 SER SER A . n A 1 41 LYS 41 108 108 LYS LYS A . n A 1 42 ARG 42 109 109 ARG ARG A . n A 1 43 SER 43 110 110 SER SER A . n A 1 44 LEU 44 111 111 LEU LEU A . n A 1 45 ALA 45 112 112 ALA ALA A . n A 1 46 ASN 46 113 113 ASN ASN A . n A 1 47 TYR 47 114 114 TYR TYR A . n A 1 48 LEU 48 115 115 LEU LEU A . n A 1 49 LEU 49 116 116 LEU LEU A . n A 1 50 LYS 50 117 117 LYS LYS A . n A 1 51 ASN 51 118 118 ASN ASN A . n A 1 52 GLY 52 119 119 GLY GLY A . n A 1 53 GLU 53 120 120 GLU GLU A . n A 1 54 THR 54 121 121 THR THR A . n A 1 55 PHE 55 122 122 PHE PHE A . n A 1 56 LEU 56 123 123 LEU LEU A . n A 1 57 LYS 57 124 124 LYS LYS A . n A 1 58 PRO 58 125 125 PRO PRO A . n A 1 59 GLU 59 126 126 GLU GLU A . n A 1 60 ASP 60 127 127 ASP ASP A . n A 1 61 PHE 61 128 128 PHE PHE A . n A 1 62 ASN 62 129 129 ASN ASN A . n A 1 63 PHE 63 130 130 PHE PHE A . n A 1 64 THR 64 131 131 THR THR A . n A 1 65 VAL 65 132 132 VAL VAL A . n A 1 66 LEU 66 133 133 LEU LEU A . n A 1 67 PRO 67 134 134 PRO PRO A . n A 1 68 LYS 68 135 135 LYS LYS A . n A 1 69 GLY 69 136 ? ? ? A . n B 2 1 DG 1 1 1 DG DG B . n B 2 2 DT 2 2 2 DT DT B . n B 2 3 DC 3 3 3 DC DC B . n B 2 4 DA 4 4 4 DA DA B . n B 2 5 DC 5 5 5 DC DC B . n B 2 6 DT 6 6 6 DT DT B . n B 2 7 DA 7 7 7 DA DA B . n B 2 8 DC 8 8 8 DC DC B . n B 2 9 5CM 9 9 9 5CM 5CM B . n B 2 10 DG 10 10 10 DG DG B . n B 2 11 DG 11 11 11 DG DG B . n B 2 12 DA 12 12 12 DA DA B . n B 2 13 DC 13 13 13 DC DC B . n B 2 14 DA 14 14 14 DA DA B . n C 3 1 DG 1 1 1 DG DG C . n C 3 2 DT 2 2 2 DT DT C . n C 3 3 DC 3 3 3 DC DC C . n C 3 4 DT 4 4 4 DT DT C . n C 3 5 DG 5 5 5 DG DG C . n C 3 6 DG 6 6 6 DG DG C . n C 3 7 DT 7 7 7 DT DT C . n C 3 8 DA 8 8 8 DA DA C . n C 3 9 DG 9 9 9 DG DG C . n C 3 10 DT 10 10 10 DT DT C . n C 3 11 DG 11 11 11 DG DG C . n C 3 12 DA 12 12 12 DA DA C . n C 3 13 DC 13 13 13 DC DC C . n C 3 14 DT 14 14 14 DT DT C . n # _pdbx_struct_mod_residue.id 1 _pdbx_struct_mod_residue.label_asym_id B _pdbx_struct_mod_residue.label_comp_id 5CM _pdbx_struct_mod_residue.label_seq_id 9 _pdbx_struct_mod_residue.auth_asym_id B _pdbx_struct_mod_residue.auth_comp_id 5CM _pdbx_struct_mod_residue.auth_seq_id 9 _pdbx_struct_mod_residue.PDB_ins_code ? _pdbx_struct_mod_residue.parent_comp_id DC _pdbx_struct_mod_residue.details ? # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N,O # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 4670 ? 1 MORE -8 ? 1 'SSA (A^2)' 10660 ? # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _pdbx_struct_special_symmetry.id _pdbx_struct_special_symmetry.PDB_model_num _pdbx_struct_special_symmetry.auth_asym_id _pdbx_struct_special_symmetry.auth_comp_id _pdbx_struct_special_symmetry.auth_seq_id _pdbx_struct_special_symmetry.PDB_ins_code _pdbx_struct_special_symmetry.label_asym_id _pdbx_struct_special_symmetry.label_comp_id _pdbx_struct_special_symmetry.label_seq_id 1 1 A HOH 320 ? M HOH . 2 1 B HOH 201 ? N HOH . # 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 2013-01-16 2 'Structure model' 1 1 2013-08-14 # _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_group.ordinal 1 _pdbx_audit_revision_group.revision_ordinal 2 _pdbx_audit_revision_group.data_content_type 'Structure model' _pdbx_audit_revision_group.group 'Database references' # loop_ _pdbx_refine_tls.pdbx_refine_id _pdbx_refine_tls.id _pdbx_refine_tls.details _pdbx_refine_tls.method _pdbx_refine_tls.origin_x _pdbx_refine_tls.origin_y _pdbx_refine_tls.origin_z _pdbx_refine_tls.T[1][1] _pdbx_refine_tls.T[2][2] _pdbx_refine_tls.T[3][3] _pdbx_refine_tls.T[1][2] _pdbx_refine_tls.T[1][3] _pdbx_refine_tls.T[2][3] _pdbx_refine_tls.L[1][1] _pdbx_refine_tls.L[2][2] _pdbx_refine_tls.L[3][3] _pdbx_refine_tls.L[1][2] _pdbx_refine_tls.L[1][3] _pdbx_refine_tls.L[2][3] _pdbx_refine_tls.S[1][1] _pdbx_refine_tls.S[1][2] _pdbx_refine_tls.S[1][3] _pdbx_refine_tls.S[2][1] _pdbx_refine_tls.S[2][2] _pdbx_refine_tls.S[2][3] _pdbx_refine_tls.S[3][1] _pdbx_refine_tls.S[3][2] _pdbx_refine_tls.S[3][3] 'X-RAY DIFFRACTION' 1 ? refined -3.3944 -11.8131 4.3750 0.2326 0.2517 0.2424 -0.0073 0.0026 -0.0245 0.6284 0.9797 1.5410 -0.4314 0.3256 -0.6242 0.0083 -0.0141 0.0059 -0.0971 0.0234 -0.0729 0.0997 -0.0137 -0.0487 'X-RAY DIFFRACTION' 2 ? refined -18.9331 -12.0063 -13.7962 0.3457 0.3937 0.3550 -0.0759 -0.0226 -0.1141 1.7749 2.1899 0.5161 1.6014 -0.4628 -1.0130 -0.0418 -0.2728 0.2781 -0.2738 -0.0546 0.3679 0.1146 0.2262 0.0383 'X-RAY DIFFRACTION' 3 ? refined -22.6605 -13.3668 -11.2981 0.3022 0.4634 0.3583 -0.0426 -0.0095 -0.0021 3.7803 0.6264 0.3422 0.2987 0.0373 0.3534 -0.2650 0.0063 -0.3741 -0.1841 0.1125 0.1463 0.0021 -0.1157 0.1730 # loop_ _pdbx_refine_tls_group.pdbx_refine_id _pdbx_refine_tls_group.id _pdbx_refine_tls_group.refine_tls_id _pdbx_refine_tls_group.beg_auth_asym_id _pdbx_refine_tls_group.beg_auth_seq_id _pdbx_refine_tls_group.end_auth_asym_id _pdbx_refine_tls_group.end_auth_seq_id _pdbx_refine_tls_group.selection_details _pdbx_refine_tls_group.beg_label_asym_id _pdbx_refine_tls_group.beg_label_seq_id _pdbx_refine_tls_group.end_label_asym_id _pdbx_refine_tls_group.end_label_seq_id _pdbx_refine_tls_group.selection 'X-RAY DIFFRACTION' 1 1 A 71 A 135 'chain A' ? ? ? ? ? 'X-RAY DIFFRACTION' 2 2 B 1 B 14 'chain B' ? ? ? ? ? 'X-RAY DIFFRACTION' 3 3 C 1 C 14 'chain C' ? ? ? ? ? # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal HKL-2000 'data collection' . ? 1 SOLVE phasing . ? 2 PHENIX refinement '(phenix.refine: 1.6.4_486)' ? 3 HKL-2000 'data reduction' . ? 4 HKL-2000 'data scaling' . ? 5 # _pdbx_validate_close_contact.id 1 _pdbx_validate_close_contact.PDB_model_num 1 _pdbx_validate_close_contact.auth_atom_id_1 OP2 _pdbx_validate_close_contact.auth_asym_id_1 B _pdbx_validate_close_contact.auth_comp_id_1 DA _pdbx_validate_close_contact.auth_seq_id_1 4 _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_2 237 _pdbx_validate_close_contact.PDB_ins_code_2 ? _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 2.19 # 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 "O3'" B DG 11 ? ? "C3'" B DG 11 ? ? 1.368 1.419 -0.051 0.006 N 2 1 C6 B DA 14 ? ? N1 B DA 14 ? ? 1.394 1.351 0.043 0.007 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 NE A ARG 79 ? ? CZ A ARG 79 ? ? NH1 A ARG 79 ? ? 115.75 120.30 -4.55 0.50 N 2 1 NE A ARG 79 ? ? CZ A ARG 79 ? ? NH2 A ARG 79 ? ? 123.92 120.30 3.62 0.50 N 3 1 "O4'" B DG 1 ? ? "C1'" B DG 1 ? ? "C2'" B DG 1 ? ? 112.59 106.80 5.79 0.50 N 4 1 "O4'" B DG 1 ? ? "C1'" B DG 1 ? ? N9 B DG 1 ? ? 110.21 108.30 1.91 0.30 N 5 1 N3 B DC 5 ? ? C2 B DC 5 ? ? O2 B DC 5 ? ? 126.23 121.90 4.33 0.70 N 6 1 C4 B DT 6 ? ? C5 B DT 6 ? ? C7 B DT 6 ? ? 124.71 119.00 5.71 0.60 N 7 1 C6 B DT 6 ? ? C5 B DT 6 ? ? C7 B DT 6 ? ? 117.73 122.90 -5.17 0.60 N 8 1 "O4'" B DC 8 ? ? "C1'" B DC 8 ? ? N1 B DC 8 ? ? 103.27 108.00 -4.73 0.70 N 9 1 "O4'" B DG 11 ? ? "C1'" B DG 11 ? ? N9 B DG 11 ? ? 113.01 108.30 4.71 0.30 N 10 1 OP1 B DA 14 ? ? P B DA 14 ? ? OP2 B DA 14 ? ? 129.40 119.60 9.80 1.50 N 11 1 "O4'" B DA 14 ? ? "C4'" B DA 14 ? ? "C3'" B DA 14 ? ? 101.58 104.50 -2.92 0.40 N 12 1 "C3'" B DA 14 ? ? "C2'" B DA 14 ? ? "C1'" B DA 14 ? ? 96.88 102.40 -5.52 0.80 N 13 1 "O4'" B DA 14 ? ? "C1'" B DA 14 ? ? "C2'" B DA 14 ? ? 110.13 106.80 3.33 0.50 N 14 1 "O4'" C DG 1 ? ? "C1'" C DG 1 ? ? N9 C DG 1 ? ? 110.56 108.30 2.26 0.30 N 15 1 C2 C DT 2 ? ? N3 C DT 2 ? ? C4 C DT 2 ? ? 123.54 127.20 -3.66 0.60 N 16 1 C5 C DT 2 ? ? C6 C DT 2 ? ? N1 C DT 2 ? ? 120.08 123.70 -3.62 0.60 N 17 1 C2 C DC 3 ? ? N3 C DC 3 ? ? C4 C DC 3 ? ? 116.74 119.90 -3.16 0.50 N 18 1 C5 C DC 3 ? ? C6 C DC 3 ? ? N1 C DC 3 ? ? 117.87 121.00 -3.13 0.50 N 19 1 "O4'" C DT 4 ? ? "C1'" C DT 4 ? ? N1 C DT 4 ? ? 114.38 108.30 6.08 0.30 N 20 1 C5 C DG 5 ? ? C6 C DG 5 ? ? N1 C DG 5 ? ? 114.85 111.50 3.35 0.50 N 21 1 "C1'" C DG 11 ? ? "O4'" C DG 11 ? ? "C4'" C DG 11 ? ? 101.68 110.10 -8.42 1.00 N 22 1 "C3'" C DG 11 ? ? "C2'" C DG 11 ? ? "C1'" C DG 11 ? ? 97.54 102.40 -4.86 0.80 N 23 1 "O4'" C DG 11 ? ? "C1'" C DG 11 ? ? N9 C DG 11 ? ? 110.60 108.30 2.30 0.30 N 24 1 C5 C DT 14 ? ? C4 C DT 14 ? ? O4 C DT 14 ? ? 120.47 124.90 -4.43 0.70 N # loop_ _pdbx_unobs_or_zero_occ_atoms.id _pdbx_unobs_or_zero_occ_atoms.PDB_model_num _pdbx_unobs_or_zero_occ_atoms.polymer_flag _pdbx_unobs_or_zero_occ_atoms.occupancy_flag _pdbx_unobs_or_zero_occ_atoms.auth_asym_id _pdbx_unobs_or_zero_occ_atoms.auth_comp_id _pdbx_unobs_or_zero_occ_atoms.auth_seq_id _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code _pdbx_unobs_or_zero_occ_atoms.auth_atom_id _pdbx_unobs_or_zero_occ_atoms.label_alt_id _pdbx_unobs_or_zero_occ_atoms.label_asym_id _pdbx_unobs_or_zero_occ_atoms.label_comp_id _pdbx_unobs_or_zero_occ_atoms.label_seq_id _pdbx_unobs_or_zero_occ_atoms.label_atom_id 1 1 Y 1 A LYS 71 ? CG ? A LYS 4 CG 2 1 Y 1 A LYS 71 ? CD ? A LYS 4 CD 3 1 Y 1 A LYS 71 ? CE ? A LYS 4 CE 4 1 Y 1 A LYS 71 ? NZ ? A LYS 4 NZ # loop_ _pdbx_unobs_or_zero_occ_residues.id _pdbx_unobs_or_zero_occ_residues.PDB_model_num _pdbx_unobs_or_zero_occ_residues.polymer_flag _pdbx_unobs_or_zero_occ_residues.occupancy_flag _pdbx_unobs_or_zero_occ_residues.auth_asym_id _pdbx_unobs_or_zero_occ_residues.auth_comp_id _pdbx_unobs_or_zero_occ_residues.auth_seq_id _pdbx_unobs_or_zero_occ_residues.PDB_ins_code _pdbx_unobs_or_zero_occ_residues.label_asym_id _pdbx_unobs_or_zero_occ_residues.label_comp_id _pdbx_unobs_or_zero_occ_residues.label_seq_id 1 1 Y 1 A SER 68 ? A SER 1 2 1 Y 1 A GLY 69 ? A GLY 2 3 1 Y 1 A HIS 70 ? A HIS 3 4 1 Y 1 A GLY 136 ? A GLY 69 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 3VXV 'double helix' 3VXV 'b-form double helix' 3VXV 'mismatched base pair' # 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 B DG 1 1_555 C DC 13 1_555 -0.225 0.035 -0.118 -25.080 -16.480 -0.391 1 B_DG1:DC13_C B 1 ? C 13 ? 19 1 1 B DT 2 1_555 C DA 12 1_555 -0.347 -0.073 0.089 -10.782 -7.031 -3.304 2 B_DT2:DA12_C B 2 ? C 12 ? 20 1 1 B DC 3 1_555 C DG 11 1_555 -0.101 -0.219 -0.062 -6.211 -6.081 -1.076 3 B_DC3:DG11_C B 3 ? C 11 ? 19 1 1 B DA 4 1_555 C DT 10 1_555 0.201 -0.153 0.118 4.348 -9.707 0.624 4 B_DA4:DT10_C B 4 ? C 10 ? 20 1 1 B DC 5 1_555 C DG 9 1_555 0.793 -0.245 0.117 4.055 -13.621 3.769 5 B_DC5:DG9_C B 5 ? C 9 ? 19 1 1 B DT 6 1_555 C DA 8 1_555 -0.128 -0.240 0.127 -4.552 -9.780 1.097 6 B_DT6:DA8_C B 6 ? C 8 ? 20 1 1 B DA 7 1_555 C DT 7 1_555 0.122 -0.145 0.064 -9.820 -7.266 0.271 7 B_DA7:DT7_C B 7 ? C 7 ? 20 1 1 B DC 8 1_555 C DG 6 1_555 0.330 -0.147 0.193 -5.872 -3.950 -1.499 8 B_DC8:DG6_C B 8 ? C 6 ? 19 1 1 B 5CM 9 1_555 C DG 5 1_555 0.357 -0.134 -0.032 -3.950 -7.467 -0.557 9 B_5CM9:DG5_C B 9 ? C 5 ? 19 1 1 B DG 10 1_555 C DT 4 1_555 -2.431 -0.584 0.269 13.254 9.223 -7.293 10 B_DG10:DT4_C B 10 ? C 4 ? 28 1 1 B DG 11 1_555 C DC 3 1_555 -0.238 -0.044 0.287 27.737 -0.384 0.181 11 B_DG11:DC3_C B 11 ? C 3 ? 19 1 1 B DA 12 1_555 C DT 2 1_555 0.149 -0.058 0.179 24.158 -17.695 2.402 12 B_DA12:DT2_C B 12 ? C 2 ? 20 1 1 B DC 13 1_555 C DG 1 1_555 0.334 -0.069 -0.142 13.623 -15.089 0.122 13 B_DC13:DG1_C B 13 ? C 1 ? 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 B DG 1 1_555 C DC 13 1_555 B DT 2 1_555 C DA 12 1_555 -0.896 -0.664 2.897 -1.467 3.402 31.750 -1.748 1.393 2.850 6.193 2.670 31.960 1 BB_DG1DT2:DA12DC13_CC B 1 ? C 13 ? B 2 ? C 12 ? 1 B DT 2 1_555 C DA 12 1_555 B DC 3 1_555 C DG 11 1_555 0.751 0.019 3.168 3.142 3.647 37.443 -0.432 -0.763 3.206 5.653 -4.870 37.740 2 BB_DT2DC3:DG11DA12_CC B 2 ? C 12 ? B 3 ? C 11 ? 1 B DC 3 1_555 C DG 11 1_555 B DA 4 1_555 C DT 10 1_555 -0.081 0.160 3.073 -1.289 8.717 28.896 -1.375 -0.093 2.993 16.977 2.511 30.182 3 BB_DC3DA4:DT10DG11_CC B 3 ? C 11 ? B 4 ? C 10 ? 1 B DA 4 1_555 C DT 10 1_555 B DC 5 1_555 C DG 9 1_555 0.874 -0.725 3.278 0.323 2.971 33.673 -1.725 -1.452 3.212 5.116 -0.556 33.801 4 BB_DA4DC5:DG9DT10_CC B 4 ? C 10 ? B 5 ? C 9 ? 1 B DC 5 1_555 C DG 9 1_555 B DT 6 1_555 C DA 8 1_555 0.124 -0.653 3.410 3.923 4.682 32.201 -1.990 0.477 3.277 8.348 -6.994 32.760 5 BB_DC5DT6:DA8DG9_CC B 5 ? C 9 ? B 6 ? C 8 ? 1 B DT 6 1_555 C DA 8 1_555 B DA 7 1_555 C DT 7 1_555 -0.073 -0.589 3.400 0.991 7.643 32.096 -2.361 0.300 3.176 13.581 -1.760 32.985 6 BB_DT6DA7:DT7DA8_CC B 6 ? C 8 ? B 7 ? C 7 ? 1 B DA 7 1_555 C DT 7 1_555 B DC 8 1_555 C DG 6 1_555 -0.537 -0.554 3.273 0.222 2.502 34.003 -1.341 0.951 3.221 4.272 -0.379 34.093 7 BB_DA7DC8:DG6DT7_CC B 7 ? C 7 ? B 8 ? C 6 ? 1 B DC 8 1_555 C DG 6 1_555 B 5CM 9 1_555 C DG 5 1_555 0.743 -0.060 3.336 3.086 -1.725 30.736 0.232 -0.777 3.390 -3.241 -5.797 30.934 8 BB_DC85CM9:DG5DG6_CC B 8 ? C 6 ? B 9 ? C 5 ? 1 B 5CM 9 1_555 C DG 5 1_555 B DG 10 1_555 C DT 4 1_555 0.110 -0.096 3.204 -5.786 -4.268 27.923 0.742 -1.486 3.099 -8.665 11.745 28.816 9 BB_5CM9DG10:DT4DG5_CC B 9 ? C 5 ? B 10 ? C 4 ? 1 B DG 10 1_555 C DT 4 1_555 B DG 11 1_555 C DC 3 1_555 0.296 -0.729 3.177 -4.143 -0.798 35.551 -1.074 -1.059 3.139 -1.301 6.756 35.792 10 BB_DG10DG11:DC3DT4_CC B 10 ? C 4 ? B 11 ? C 3 ? 1 B DG 11 1_555 C DC 3 1_555 B DA 12 1_555 C DT 2 1_555 -0.893 -0.723 3.434 -4.511 3.962 37.510 -1.645 0.765 3.423 6.114 6.960 37.971 11 BB_DG11DA12:DT2DC3_CC B 11 ? C 3 ? B 12 ? C 2 ? 1 B DA 12 1_555 C DT 2 1_555 B DC 13 1_555 C DG 1 1_555 0.197 -1.291 3.498 -1.517 5.261 33.248 -3.118 -0.596 3.250 9.118 2.629 33.683 12 BB_DA12DC13:DG1DT2_CC B 12 ? C 2 ? B 13 ? C 1 ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 4 'ACETATE ION' ACT 5 1,2-ETHANEDIOL EDO 6 water HOH # 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 D 4 ACT 1 201 2 ACT ACT A . E 4 ACT 1 202 3 ACT ACT A . F 5 EDO 1 203 11 EDO EDO A . G 5 EDO 1 204 12 EDO EDO A . H 5 EDO 1 205 13 EDO EDO A . I 5 EDO 1 206 14 EDO EDO A . J 5 EDO 1 207 21 EDO EDO A . K 4 ACT 1 101 1 ACT ACT B . L 5 EDO 1 101 19 EDO EDO C . M 6 HOH 1 301 2 HOH HOH A . M 6 HOH 2 302 3 HOH HOH A . M 6 HOH 3 303 4 HOH HOH A . M 6 HOH 4 304 6 HOH HOH A . M 6 HOH 5 305 7 HOH HOH A . M 6 HOH 6 306 8 HOH HOH A . M 6 HOH 7 307 10 HOH HOH A . M 6 HOH 8 308 12 HOH HOH A . M 6 HOH 9 309 14 HOH HOH A . M 6 HOH 10 310 15 HOH HOH A . M 6 HOH 11 311 18 HOH HOH A . M 6 HOH 12 312 19 HOH HOH A . M 6 HOH 13 313 23 HOH HOH A . M 6 HOH 14 314 26 HOH HOH A . M 6 HOH 15 315 29 HOH HOH A . M 6 HOH 16 316 36 HOH HOH A . M 6 HOH 17 317 39 HOH HOH A . M 6 HOH 18 318 42 HOH HOH A . M 6 HOH 19 319 43 HOH HOH A . M 6 HOH 20 320 46 HOH HOH A . M 6 HOH 21 321 48 HOH HOH A . M 6 HOH 22 322 49 HOH HOH A . M 6 HOH 23 323 50 HOH HOH A . M 6 HOH 24 324 53 HOH HOH A . M 6 HOH 25 325 57 HOH HOH A . M 6 HOH 26 326 60 HOH HOH A . M 6 HOH 27 327 63 HOH HOH A . M 6 HOH 28 328 69 HOH HOH A . M 6 HOH 29 329 70 HOH HOH A . M 6 HOH 30 330 71 HOH HOH A . M 6 HOH 31 331 75 HOH HOH A . M 6 HOH 32 332 80 HOH HOH A . M 6 HOH 33 333 81 HOH HOH A . M 6 HOH 34 334 82 HOH HOH A . M 6 HOH 35 335 91 HOH HOH A . M 6 HOH 36 336 96 HOH HOH A . M 6 HOH 37 337 97 HOH HOH A . M 6 HOH 38 338 99 HOH HOH A . M 6 HOH 39 339 100 HOH HOH A . M 6 HOH 40 340 101 HOH HOH A . M 6 HOH 41 341 102 HOH HOH A . M 6 HOH 42 342 105 HOH HOH A . M 6 HOH 43 343 106 HOH HOH A . M 6 HOH 44 344 107 HOH HOH A . M 6 HOH 45 345 112 HOH HOH A . M 6 HOH 46 346 117 HOH HOH A . M 6 HOH 47 347 123 HOH HOH A . M 6 HOH 48 348 126 HOH HOH A . M 6 HOH 49 349 129 HOH HOH A . M 6 HOH 50 350 130 HOH HOH A . M 6 HOH 51 351 131 HOH HOH A . M 6 HOH 52 352 133 HOH HOH A . M 6 HOH 53 353 137 HOH HOH A . M 6 HOH 54 354 139 HOH HOH A . M 6 HOH 55 355 141 HOH HOH A . M 6 HOH 56 356 143 HOH HOH A . M 6 HOH 57 357 144 HOH HOH A . M 6 HOH 58 358 148 HOH HOH A . M 6 HOH 59 359 149 HOH HOH A . M 6 HOH 60 360 151 HOH HOH A . M 6 HOH 61 361 152 HOH HOH A . M 6 HOH 62 362 9 HOH HOH A . N 6 HOH 1 201 13 HOH HOH B . N 6 HOH 2 202 16 HOH HOH B . N 6 HOH 3 203 20 HOH HOH B . N 6 HOH 4 204 21 HOH HOH B . N 6 HOH 5 205 22 HOH HOH B . N 6 HOH 6 206 27 HOH HOH B . N 6 HOH 7 207 28 HOH HOH B . N 6 HOH 8 208 31 HOH HOH B . N 6 HOH 9 209 33 HOH HOH B . N 6 HOH 10 210 35 HOH HOH B . N 6 HOH 11 211 38 HOH HOH B . N 6 HOH 12 212 41 HOH HOH B . N 6 HOH 13 213 44 HOH HOH B . N 6 HOH 14 214 54 HOH HOH B . N 6 HOH 15 215 59 HOH HOH B . N 6 HOH 16 216 61 HOH HOH B . N 6 HOH 17 217 65 HOH HOH B . N 6 HOH 18 218 66 HOH HOH B . N 6 HOH 19 219 67 HOH HOH B . N 6 HOH 20 220 68 HOH HOH B . N 6 HOH 21 221 73 HOH HOH B . N 6 HOH 22 222 76 HOH HOH B . N 6 HOH 23 223 77 HOH HOH B . N 6 HOH 24 224 83 HOH HOH B . N 6 HOH 25 225 84 HOH HOH B . N 6 HOH 26 226 87 HOH HOH B . N 6 HOH 27 227 89 HOH HOH B . N 6 HOH 28 228 90 HOH HOH B . N 6 HOH 29 229 92 HOH HOH B . N 6 HOH 30 230 94 HOH HOH B . N 6 HOH 31 231 95 HOH HOH B . N 6 HOH 32 232 108 HOH HOH B . N 6 HOH 33 233 110 HOH HOH B . N 6 HOH 34 234 111 HOH HOH B . N 6 HOH 35 235 113 HOH HOH B . N 6 HOH 36 236 114 HOH HOH B . N 6 HOH 37 237 115 HOH HOH B . N 6 HOH 38 238 116 HOH HOH B . N 6 HOH 39 239 119 HOH HOH B . N 6 HOH 40 240 120 HOH HOH B . N 6 HOH 41 241 127 HOH HOH B . N 6 HOH 42 242 128 HOH HOH B . N 6 HOH 43 243 132 HOH HOH B . N 6 HOH 44 244 134 HOH HOH B . N 6 HOH 45 245 135 HOH HOH B . N 6 HOH 46 246 138 HOH HOH B . N 6 HOH 47 247 146 HOH HOH B . N 6 HOH 48 248 147 HOH HOH B . N 6 HOH 49 249 153 HOH HOH B . N 6 HOH 50 250 154 HOH HOH B . N 6 HOH 51 251 11 HOH HOH B . O 6 HOH 1 201 40 HOH HOH C . O 6 HOH 2 202 1 HOH HOH C . O 6 HOH 3 203 5 HOH HOH C . O 6 HOH 4 204 17 HOH HOH C . O 6 HOH 5 205 24 HOH HOH C . O 6 HOH 6 206 25 HOH HOH C . O 6 HOH 7 207 30 HOH HOH C . O 6 HOH 8 208 32 HOH HOH C . O 6 HOH 9 209 34 HOH HOH C . O 6 HOH 10 210 37 HOH HOH C . O 6 HOH 11 211 45 HOH HOH C . O 6 HOH 12 212 47 HOH HOH C . O 6 HOH 13 213 51 HOH HOH C . O 6 HOH 14 214 52 HOH HOH C . O 6 HOH 15 215 55 HOH HOH C . O 6 HOH 16 216 56 HOH HOH C . O 6 HOH 17 217 58 HOH HOH C . O 6 HOH 18 218 62 HOH HOH C . O 6 HOH 19 219 64 HOH HOH C . O 6 HOH 20 220 72 HOH HOH C . O 6 HOH 21 221 74 HOH HOH C . O 6 HOH 22 222 78 HOH HOH C . O 6 HOH 23 223 79 HOH HOH C . O 6 HOH 24 224 85 HOH HOH C . O 6 HOH 25 225 86 HOH HOH C . O 6 HOH 26 226 88 HOH HOH C . O 6 HOH 27 227 93 HOH HOH C . O 6 HOH 28 228 98 HOH HOH C . O 6 HOH 29 229 103 HOH HOH C . O 6 HOH 30 230 104 HOH HOH C . O 6 HOH 31 231 109 HOH HOH C . O 6 HOH 32 232 118 HOH HOH C . O 6 HOH 33 233 121 HOH HOH C . O 6 HOH 34 234 122 HOH HOH C . O 6 HOH 35 235 124 HOH HOH C . O 6 HOH 36 236 125 HOH HOH C . O 6 HOH 37 237 136 HOH HOH C . O 6 HOH 38 238 140 HOH HOH C . O 6 HOH 39 239 142 HOH HOH C . O 6 HOH 40 240 145 HOH HOH C . O 6 HOH 41 241 150 HOH HOH C . #