data_UDBA41 # _entry.id UDBA41 # _audit.revision_id 1 _audit.creation_date 2001-10-03 _audit.update_record ; This preliminary mmCIF data file was originally created by the Nucleic Acid Database Project and is being released as part of the RCSB PDB data uniformity project. This data file is provided for test purposes. This file is not the author approved archival version of this entry which can be obtained in PDB format from ftp://ftp.rcsb.org or one of the PDB ftp mirror sites. ; # loop_ _audit_conform.dict_name _audit_conform.dict_version _audit_conform.dict_location cif_mm.dic 2.0.03 http://pdb.rutgers.edu/mmcif/dictionaries/ascii/cif_mm.dic cif_pdbx.dic 0.8.07 http://pdb.rutgers.edu/mmcif/dictionaries/ascii/pdbx_exchange.dic # _database.entry_id UDBA41 _database.code_CSD ? # loop_ _database_2.database_id _database_2.database_code NDB UDBA41 RCSB UDBA41 # loop_ _database_PDB_rev.num _database_PDB_rev.date _database_PDB_rev.date_original _database_PDB_rev.status _database_PDB_rev.replaces _database_PDB_rev.mod_type 1 1995-09-11 1995-09-11 ? ? 0 2 2001-09-21 ? ? ? 5 # loop_ _audit_author.name 'Szabo, T.' 'Noreus, D.' 'Norrestam, R.' 'Stawinski, J.' # _citation.id primary _citation.title ;Molecular and Crystal Structure of Sp-thymidin-3'-yl 4-thiothymidin-5'-yl Methylphosphonate ; _citation.journal_abbrev 'Nucleic Acids Res.' _citation.journal_volume 21 _citation.page_first 3921 _citation.page_last 3926 _citation.year 1993 _citation.journal_id_ASTM NARHAD _citation.country UK _citation.journal_id_ISSN 0305-1048 _citation.journal_id_CSD 0389 _citation.book_publisher ? # loop_ _citation_author.citation_id _citation_author.name primary 'Szabo, T.' primary 'Noreus, D.' primary 'Norrestam, R.' primary 'Stawinski, J.' # _cell.entry_id UDBA41 _cell.length_a 13.241 _cell.length_b 13.844 _cell.length_c 14.944 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id UDBA41 _symmetry.space_group_name_H-M 'P 21 21 21' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.details 1 polymer syn '5'-D(*TP(CH3)*(S)T)-3'' 563.434 1 ? 2 non-polymer syn 'METHYL GROUP' 15.035 1 ? 3 non-polymer syn 'SULFUR ATOM' 32.060 1 ? 4 non-polymer syn METHANOL 32.042 1 ? # loop_ _entity_keywords.entity_id _entity_keywords.text _entity_keywords.pdbx_mutation _entity_keywords.pdbx_fragment _entity_keywords.pdbx_ec 1 ? ? ? ? 2 ? ? ? ? 3 ? ? ? ? 4 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id 1 1 +T 1 2 +T # 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 T 'DNA linking' y 'THYMIDINE-5'-MONOPHOSPHATE' ? 'C10 H15 N2 O8 P1' 322.211 +T 'DNA linking' y 'THYMIDINE-5'-MONOPHOSPHATE' ? 'C10 H15 N2 O8 P1' 322.211 CH3 non-polymer . 'METHYL GROUP' ? 'C1 H3' 15.035 S non-polymer . 'SULFUR ATOM' ? S1 32.060 MOH non-polymer . METHANOL ? 'C1 H4 O1' 32.042 # _exptl.entry_id UDBA41 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number ? # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol ? _exptl_crystal.density_Matthews ? _exptl_crystal.description ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method EVAPORATION _exptl_crystal_grow.temp ? _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH ? _exptl_crystal_grow.pdbx_details ? _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.id 1 _diffrn.ambient_temp 173.00 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector ? _diffrn_detector.type ? _diffrn_detector.pdbx_collection_date ? _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 'SINGLE WAVELENGTH' # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.7100 # _diffrn_source.diffrn_id 1 _diffrn_source.source ? _diffrn_source.type ? _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? # _computing.entry_id UDBA41 _computing.data_collection ? _computing.data_reduction ? _computing.structure_solution ? _computing.structure_refinement ? _computing.pdbx_structure_refinement_method 'FULL-MATRIX LEAST SQUARES' # _refine.entry_id UDBA41 _refine.ls_number_reflns_obs 1237 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I 3.000 _refine.pdbx_ls_sigma_F ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low ? _refine.ls_d_res_high ? _refine.ls_percent_reflns_obs ? _refine.ls_R_factor_obs 0.0580000 _refine.ls_R_factor_all ? _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_Free ? _refine.ls_redundancy_reflns_obs ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? # _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 35 _refine_hist.pdbx_number_atoms_ligand 2 _refine_hist.number_atoms_solvent 2 _refine_hist.number_atoms_total 39 _refine_hist.d_res_high . _refine_hist.d_res_low . # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number o_bond_d ? ? ? ? o_bond_d_na ? ? ? ? o_bond_d_prot ? ? ? ? o_angle_d ? ? ? ? o_angle_d_na ? ? ? ? o_angle_d_prot ? ? ? ? o_angle_deg ? ? ? ? o_angle_deg_na ? ? ? ? o_angle_deg_prot ? ? ? ? o_dihedral_angle_d ? ? ? ? o_dihedral_angle_d_na ? ? ? ? o_dihedral_angle_d_prot ? ? ? ? o_improper_angle_d ? ? ? ? o_improper_angle_d_na ? ? ? ? o_improper_angle_d_prot ? ? ? ? o_mcbond_it ? ? ? ? o_mcangle_it ? ? ? ? o_scbond_it ? ? ? ? o_scangle_it ? ? ? ? # _struct.entry_id UDBA41 _struct.title ;MOLECULAR AND CRYSTAL STRUCTURE OF SP-THYMIDIN-3'-YL 4-THIOTHYMIDIN-5'-YL METHYLPHOSPHONATE ; _struct.pdbx_model_details ? # _struct_keywords.entry_id UDBA41 _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'U-DNA, SINGLE STRAND' # loop_ _struct_asym.id _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N 1 ? B N 2 ? C N 3 ? D N 4 ? # _struct_biol.id 1 _struct_biol.pdbx_parent_biol_id ? _struct_biol.details ? # loop_ _struct_biol_gen.biol_id _struct_biol_gen.asym_id _struct_biol_gen.symmetry _struct_biol_gen.details _struct_biol_gen.pdbx_full_symmetry_operation 1 A 1_555 ? x,y,z 1 B 1_555 ? x,y,z 1 C 1_555 ? x,y,z 1 D 1_555 ? x,y,z # loop_ _struct_conn.id _struct_conn.conn_type_id _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 covale1 covale ? C S . S ? ? ? 1_555 A +T 2 C4 ? ? A S 2 A +T 2 1_555 ? ? ? ? ? ? ? covale2 covale ? B CH3 . C ? ? ? 1_555 A +T 2 P ? ? A CH3 2 A +T 2 1_555 ? ? ? ? ? ? ? covale_base1 covale_base ? C S . S ? ? ? 1_555 A +T 2 C4 ? ? A S 2 A +T 2 1_555 ? ? ? ? ? ? ? covale_phosphate1 covale_phosphate ? B CH3 . C ? ? ? 1_555 A +T 2 P ? ? A CH3 2 A +T 2 1_555 ? ? ? ? ? ? ? modres1 modres ? A +T 2 ? ? ? T 1_555 ? ? ? ? ? ? A +T 2 ? ? ? 1_555 ? ? ? ? ? ? 'THYMINE MODIFIED WITH CH3-S' # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? covale_base ? ? covale_phosphate ? ? modres ? ? # _database_PDB_matrix.entry_id UDBA41 _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 UDBA41 _atom_sites.Cartn_transform_axes ? _atom_sites.fract_transf_matrix[1][1] 0.075523 _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] 0.072233 _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] 0.066916 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # _atom_sites_alt.id . _atom_sites_alt.details ? # loop_ _atom_type.symbol O C N P S # 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.Cartn_x_esd _atom_site.Cartn_y_esd _atom_site.Cartn_z_esd _atom_site.occupancy_esd _atom_site.B_iso_or_equiv_esd _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 O O5* . T A 1 1 ? 8.333 2.824 6.900 10.00 3.16 ? ? ? ? ? 1 T A O5* 1 ATOM 2 C C5* . T A 1 1 ? 8.060 1.815 5.880 10.00 3.32 ? ? ? ? ? 1 T A C5* 1 ATOM 3 C C4* . T A 1 1 ? 6.583 1.696 5.582 10.00 1.42 ? ? ? ? ? 1 T A C4* 1 ATOM 4 O O4* . T A 1 1 ? 5.886 1.060 6.710 10.00 2.05 ? ? ? ? ? 1 T A O4* 1 ATOM 5 C C3* . T A 1 1 ? 5.894 3.040 5.369 10.00 2.05 ? ? ? ? ? 1 T A C3* 1 ATOM 6 O O3* . T A 1 1 ? 4.935 2.935 4.252 10.00 1.66 ? ? ? ? ? 1 T A O3* 1 ATOM 7 C C2* . T A 1 1 ? 5.119 3.346 6.665 10.00 1.89 ? ? ? ? ? 1 T A C2* 1 ATOM 8 C C1* . T A 1 1 ? 4.939 1.944 7.303 10.00 2.13 ? ? ? ? ? 1 T A C1* 1 ATOM 9 N N1 . T A 1 1 ? 5.224 1.962 8.793 10.00 1.26 ? ? ? ? ? 1 T A N1 1 ATOM 10 C C2 . T A 1 1 ? 4.136 2.056 9.673 10.00 1.97 ? ? ? ? ? 1 T A C2 1 ATOM 11 O O2 . T A 1 1 ? 2.988 2.115 9.297 10.00 2.21 ? ? ? ? ? 1 T A O2 1 ATOM 12 N N3 . T A 1 1 ? 4.520 2.120 10.985 10.00 1.42 ? ? ? ? ? 1 T A N3 1 ATOM 13 C C4 . T A 1 1 ? 5.796 2.162 11.510 10.00 1.58 ? ? ? ? ? 1 T A C4 1 ATOM 14 O O4 . T A 1 1 ? 5.956 2.262 12.723 10.00 2.05 ? ? ? ? ? 1 T A O4 1 ATOM 15 C C5 . T A 1 1 ? 6.847 2.006 10.544 10.00 1.82 ? ? ? ? ? 1 T A C5 1 ATOM 16 C C5M . T A 1 1 ? 8.359 1.964 11.008 10.00 2.53 ? ? ? ? ? 1 T A C5M 1 ATOM 17 C C6 . T A 1 1 ? 6.526 1.946 9.238 10.00 1.58 ? ? ? ? ? 1 T A C6 1 ATOM 18 P P . +T A 1 2 ? 5.484 3.350 2.845 10.00 1.82 ? ? ? ? ? 2 +T A P 1 ATOM 19 O O1P . +T A 1 2 ? 6.873 2.892 2.585 10.00 2.29 ? ? ? ? ? 2 +T A O1P 1 ATOM 20 O O5* . +T A 1 2 ? 4.416 2.715 1.899 10.00 2.53 ? ? ? ? ? 2 +T A O5* 1 ATOM 21 C C5* . +T A 1 2 ? 4.765 1.765 0.853 10.00 2.21 ? ? ? ? ? 2 +T A C5* 1 ATOM 22 C C4* . +T A 1 2 ? 3.564 1.551 -0.048 10.00 1.89 ? ? ? ? ? 2 +T A C4* 1 ATOM 23 O O4* . +T A 1 2 ? 2.529 0.885 0.671 10.00 1.42 ? ? ? ? ? 2 +T A O4* 1 ATOM 24 C C3* . +T A 1 2 ? 2.951 2.866 -0.665 10.00 1.74 ? ? ? ? ? 2 +T A C3* 1 ATOM 25 O O3* . +T A 1 2 ? 2.492 2.502 -1.982 10.00 1.42 ? ? ? ? ? 2 +T A O3* 1 ATOM 26 C C2* . +T A 1 2 ? 1.770 3.075 0.263 10.00 1.50 ? ? ? ? ? 2 +T A C2* 1 ATOM 27 C C1* . +T A 1 2 ? 1.321 1.649 0.556 10.00 1.74 ? ? ? ? ? 2 +T A C1* 1 ATOM 28 N N1 . +T A 1 2 ? 0.564 1.501 1.829 10.00 1.42 ? ? ? ? ? 2 +T A N1 1 ATOM 29 C C2 . +T A 1 2 ? -0.809 1.469 1.728 10.00 1.26 ? ? ? ? ? 2 +T A C2 1 ATOM 30 O O2 . +T A 1 2 ? -1.410 1.503 0.666 10.00 2.21 ? ? ? ? ? 2 +T A O2 1 ATOM 31 N N3 . +T A 1 2 ? -1.447 1.377 2.922 10.00 1.42 ? ? ? ? ? 2 +T A N3 1 ATOM 32 C C4 . +T A 1 2 ? -0.826 1.376 4.172 10.00 2.21 ? ? ? ? ? 2 +T A C4 1 ATOM 33 C C5 . +T A 1 2 ? 0.592 1.423 4.177 10.00 1.58 ? ? ? ? ? 2 +T A C5 1 ATOM 34 C C5M . +T A 1 2 ? 1.341 1.382 5.474 10.00 2.61 ? ? ? ? ? 2 +T A C5M 1 ATOM 35 C C6 . +T A 1 2 ? 1.194 1.492 3.029 10.00 1.89 ? ? ? ? ? 2 +T A C6 1 HETATM 36 C C . CH3 B 2 . ? 5.277 5.135 2.714 10.00 2.61 ? ? ? ? ? 2 CH3 A C 1 HETATM 37 S S . S C 3 . ? -1.793 1.290 5.538 10.00 2.61 ? ? ? ? ? 2 S A S 1 HETATM 38 C C . MOH D 4 . ? 8.726 0.223 1.260 10.00 3.95 ? ? ? ? ? 3 MOH ? C 1 HETATM 39 O O . MOH D 4 . ? 8.931 0.946 2.494 10.00 2.92 ? ? ? ? ? 3 MOH ? O 1 # _atom_site_anisotrop.id ? _atom_site_anisotrop.type_symbol ? _atom_site_anisotrop.pdbx_label_atom_id ? _atom_site_anisotrop.pdbx_label_alt_id ? _atom_site_anisotrop.pdbx_label_comp_id ? _atom_site_anisotrop.pdbx_label_asym_id ? _atom_site_anisotrop.pdbx_label_seq_id ? _atom_site_anisotrop.U[1][1] ? _atom_site_anisotrop.U[1][2] ? _atom_site_anisotrop.U[1][3] ? _atom_site_anisotrop.U[2][2] ? _atom_site_anisotrop.U[2][3] ? _atom_site_anisotrop.U[3][3] ? _atom_site_anisotrop.U[1][1]_esd ? _atom_site_anisotrop.U[1][2]_esd ? _atom_site_anisotrop.U[1][3]_esd ? _atom_site_anisotrop.U[2][2]_esd ? _atom_site_anisotrop.U[2][3]_esd ? _atom_site_anisotrop.U[3][3]_esd ? _atom_site_anisotrop.pdbx_auth_seq_id ? _atom_site_anisotrop.pdbx_auth_comp_id ? _atom_site_anisotrop.pdbx_auth_asym_id ? # 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 A 1 1 +T 1 1 1 T T A A 1 2 +T 2 2 2 +T +T A #