data_279D # _entry.id 279D # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.387 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 279D pdb_0000279d 10.2210/pdb279d/pdb RCSB ZDJ050 ? ? WWPDB D_1000177691 ? ? # 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 1996-06-27 2 'Structure model' 1 1 2008-05-22 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2024-02-14 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' 3 4 'Structure model' 'Data collection' 4 4 'Structure model' 'Database references' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 4 'Structure model' chem_comp_atom 2 4 'Structure model' chem_comp_bond 3 4 'Structure model' database_2 # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 4 'Structure model' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 279D _pdbx_database_status.recvd_initial_deposition_date 1996-05-21 _pdbx_database_status.deposit_site NDB _pdbx_database_status.process_site NDB _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Ban, C.' 1 'Ramakrishnan, B.' 2 'Sundaralingam, M.' 3 # _citation.id primary _citation.title ;Crystal structure of the self-complementary 5'-purine start decamer d(GCGCGCGCGC) in the Z-DNA conformation. I. ; _citation.journal_abbrev Biophys.J. _citation.journal_volume 71 _citation.page_first 1215 _citation.page_last 1221 _citation.year 1996 _citation.journal_id_ASTM BIOJAU _citation.country US _citation.journal_id_ISSN 0006-3495 _citation.journal_id_CSD 0030 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 8873995 _citation.pdbx_database_id_DOI ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Ban, C.' 1 ? primary 'Ramakrishnan, B.' 2 ? primary 'Sundaralingam, M.' 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 nat ;DNA (5'-D(*GP*CP*GP*CP*GP*CP*GP*CP*GP*C)-3' ; 573.430 1 ? ? ? ? 2 water nat water 18.015 14 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code '(DG)(DC)' _entity_poly.pdbx_seq_one_letter_code_can GC _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DG n 1 2 DC n # 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 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 # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 DG 1 1 1 DG G A . n A 1 2 DC 2 2 2 DC C A . n # 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 B 2 HOH 1 3 3 HOH HOH A . B 2 HOH 2 4 4 HOH HOH A . B 2 HOH 3 5 5 HOH HOH A . B 2 HOH 4 6 6 HOH HOH A . B 2 HOH 5 7 7 HOH HOH A . B 2 HOH 6 8 8 HOH HOH A . B 2 HOH 7 9 9 HOH HOH A . B 2 HOH 8 10 10 HOH HOH A . B 2 HOH 9 11 11 HOH HOH A . B 2 HOH 10 12 12 HOH HOH A . B 2 HOH 11 13 13 HOH HOH A . B 2 HOH 12 14 14 HOH HOH A . B 2 HOH 13 15 15 HOH HOH A . B 2 HOH 14 16 16 HOH HOH A . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal X-PLOR refinement . ? 1 XENGEN 'data reduction' 'V. 2.0' ? 2 # _cell.entry_id 279D _cell.length_a 18.100 _cell.length_b 18.100 _cell.length_c 43.100 _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 279D _symmetry.space_group_name_H-M 'P 65 2 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 # _exptl.entry_id 279D _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number ? # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 30.78 _exptl_crystal.density_Matthews 1.78 _exptl_crystal.description ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp ? _exptl_crystal_grow.temp_details 'ROOM TEMPERATURE' _exptl_crystal_grow.pH 7.00 _exptl_crystal_grow.pdbx_details 'pH 7.00, VAPOR DIFFUSION, HANGING DROP' _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 'NA CACODYLATE' ? ? ? 1 4 1 MGCL2 ? ? ? 1 5 1 SPERMINE_HCL ? ? ? 1 6 2 WATER ? ? ? 1 7 2 MPD ? ? ? # _diffrn.id 1 _diffrn.ambient_temp ? _diffrn.ambient_temp_details 'ROOM TEMPERATURE' _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'AREA DETECTOR' _diffrn_detector.type SIEMENS-NICOLET _diffrn_detector.pdbx_collection_date 1994-04-13 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator GRAPHITE _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 'ROTATING ANODE' _diffrn_source.type MACSCIENCE _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list ? # _reflns.entry_id 279D _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F 1.000 _reflns.d_resolution_low 20.000 _reflns.d_resolution_high 1.900 _reflns.number_obs 401 _reflns.number_all 2020 _reflns.percent_possible_obs 96.400 _reflns.pdbx_Rmerge_I_obs 0.0220000 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 5.000 _reflns.R_free_details ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _refine.entry_id 279D _refine.ls_number_reflns_obs 340 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 1.000 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 8.000 _refine.ls_d_res_high 1.900 _refine.ls_percent_reflns_obs ? _refine.ls_R_factor_obs 0.1860000 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.1860000 _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 ? _refine.pdbx_method_to_determine_struct ? _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 41 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 14 _refine_hist.number_atoms_total 55 _refine_hist.d_res_high 1.900 _refine_hist.d_res_low 8.000 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function x_bond_d 0.012 ? ? ? '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 3.30 ? ? ? 'X-RAY DIFFRACTION' ? x_angle_deg_na ? ? ? ? 'X-RAY DIFFRACTION' ? x_angle_deg_prot ? ? ? ? 'X-RAY DIFFRACTION' ? x_dihedral_angle_d 31.0 ? ? ? 'X-RAY DIFFRACTION' ? x_dihedral_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? x_dihedral_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? x_improper_angle_d 3.40 ? ? ? '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 PARAM11.DAT _pdbx_xplor_file.topol_file ? _pdbx_xplor_file.pdbx_refine_id 'X-RAY DIFFRACTION' # _database_PDB_matrix.entry_id 279D _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 279D _struct.title ;CRYSTAL STRUCTURE OF THE SELF-COMPLEMENTARY 5'-PURINE START DECAMER D(GCGCGCGCGC) IN THE Z-DNA CONFORMATION-PART I ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 279D _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'Z-DNA, DOUBLE HELIX, 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 2 ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 279D _struct_ref.pdbx_db_accession 279D _struct_ref.pdbx_db_isoform ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 279D _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 2 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 279D _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 2 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 2 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dodecameric _pdbx_struct_assembly.oligomeric_count 12 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4,5,6,7,8,9,10,11,12 _pdbx_struct_assembly_gen.asym_id_list A,B # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 2 'crystal symmetry operation' 2_554 -y,x-y,z-1/3 -0.5000000000 -0.8660254038 0.0000000000 0.0000000000 0.8660254038 -0.5000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 -14.3666666667 3 'crystal symmetry operation' 3_555 -x+y,-x,z+1/3 -0.5000000000 0.8660254038 0.0000000000 0.0000000000 -0.8660254038 -0.5000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 14.3666666667 4 'crystal symmetry operation' 4_555 -x,-y,z+1/2 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 21.5500000000 5 'crystal symmetry operation' 5_555 y,-x+y,z+1/6 0.5000000000 0.8660254038 0.0000000000 0.0000000000 -0.8660254038 0.5000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 7.1833333333 6 'crystal symmetry operation' 6_554 x-y,x,z-1/6 0.5000000000 -0.8660254038 0.0000000000 0.0000000000 0.8660254038 0.5000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 -7.1833333333 7 'crystal symmetry operation' 7_557 y,x,-z+8/3 -0.5000000000 0.8660254038 0.0000000000 0.0000000000 0.8660254038 0.5000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 114.9333333333 8 'crystal symmetry operation' 8_557 x-y,-y,-z+2 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 86.2000000000 9 'crystal symmetry operation' 9_557 -x,-x+y,-z+7/3 -0.5000000000 -0.8660254038 0.0000000000 0.0000000000 -0.8660254038 0.5000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 100.5666666667 10 'crystal symmetry operation' 10_557 -y,-x,-z+13/6 0.5000000000 -0.8660254038 0.0000000000 0.0000000000 -0.8660254038 -0.5000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 93.3833333333 11 'crystal symmetry operation' 11_557 -x+y,y,-z+5/2 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 107.7500000000 12 'crystal symmetry operation' 12_557 x,x-y,-z+17/6 0.5000000000 0.8660254038 0.0000000000 0.0000000000 0.8660254038 -0.5000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 122.1166666667 # _struct_biol.id 1 _struct_biol.pdbx_parent_biol_id ? _struct_biol.details ? # _pdbx_validate_symm_contact.id 1 _pdbx_validate_symm_contact.PDB_model_num 1 _pdbx_validate_symm_contact.auth_atom_id_1 P _pdbx_validate_symm_contact.auth_asym_id_1 A _pdbx_validate_symm_contact.auth_comp_id_1 DG _pdbx_validate_symm_contact.auth_seq_id_1 1 _pdbx_validate_symm_contact.PDB_ins_code_1 ? _pdbx_validate_symm_contact.label_alt_id_1 ? _pdbx_validate_symm_contact.site_symmetry_1 1_555 _pdbx_validate_symm_contact.auth_atom_id_2 "O3'" _pdbx_validate_symm_contact.auth_asym_id_2 A _pdbx_validate_symm_contact.auth_comp_id_2 DC _pdbx_validate_symm_contact.auth_seq_id_2 2 _pdbx_validate_symm_contact.PDB_ins_code_2 ? _pdbx_validate_symm_contact.label_alt_id_2 ? _pdbx_validate_symm_contact.site_symmetry_2 6_554 _pdbx_validate_symm_contact.dist 1.63 # 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 "C5'" A DG 1 ? ? "C4'" A DG 1 ? ? 1.412 1.509 -0.097 0.011 N 2 1 "C4'" A DG 1 ? ? "C3'" A DG 1 ? ? 1.373 1.521 -0.148 0.010 N 3 1 "O4'" A DG 1 ? ? "C4'" A DG 1 ? ? 1.362 1.446 -0.084 0.010 N 4 1 C6 A DG 1 ? ? O6 A DG 1 ? ? 1.303 1.237 0.066 0.009 N 5 1 "O3'" A DC 2 ? ? "C3'" A DC 2 ? ? 1.352 1.419 -0.067 0.006 N 6 1 C4 A DC 2 ? ? N4 A DC 2 ? ? 1.248 1.335 -0.087 0.009 N 7 1 C4 A DC 2 ? ? C5 A DC 2 ? ? 1.368 1.425 -0.057 0.008 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 "O5'" A DG 1 ? ? P A DG 1 ? ? OP1 A DG 1 ? ? 119.46 110.70 8.76 1.20 N 2 1 "O5'" A DG 1 ? ? "C5'" A DG 1 ? ? "C4'" A DG 1 ? ? 95.18 109.40 -14.22 0.80 N 3 1 "O4'" A DG 1 ? ? "C4'" A DG 1 ? ? "C3'" A DG 1 ? ? 100.34 104.50 -4.16 0.40 N 4 1 "C5'" A DG 1 ? ? "C4'" A DG 1 ? ? "C3'" A DG 1 ? ? 94.49 114.10 -19.61 1.80 N 5 1 "C1'" A DG 1 ? ? "O4'" A DG 1 ? ? "C4'" A DG 1 ? ? 115.76 110.30 5.46 0.70 N 6 1 "C4'" A DG 1 ? ? "C3'" A DG 1 ? ? "C2'" A DG 1 ? ? 108.82 103.10 5.72 0.90 N 7 1 "O4'" A DG 1 ? ? "C1'" A DG 1 ? ? "C2'" A DG 1 ? ? 100.47 105.90 -5.43 0.80 N 8 1 "O4'" A DG 1 ? ? "C1'" A DG 1 ? ? N9 A DG 1 ? ? 99.77 108.00 -8.23 0.70 N 9 1 C2 A DG 1 ? ? N3 A DG 1 ? ? C4 A DG 1 ? ? 115.59 111.90 3.69 0.50 N 10 1 N1 A DG 1 ? ? C2 A DG 1 ? ? N2 A DG 1 ? ? 107.58 116.20 -8.62 0.90 N 11 1 N3 A DG 1 ? ? C2 A DG 1 ? ? N2 A DG 1 ? ? 130.63 119.90 10.73 0.70 N 12 1 N1 A DG 1 ? ? C6 A DG 1 ? ? O6 A DG 1 ? ? 116.27 119.90 -3.63 0.60 N 13 1 P A DC 2 ? ? "O5'" A DC 2 ? ? "C5'" A DC 2 ? ? 110.17 120.90 -10.73 1.60 N 14 1 "O4'" A DC 2 ? ? "C4'" A DC 2 ? ? "C3'" A DC 2 ? ? 113.88 106.00 7.88 0.60 N 15 1 "C5'" A DC 2 ? ? "C4'" A DC 2 ? ? "O4'" A DC 2 ? ? 96.92 109.30 -12.38 1.90 N 16 1 "C1'" A DC 2 ? ? "O4'" A DC 2 ? ? "C4'" A DC 2 ? ? 98.01 110.10 -12.09 1.00 N 17 1 "C4'" A DC 2 ? ? "C3'" A DC 2 ? ? "C2'" A DC 2 ? ? 95.74 102.20 -6.46 0.70 N 18 1 "O4'" A DC 2 ? ? "C1'" A DC 2 ? ? "C2'" A DC 2 ? ? 112.49 106.80 5.69 0.50 N 19 1 C6 A DC 2 ? ? N1 A DC 2 ? ? C2 A DC 2 ? ? 123.35 120.30 3.05 0.40 N 20 1 N3 A DC 2 ? ? C4 A DC 2 ? ? C5 A DC 2 ? ? 126.34 121.90 4.44 0.40 N 21 1 N1 A DC 2 ? ? C2 A DC 2 ? ? O2 A DC 2 ? ? 124.57 118.90 5.67 0.60 N 22 1 C5 A DC 2 ? ? C4 A DC 2 ? ? N4 A DC 2 ? ? 114.26 120.20 -5.94 0.70 N # 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 5 ? B HOH . 2 1 A HOH 10 ? B HOH . 3 1 A HOH 12 ? B HOH . # loop_ _refine_B_iso.class _refine_B_iso.details _refine_B_iso.treatment _refine_B_iso.pdbx_refine_id 'ALL ATOMS' TF isotropic 'X-RAY DIFFRACTION' 'ALL WATERS' TF isotropic 'X-RAY DIFFRACTION' # loop_ _refine_occupancy.class _refine_occupancy.treatment _refine_occupancy.pdbx_refine_id 'ALL ATOMS' fix 'X-RAY DIFFRACTION' 'ALL WATERS' fix 'X-RAY DIFFRACTION' # 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 DC OP3 O N N 1 DC P P N N 2 DC OP1 O N N 3 DC OP2 O N N 4 DC "O5'" O N N 5 DC "C5'" C N N 6 DC "C4'" C N R 7 DC "O4'" O N N 8 DC "C3'" C N S 9 DC "O3'" O N N 10 DC "C2'" C N N 11 DC "C1'" C N R 12 DC N1 N N N 13 DC C2 C N N 14 DC O2 O N N 15 DC N3 N N N 16 DC C4 C N N 17 DC N4 N N N 18 DC C5 C N N 19 DC C6 C N N 20 DC HOP3 H N N 21 DC HOP2 H N N 22 DC "H5'" H N N 23 DC "H5''" H N N 24 DC "H4'" H N N 25 DC "H3'" H N N 26 DC "HO3'" H N N 27 DC "H2'" H N N 28 DC "H2''" H N N 29 DC "H1'" H N N 30 DC H41 H N N 31 DC H42 H N N 32 DC H5 H N N 33 DC H6 H N N 34 DG OP3 O N N 35 DG P P N N 36 DG OP1 O N N 37 DG OP2 O N N 38 DG "O5'" O N N 39 DG "C5'" C N N 40 DG "C4'" C N R 41 DG "O4'" O N N 42 DG "C3'" C N S 43 DG "O3'" O N N 44 DG "C2'" C N N 45 DG "C1'" C N R 46 DG N9 N Y N 47 DG C8 C Y N 48 DG N7 N Y N 49 DG C5 C Y N 50 DG C6 C N N 51 DG O6 O N N 52 DG N1 N N N 53 DG C2 C N N 54 DG N2 N N N 55 DG N3 N N N 56 DG C4 C Y N 57 DG HOP3 H N N 58 DG HOP2 H N N 59 DG "H5'" H N N 60 DG "H5''" H N N 61 DG "H4'" H N N 62 DG "H3'" H N N 63 DG "HO3'" H N N 64 DG "H2'" H N N 65 DG "H2''" H N N 66 DG "H1'" H N N 67 DG H8 H N N 68 DG H1 H N N 69 DG H21 H N N 70 DG H22 H N N 71 HOH O O N N 72 HOH H1 H N N 73 HOH H2 H N N 74 # 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 DC OP3 P sing N N 1 DC OP3 HOP3 sing N N 2 DC P OP1 doub N N 3 DC P OP2 sing N N 4 DC P "O5'" sing N N 5 DC OP2 HOP2 sing N N 6 DC "O5'" "C5'" sing N N 7 DC "C5'" "C4'" sing N N 8 DC "C5'" "H5'" sing N N 9 DC "C5'" "H5''" sing N N 10 DC "C4'" "O4'" sing N N 11 DC "C4'" "C3'" sing N N 12 DC "C4'" "H4'" sing N N 13 DC "O4'" "C1'" sing N N 14 DC "C3'" "O3'" sing N N 15 DC "C3'" "C2'" sing N N 16 DC "C3'" "H3'" sing N N 17 DC "O3'" "HO3'" sing N N 18 DC "C2'" "C1'" sing N N 19 DC "C2'" "H2'" sing N N 20 DC "C2'" "H2''" sing N N 21 DC "C1'" N1 sing N N 22 DC "C1'" "H1'" sing N N 23 DC N1 C2 sing N N 24 DC N1 C6 sing N N 25 DC C2 O2 doub N N 26 DC C2 N3 sing N N 27 DC N3 C4 doub N N 28 DC C4 N4 sing N N 29 DC C4 C5 sing N N 30 DC N4 H41 sing N N 31 DC N4 H42 sing N N 32 DC C5 C6 doub N N 33 DC C5 H5 sing N N 34 DC C6 H6 sing N N 35 DG OP3 P sing N N 36 DG OP3 HOP3 sing N N 37 DG P OP1 doub N N 38 DG P OP2 sing N N 39 DG P "O5'" sing N N 40 DG OP2 HOP2 sing N N 41 DG "O5'" "C5'" sing N N 42 DG "C5'" "C4'" sing N N 43 DG "C5'" "H5'" sing N N 44 DG "C5'" "H5''" sing N N 45 DG "C4'" "O4'" sing N N 46 DG "C4'" "C3'" sing N N 47 DG "C4'" "H4'" sing N N 48 DG "O4'" "C1'" sing N N 49 DG "C3'" "O3'" sing N N 50 DG "C3'" "C2'" sing N N 51 DG "C3'" "H3'" sing N N 52 DG "O3'" "HO3'" sing N N 53 DG "C2'" "C1'" sing N N 54 DG "C2'" "H2'" sing N N 55 DG "C2'" "H2''" sing N N 56 DG "C1'" N9 sing N N 57 DG "C1'" "H1'" sing N N 58 DG N9 C8 sing Y N 59 DG N9 C4 sing Y N 60 DG C8 N7 doub Y N 61 DG C8 H8 sing N N 62 DG N7 C5 sing Y N 63 DG C5 C6 sing N N 64 DG C5 C4 doub Y N 65 DG C6 O6 doub N N 66 DG C6 N1 sing N N 67 DG N1 C2 sing N N 68 DG N1 H1 sing N N 69 DG C2 N2 sing N N 70 DG C2 N3 doub N N 71 DG N2 H21 sing N N 72 DG N2 H22 sing N N 73 DG N3 C4 sing N N 74 HOH O H1 sing N N 75 HOH O H2 sing N N 76 # _atom_sites.entry_id 279D _atom_sites.fract_transf_matrix[1][1] 0.055249 _atom_sites.fract_transf_matrix[1][2] 0.031898 _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] 0.063796 _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] 0.023202 _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 # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_alt_id _atom_site.label_comp_id _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.label_seq_id _atom_site.pdbx_PDB_ins_code _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_seq_id _atom_site.auth_comp_id _atom_site.auth_asym_id _atom_site.auth_atom_id _atom_site.pdbx_PDB_model_num ATOM 1 P P . DG A 1 1 ? -4.154 -4.171 44.411 1.00 39.15 ? 1 DG A P 1 ATOM 2 O OP1 . DG A 1 1 ? -4.757 -2.761 44.368 1.00 35.41 ? 1 DG A OP1 1 ATOM 3 O OP2 . DG A 1 1 ? -3.954 -4.816 43.079 1.00 34.78 ? 1 DG A OP2 1 ATOM 4 O "O5'" . DG A 1 1 ? -4.596 -5.183 45.575 1.00 33.19 ? 1 DG A "O5'" 1 ATOM 5 C "C5'" . DG A 1 1 ? -4.529 -4.758 46.850 1.00 22.04 ? 1 DG A "C5'" 1 ATOM 6 C "C4'" . DG A 1 1 ? -4.613 -6.048 47.419 1.00 14.72 ? 1 DG A "C4'" 1 ATOM 7 O "O4'" . DG A 1 1 ? -3.432 -6.726 47.419 1.00 14.85 ? 1 DG A "O4'" 1 ATOM 8 C "C3'" . DG A 1 1 ? -4.636 -5.593 48.714 1.00 16.80 ? 1 DG A "C3'" 1 ATOM 9 O "O3'" . DG A 1 1 ? -6.009 -5.291 48.911 1.00 26.82 ? 1 DG A "O3'" 1 ATOM 10 C "C2'" . DG A 1 1 ? -3.960 -6.599 49.591 1.00 15.56 ? 1 DG A "C2'" 1 ATOM 11 C "C1'" . DG A 1 1 ? -3.129 -7.399 48.580 1.00 13.57 ? 1 DG A "C1'" 1 ATOM 12 N N9 . DG A 1 1 ? -1.709 -7.220 48.601 1.00 12.75 ? 1 DG A N9 1 ATOM 13 C C8 . DG A 1 1 ? -0.705 -8.161 48.650 1.00 25.18 ? 1 DG A C8 1 ATOM 14 N N7 . DG A 1 1 ? 0.491 -7.627 48.670 1.00 26.96 ? 1 DG A N7 1 ATOM 15 C C5 . DG A 1 1 ? 0.243 -6.265 48.605 1.00 24.08 ? 1 DG A C5 1 ATOM 16 C C6 . DG A 1 1 ? 1.134 -5.191 48.485 1.00 23.18 ? 1 DG A C6 1 ATOM 17 O O6 . DG A 1 1 ? 2.420 -5.183 48.695 1.00 25.26 ? 1 DG A O6 1 ATOM 18 N N1 . DG A 1 1 ? 0.529 -3.960 48.361 1.00 17.36 ? 1 DG A N1 1 ATOM 19 C C2 . DG A 1 1 ? -0.805 -3.788 48.350 1.00 17.21 ? 1 DG A C2 1 ATOM 20 N N2 . DG A 1 1 ? -1.047 -2.473 48.114 1.00 15.58 ? 1 DG A N2 1 ATOM 21 N N3 . DG A 1 1 ? -1.654 -4.831 48.466 1.00 16.67 ? 1 DG A N3 1 ATOM 22 C C4 . DG A 1 1 ? -1.084 -6.024 48.582 1.00 15.38 ? 1 DG A C4 1 ATOM 23 P P . DC A 1 2 ? -6.504 -4.558 50.291 1.00 31.12 ? 2 DC A P 1 ATOM 24 O OP1 . DC A 1 2 ? -6.224 -5.436 51.495 1.00 30.97 ? 2 DC A OP1 1 ATOM 25 O OP2 . DC A 1 2 ? -7.913 -4.137 50.002 1.00 33.46 ? 2 DC A OP2 1 ATOM 26 O "O5'" . DC A 1 2 ? -5.754 -3.150 50.602 1.00 25.67 ? 2 DC A "O5'" 1 ATOM 27 C "C5'" . DC A 1 2 ? -5.478 -3.038 51.993 1.00 19.91 ? 2 DC A "C5'" 1 ATOM 28 C "C4'" . DC A 1 2 ? -4.897 -1.777 52.433 1.00 14.48 ? 2 DC A "C4'" 1 ATOM 29 O "O4'" . DC A 1 2 ? -3.710 -2.345 53.078 1.00 17.58 ? 2 DC A "O4'" 1 ATOM 30 C "C3'" . DC A 1 2 ? -4.583 -0.831 51.301 1.00 9.30 ? 2 DC A "C3'" 1 ATOM 31 O "O3'" . DC A 1 2 ? -4.423 0.481 51.584 1.00 15.49 ? 2 DC A "O3'" 1 ATOM 32 C "C2'" . DC A 1 2 ? -3.377 -1.575 50.814 1.00 7.47 ? 2 DC A "C2'" 1 ATOM 33 C "C1'" . DC A 1 2 ? -2.754 -1.950 52.114 1.00 4.63 ? 2 DC A "C1'" 1 ATOM 34 N N1 . DC A 1 2 ? -1.866 -3.031 52.032 1.00 14.10 ? 2 DC A N1 1 ATOM 35 C C2 . DC A 1 2 ? -0.542 -2.666 52.205 1.00 11.15 ? 2 DC A C2 1 ATOM 36 O O2 . DC A 1 2 ? -0.156 -1.534 52.315 1.00 9.08 ? 2 DC A O2 1 ATOM 37 N N3 . DC A 1 2 ? 0.340 -3.660 52.289 1.00 11.32 ? 2 DC A N3 1 ATOM 38 C C4 . DC A 1 2 ? -0.103 -4.914 52.168 1.00 7.50 ? 2 DC A C4 1 ATOM 39 N N4 . DC A 1 2 ? 0.703 -5.861 52.271 1.00 10.66 ? 2 DC A N4 1 ATOM 40 C C5 . DC A 1 2 ? -1.398 -5.299 51.954 1.00 10.36 ? 2 DC A C5 1 ATOM 41 C C6 . DC A 1 2 ? -2.266 -4.296 51.896 1.00 9.55 ? 2 DC A C6 1 HETATM 42 O O . HOH B 2 . ? 0.098 -9.219 52.539 1.00 26.86 ? 3 HOH A O 1 HETATM 43 O O . HOH B 2 . ? -5.825 -5.195 38.303 1.00 35.23 ? 4 HOH A O 1 HETATM 44 O O . HOH B 2 . ? 4.353 -7.537 50.286 0.50 36.82 ? 5 HOH A O 1 HETATM 45 O O . HOH B 2 . ? -3.508 -3.593 40.263 1.00 45.77 ? 6 HOH A O 1 HETATM 46 O O . HOH B 2 . ? -5.771 -8.607 40.257 1.00 46.59 ? 7 HOH A O 1 HETATM 47 O O . HOH B 2 . ? -4.793 -1.362 41.341 1.00 55.05 ? 8 HOH A O 1 HETATM 48 O O . HOH B 2 . ? -1.074 -3.782 39.504 1.00 83.31 ? 9 HOH A O 1 HETATM 49 O O . HOH B 2 . ? -1.157 0.646 46.694 0.50 64.86 ? 10 HOH A O 1 HETATM 50 O O . HOH B 2 . ? -6.186 -5.297 41.235 1.00 86.28 ? 11 HOH A O 1 HETATM 51 O O . HOH B 2 . ? -0.542 0.943 50.277 0.50 75.46 ? 12 HOH A O 1 HETATM 52 O O . HOH B 2 . ? 5.341 -9.793 49.081 1.00 81.43 ? 13 HOH A O 1 HETATM 53 O O . HOH B 2 . ? -7.180 -2.999 48.044 1.00 99.14 ? 14 HOH A O 1 HETATM 54 O O . HOH B 2 . ? -3.653 -6.413 40.043 1.00 96.55 ? 15 HOH A O 1 HETATM 55 O O . HOH B 2 . ? 6.258 -7.344 47.761 1.00 94.66 ? 16 HOH A O 1 #