data_UDB021 # _entry.id UDB021 # _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 UDB021 _database.code_CSD ? # loop_ _database_2.database_id _database_2.database_code NDB UDB021 RCSB UDB021 # 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 1995-10-26 1995-10-26 ? ? 0 2 2001-09-21 ? ? ? 5 # loop_ _audit_author.name 'Krishnan, R.' 'Seshadri, T.P.' # _citation.id primary _citation.title ;Crystal Structure of Guanylyl-2',5'-Cytidine Dihydrate: An Analogue of msDNA- RNA Junction in Stigmatella aurantiaca ; _citation.journal_abbrev Biopolymers _citation.journal_volume 34 _citation.page_first 1637 _citation.page_last 1646 _citation.year 1994 _citation.journal_id_ASTM BIPMAA _citation.country US _citation.journal_id_ISSN 0006-3525 _citation.journal_id_CSD 0161 _citation.book_publisher ? # loop_ _citation_author.citation_id _citation_author.name primary 'Krishnan, R.' primary 'Seshadri, T.P.' # _cell.entry_id UDB021 _cell.length_a 8.376 _cell.length_b 16.231 _cell.length_c 18.671 _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 UDB021 _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 nat ;DNA (5'-D(*GP*)-2'-5'-R(*C)-3') ; 605.434 1 ? 2 water nat water 18.015 2 ? # _entity_poly.entity_id 1 _entity_poly.type polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id 1 1 G 1 2 C # 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 G 'RNA linking' y 'GUANOSINE-5'-MONOPHOSPHATE' ? 'C10 H14 N5 O8 P1' 363.223 C 'RNA linking' y 'CYTIDINE-5'-MONOPHOSPHATE' ? 'C9 H14 N3 O8 P1' 323.199 HOH non-polymer . WATER ? 'H2 O1' 18.015 # _exptl.entry_id UDB021 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number ? # _exptl_crystal.id 1 _exptl_crystal.density_meas 1.6200 _exptl_crystal.density_Matthews ? _exptl_crystal.density_percent_sol ? _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 4.50 _exptl_crystal_grow.pdbx_details ? _exptl_crystal_grow.pdbx_pH_range ? # _exptl_crystal_grow_comp.crystal_id 1 _exptl_crystal_grow_comp.id 1 _exptl_crystal_grow_comp.sol_id 1 _exptl_crystal_grow_comp.name WATER _exptl_crystal_grow_comp.volume 1 _exptl_crystal_grow_comp.conc 2 _exptl_crystal_grow_comp.details 3 # _diffrn.id 1 _diffrn.ambient_temp ? _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector DIFFRACTOMETER _diffrn_detector.type 'ENRAF-NONIUS CAD4' _diffrn_detector.pdbx_collection_date ? _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' # _diffrn_radiation_wavelength.id 1 # _diffrn_source.diffrn_id 1 _diffrn_source.source ? _diffrn_source.type ? _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? # _reflns.entry_id UDB021 _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F 3.000 _reflns.d_resolution_low ? _reflns.d_resolution_high 0.850 _reflns.number_obs 1699 _reflns.number_all 2354 _reflns.percent_possible_obs ? _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_av_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy ? _reflns.R_free_details ? # _refine.entry_id UDB021 _refine.ls_number_reflns_obs 1699 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 3.000 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low ? _refine.ls_d_res_high 0.850 _refine.ls_percent_reflns_obs ? _refine.ls_R_factor_obs 0.0540000 _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 40 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 2 _refine_hist.number_atoms_total 42 _refine_hist.d_res_high 0.850 _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 UDB021 _struct.title ;CRYSTAL STRUCTURE OF GUANYLYL-2',5'-CYTIDINE DIHYDRATE: AN ANALOGUE OF MSDNA-RNA JUNCTION IN STIGMATELLA AURANTIACA ; _struct.pdbx_model_details ? # _struct_keywords.entry_id UDB021 _struct_keywords.pdbx_keywords DNA _struct_keywords.text ;U-DNA, SINGLE STRAND, 2'-5' PHOSPHODIESTER BOND ; # loop_ _struct_asym.id _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N 1 ? B N 2 ? # _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 # _database_PDB_matrix.entry_id UDB021 _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 UDB021 _atom_sites.Cartn_transform_axes ? _atom_sites.fract_transf_matrix[1][1] 0.119389 _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] 0.061610 _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] 0.053559 _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 # 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* . G A 1 1 ? -0.888 -5.614 -2.308 1.00 3.60 ? ? ? ? ? 1 G A O5* 1 ATOM 2 C C5* . G A 1 1 ? -1.491 -4.595 -1.510 1.00 2.80 ? ? ? ? ? 1 G A C5* 1 ATOM 3 C C4* . G A 1 1 ? -2.195 -5.145 -0.344 1.00 2.20 ? ? ? ? ? 1 G A C4* 1 ATOM 4 O O4* . G A 1 1 ? -3.325 -5.968 -0.771 1.00 2.70 ? ? ? ? ? 1 G A O4* 1 ATOM 5 C C3* . G A 1 1 ? -1.365 -6.069 0.575 1.00 2.10 ? ? ? ? ? 1 G A C3* 1 ATOM 6 O O3* . G A 1 1 ? -1.809 -5.989 1.912 1.00 3.10 ? ? ? ? ? 1 G A O3* 1 ATOM 7 C C2* . G A 1 1 ? -1.717 -7.447 0.039 1.00 1.90 ? ? ? ? ? 1 G A C2* 1 ATOM 8 O O2* . G A 1 1 ? -1.533 -8.505 0.975 1.00 2.00 ? ? ? ? ? 1 G A O2* 1 ATOM 9 C C1* . G A 1 1 ? -3.191 -7.278 -0.260 1.00 2.20 ? ? ? ? ? 1 G A C1* 1 ATOM 10 N N9 . G A 1 1 ? -3.736 -8.213 -1.210 1.00 2.10 ? ? ? ? ? 1 G A N9 1 ATOM 11 C C8 . G A 1 1 ? -4.649 -9.222 -0.907 1.00 2.70 ? ? ? ? ? 1 G A C8 1 ATOM 12 N N7 . G A 1 1 ? -4.900 -10.002 -1.906 1.00 3.20 ? ? ? ? ? 1 G A N7 1 ATOM 13 C C5 . G A 1 1 ? -4.146 -9.487 -2.944 1.00 2.40 ? ? ? ? ? 1 G A C5 1 ATOM 14 C C6 . G A 1 1 ? -4.020 -9.903 -4.292 1.00 3.00 ? ? ? ? ? 1 G A C6 1 ATOM 15 O O6 . G A 1 1 ? -4.573 -10.859 -4.897 1.00 3.20 ? ? ? ? ? 1 G A O6 1 ATOM 16 N N1 . G A 1 1 ? -3.183 -9.068 -5.034 1.00 2.40 ? ? ? ? ? 1 G A N1 1 ATOM 17 C C2 . G A 1 1 ? -2.463 -8.016 -4.526 1.00 2.00 ? ? ? ? ? 1 G A C2 1 ATOM 18 N N2 . G A 1 1 ? -1.625 -7.406 -5.409 1.00 3.90 ? ? ? ? ? 1 G A N2 1 ATOM 19 N N3 . G A 1 1 ? -2.555 -7.633 -3.275 1.00 1.90 ? ? ? ? ? 1 G A N3 1 ATOM 20 C C4 . G A 1 1 ? -3.401 -8.385 -2.521 1.00 2.00 ? ? ? ? ? 1 G A C4 1 ATOM 21 P P . C A 1 2 ? -0.204 -9.382 0.935 1.00 1.90 ? ? ? ? ? 2 C A P 1 ATOM 22 O O1P . C A 1 2 ? -0.410 -10.425 1.981 1.00 2.60 ? ? ? ? ? 2 C A O1P 1 ATOM 23 O O2P . C A 1 2 ? 0.997 -8.494 1.049 1.00 2.90 ? ? ? ? ? 2 C A O2P 1 ATOM 24 O O5* . C A 1 2 ? -0.159 -9.993 -0.517 1.00 2.20 ? ? ? ? ? 2 C A O5* 1 ATOM 25 C C5* . C A 1 2 ? -1.047 -11.071 -0.808 1.00 3.10 ? ? ? ? ? 2 C A C5* 1 ATOM 26 C C4* . C A 1 2 ? -0.745 -11.594 -2.241 1.00 2.10 ? ? ? ? ? 2 C A C4* 1 ATOM 27 O O4* . C A 1 2 ? -0.997 -10.544 -3.217 1.00 2.20 ? ? ? ? ? 2 C A O4* 1 ATOM 28 C C3* . C A 1 2 ? 0.678 -11.990 -2.545 1.00 1.90 ? ? ? ? ? 2 C A C3* 1 ATOM 29 O O3* . C A 1 2 ? 1.005 -13.248 -1.979 1.00 3.10 ? ? ? ? ? 2 C A O3* 1 ATOM 30 C C2* . C A 1 2 ? 0.712 -11.920 -4.063 1.00 2.10 ? ? ? ? ? 2 C A C2* 1 ATOM 31 O O2* . C A 1 2 ? 0.050 -13.076 -4.554 1.00 2.50 ? ? ? ? ? 2 C A O2* 1 ATOM 32 C C1* . C A 1 2 ? -0.142 -10.683 -4.317 1.00 2.20 ? ? ? ? ? 2 C A C1* 1 ATOM 33 N N1 . C A 1 2 ? 0.653 -9.453 -4.479 1.00 2.20 ? ? ? ? ? 2 C A N1 1 ATOM 34 C C2 . C A 1 2 ? 1.148 -9.185 -5.725 1.00 2.40 ? ? ? ? ? 2 C A C2 1 ATOM 35 O O2 . C A 1 2 ? 0.921 -9.901 -6.694 1.00 3.30 ? ? ? ? ? 2 C A O2 1 ATOM 36 N N3 . C A 1 2 ? 1.952 -8.042 -5.870 1.00 2.20 ? ? ? ? ? 2 C A N3 1 ATOM 37 C C4 . C A 1 2 ? 2.211 -7.195 -4.843 1.00 2.00 ? ? ? ? ? 2 C A C4 1 ATOM 38 N N4 . C A 1 2 ? 3.007 -6.182 -5.077 1.00 2.90 ? ? ? ? ? 2 C A N4 1 ATOM 39 C C5 . C A 1 2 ? 1.625 -7.457 -3.583 1.00 2.30 ? ? ? ? ? 2 C A C5 1 ATOM 40 C C6 . C A 1 2 ? 0.888 -8.573 -3.441 1.00 2.10 ? ? ? ? ? 2 C A C6 1 HETATM 41 O O . HOH B 2 . ? -4.908 -4.528 -2.752 1.00 4.60 ? ? ? ? ? 3 HOH ? O 1 HETATM 42 O O . HOH B 2 . ? 2.027 -6.272 -0.232 1.00 6.20 ? ? ? ? ? 4 HOH ? 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 G 1 1 1 G G A A 1 2 C 2 2 2 C C A #