data_415D # _entry.id 415D # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.280 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 415D RCSB UD0001 WWPDB D_1000179215 # _pdbx_database_PDB_obs_spr.id OBSLTE _pdbx_database_PDB_obs_spr.date 2003-08-26 _pdbx_database_PDB_obs_spr.pdb_id 1O55 _pdbx_database_PDB_obs_spr.replace_pdb_id 415D _pdbx_database_PDB_obs_spr.details ? # _pdbx_database_status.status_code OBS _pdbx_database_status.entry_id 415D _pdbx_database_status.recvd_initial_deposition_date 1998-07-13 _pdbx_database_status.deposit_site NDB _pdbx_database_status.process_site NDB _pdbx_database_status.status_code_sf OBS _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.SG_entry ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Gao, Y.-G.' 1 'Robinson, H.' 2 'Liaw, Y.-C.' 3 'van Boom, J.H.' 4 'van der Marel, G.A.' 5 'Wang, A.H.-J.' 6 # _citation.id primary _citation.title 'Molecular structure of two crystal forms of cyclic triadenylic acid at 1A resolution.' _citation.journal_abbrev J.Biomol.Struct.Dyn. _citation.journal_volume 16 _citation.page_first 69 _citation.page_last 76 _citation.year 1998 _citation.journal_id_ASTM JBSDD6 _citation.country US _citation.journal_id_ISSN 0739-1102 _citation.journal_id_CSD 0646 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 9745896 _citation.pdbx_database_id_DOI ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Gao, Y.G.' 1 primary 'Robinson, H.' 2 primary 'Guan, Y.' 3 primary 'Liaw, Y.C.' 4 primary 'van Boom, J.H.' 5 primary 'van der Marel, G.A.' 6 primary 'Wang, A.H.' 7 # _cell.entry_id 415D _cell.length_a 22.637 _cell.length_b 22.637 _cell.length_c 44.581 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 36 _cell.pdbx_unique_axis ? # _symmetry.entry_id 415D _symmetry.space_group_name_H-M 'H 3 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting hexagonal _symmetry.Int_Tables_number 155 # 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 non-polymer man "ADENOSINE-5'-MONOPHOSPHATE" 347.221 2 ? ? ? ? 2 non-polymer syn 'COBALT ION,6 WATERS COORDINATED' 167.025 1 ? ? ? ? 3 water nat water 18.015 17 ? ? ? ? # _entity_keywords.entity_id 1 _entity_keywords.text 'CYCLIC TRINUCLEOTIDE' # 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 A 'RNA linking' y "ADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 HOH non-polymer . WATER ? 'H2 O' 18.015 OCO non-polymer . 'COBALT ION,6 WATERS COORDINATED' ? 'Co H12 O6 3' 167.025 # _exptl.entry_id 415D _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 1.67 _exptl_crystal.density_percent_sol 26.0000 _exptl_crystal.description ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 298.00 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 4.50 _exptl_crystal_grow.pdbx_details ? _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 COCL3 ? ? ? 1 2 1 GLYCINE ? ? ? 1 3 1 MPD ? ? ? 1 4 2 MPD ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 123.00 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'IMAGE PLATE' _diffrn_detector.type RIGAKU _diffrn_detector.pdbx_collection_date 1997-12-29 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol ? _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.5418 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source 'ROTATING ANODE' _diffrn_source.type 'RIGAKU RU200' _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list ? # _reflns.entry_id 415D _reflns.observed_criterion_sigma_I 0.000 _reflns.observed_criterion_sigma_F 0.000 _reflns.d_resolution_low 10.000 _reflns.d_resolution_high 1.040 _reflns.number_obs 2198 _reflns.number_all 2198 _reflns.percent_possible_obs 95.400 _reflns.pdbx_Rmerge_I_obs 0.0440000 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_av_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 3.500 _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_netI_over_sigmaI ? # _refine.entry_id 415D _refine.ls_number_reflns_obs ? _refine.ls_number_reflns_all 2198 _refine.pdbx_ls_sigma_I 0.00 _refine.pdbx_ls_sigma_F 0.00 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 10.000 _refine.ls_d_res_high 1.040 _refine.ls_percent_reflns_obs 97.200 _refine.ls_R_factor_obs 0.1380000 _refine.ls_R_factor_all 0.1440000 _refine.ls_R_factor_R_work ? _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.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _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_ML ? _refine.pdbx_overall_phase_error ? _refine.overall_SU_B ? _refine.overall_SU_R_Cruickshank_DPI ? _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.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 42 _refine_hist.pdbx_number_atoms_ligand 7 _refine_hist.number_atoms_solvent 17 _refine_hist.number_atoms_total 66 _refine_hist.d_res_high 1.040 _refine_hist.d_res_low 10.000 _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function s_bond_d 0.016 ? ? ? 'X-RAY DIFFRACTION' ? s_angle_d 0.031 ? ? ? 'X-RAY DIFFRACTION' ? s_similar_dist ? ? ? ? 'X-RAY DIFFRACTION' ? s_from_restr_planes ? ? ? ? 'X-RAY DIFFRACTION' ? s_zero_chiral_vol ? ? ? ? 'X-RAY DIFFRACTION' ? s_non_zero_chiral_vol ? ? ? ? 'X-RAY DIFFRACTION' ? s_anti_bump_dis_restr ? ? ? ? 'X-RAY DIFFRACTION' ? s_rigid_bond_adp_cmpnt ? ? ? ? 'X-RAY DIFFRACTION' ? s_similar_adp_cmpnt ? ? ? ? 'X-RAY DIFFRACTION' ? s_approx_iso_adps ? ? ? ? 'X-RAY DIFFRACTION' ? # _pdbx_refine.entry_id 415D _pdbx_refine.R_factor_all_no_cutoff ? _pdbx_refine.R_factor_obs_no_cutoff ? _pdbx_refine.free_R_factor_no_cutoff ? _pdbx_refine.free_R_val_test_set_size_perc_no_cutoff ? _pdbx_refine.free_R_val_test_set_ct_no_cutoff ? _pdbx_refine.R_factor_all_4sig_cutoff 0.1380000 _pdbx_refine.R_factor_obs_4sig_cutoff ? _pdbx_refine.free_R_factor_4sig_cutoff ? _pdbx_refine.free_R_val_test_set_size_perc_4sig_cutoff ? _pdbx_refine.free_R_val_test_set_ct_4sig_cutoff ? _pdbx_refine.number_reflns_obs_4sig_cutoff ? _pdbx_refine.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine.free_R_error_no_cutoff ? # _struct.entry_id 415D _struct.title 'MOLECULAR STRUCTURE OF TWO CRYSTAL FORMS OF CYCLIC TRIADENYLIC ACID AT 1 ANGSTROM RESOLUTION' _struct.pdbx_descriptor "5'-CD(*AP*AP*AP)-3'" _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 415D _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'CYCLIC TRINUCLEOTIDE, 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 ? # loop_ _struct_biol.id 1 2 # _database_PDB_matrix.entry_id 415D _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 415D _atom_sites.fract_transf_matrix[1][1] 0.044175 _atom_sites.fract_transf_matrix[1][2] 0.025505 _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] 0.051009 _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] 0.022431 _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 CO N O P # 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 A 1 A 1 2 2 A A A . B 1 A 1 5 5 A A B . C 2 OCO 1 7 7 OCO OCO ? . D 3 HOH 1 101 101 HOH HOH ? . D 3 HOH 2 102 102 HOH HOH ? . D 3 HOH 3 103 103 HOH HOH ? . D 3 HOH 4 104 104 HOH HOH ? . D 3 HOH 5 105 105 HOH HOH ? . D 3 HOH 6 106 106 HOH HOH ? . D 3 HOH 7 107 107 HOH HOH ? . D 3 HOH 8 108 108 HOH HOH ? . D 3 HOH 9 109 109 HOH HOH ? . D 3 HOH 10 110 110 HOH HOH ? . D 3 HOH 11 111 111 HOH HOH ? . D 3 HOH 12 112 112 HOH HOH ? . D 3 HOH 13 113 113 HOH HOH ? . D 3 HOH 14 114 114 HOH HOH ? . D 3 HOH 15 115 115 HOH HOH ? . D 3 HOH 16 116 116 HOH HOH ? . D 3 HOH 17 117 117 HOH HOH ? . # 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 . HOH 101 ? D HOH . 2 1 . HOH 103 ? D HOH . 3 1 . HOH 105 ? D HOH . 4 1 . HOH 106 ? D HOH . 5 1 . HOH 107 ? D HOH . 6 1 . HOH 111 ? D HOH . 7 1 . HOH 117 ? D 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 1998-07-22 2 'Structure model' 1 1 2003-08-26 # loop_ _pdbx_audit_revision_details.ordinal _pdbx_audit_revision_details.revision_ordinal _pdbx_audit_revision_details.data_content_type _pdbx_audit_revision_details.provider _pdbx_audit_revision_details.type _pdbx_audit_revision_details.description 1 1 'Structure model' repository 'Initial release' ? 2 2 'Structure model' repository Obsolete ? # loop_ _software.classification _software.name _software.version _software.citation_id _software.pdbx_ordinal 'data collection' BIOTEX . ? 1 phasing SHELXS . ? 2 refinement SHELXL-97 . ? 3 # 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 P A A 2 ? ? 1_555 O3* A A 2 ? ? 3_565 1.61 2 1 P B A 5 ? ? 1_555 O3* B A 5 ? ? 3_555 1.62 # 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 N 1 A A 2 ? OP3 ? A A 1 OP3 2 1 N 1 A A 2 ? OP1 ? A A 1 OP1 3 1 N 1 A A 2 ? OP2 ? A A 1 OP2 4 1 N 1 A A 2 ? "O5'" ? A A 1 "O5'" 5 1 N 1 A A 2 ? "C5'" ? A A 1 "C5'" 6 1 N 1 A A 2 ? "C4'" ? A A 1 "C4'" 7 1 N 1 A A 2 ? "O4'" ? A A 1 "O4'" 8 1 N 1 A A 2 ? "C3'" ? A A 1 "C3'" 9 1 N 1 A A 2 ? "O3'" ? A A 1 "O3'" 10 1 N 1 A A 2 ? "C2'" ? A A 1 "C2'" 11 1 N 1 A A 2 ? "O2'" ? A A 1 "O2'" 12 1 N 1 A A 2 ? "C1'" ? A A 1 "C1'" 13 1 N 1 B A 5 ? OP3 ? B A 1 OP3 14 1 N 1 B A 5 ? OP1 ? B A 1 OP1 15 1 N 1 B A 5 ? OP2 ? B A 1 OP2 16 1 N 1 B A 5 ? "O5'" ? B A 1 "O5'" 17 1 N 1 B A 5 ? "C5'" ? B A 1 "C5'" 18 1 N 1 B A 5 ? "C4'" ? B A 1 "C4'" 19 1 N 1 B A 5 ? "O4'" ? B A 1 "O4'" 20 1 N 1 B A 5 ? "C3'" ? B A 1 "C3'" 21 1 N 1 B A 5 ? "O3'" ? B A 1 "O3'" 22 1 N 1 B A 5 ? "C2'" ? B A 1 "C2'" 23 1 N 1 B A 5 ? "O2'" ? B A 1 "O2'" 24 1 N 1 B A 5 ? "C1'" ? B A 1 "C1'" # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 1 "ADENOSINE-5'-MONOPHOSPHATE" A 2 'COBALT ION,6 WATERS COORDINATED' OCO 3 water HOH #