data_URB020 # _entry.id URB020 # _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 URB020 _database.code_CSD ADURPO10 # loop_ _database_2.database_id _database_2.database_code NDB URB020 RCSB URB020 # 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 1994-10-04 1994-10-04 ? ? 0 2 2001-09-21 ? ? ? 5 # loop_ _audit_author.name 'Shefter, E.' 'Barlow, M.' 'Sparks, R.A.' 'Trueblood, K.N.' # _citation.id primary _citation.title ;The Crystal and Molecular Structure of a Dinucleoside Phosphate: Beta- Adenosine-2'-Beta-Uridine-5'-Phosphoric Acid ; _citation.journal_abbrev 'Acta Crystallogr.,Sect.B' _citation.journal_volume 25 _citation.page_first 895 _citation.page_last 909 _citation.year 1969 _citation.journal_id_ASTM ASBSDK _citation.country DK _citation.journal_id_ISSN 0108-7681 _citation.journal_id_CSD 0622 _citation.book_publisher ? # loop_ _citation_author.citation_id _citation_author.name primary 'Shefter, E.' primary 'Barlow, M.' primary 'Sparks, R.A.' primary 'Trueblood, K.N.' # _cell.entry_id URB020 _cell.length_a 9.783 _cell.length_b 16.013 _cell.length_c 8.718 _cell.angle_alpha 90.00 _cell.angle_beta 90.79 _cell.angle_gamma 90.00 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id URB020 _symmetry.space_group_name_H-M 'P 1 21 1' _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 ;RNA (5'-R(*AP*U)-3') ; 590.419 1 ? 2 water nat water 18.015 3 ? # _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 A 1 2 U # 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 P1' 347.224 U 'RNA linking' y 'URIDINE-5'-MONOPHOSPHATE' ? 'C9 H13 N2 O9 P1' 324.183 HOH non-polymer . WATER ? 'H2 O1' 18.015 # _exptl.entry_id URB020 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number ? # _exptl_crystal.id 1 _exptl_crystal.density_meas 1.5600 _exptl_crystal.density_Matthews ? _exptl_crystal.density_percent_sol ? _exptl_crystal.description ? # _exptl_crystal_grow_comp.crystal_id 1 _exptl_crystal_grow_comp.id 1 _exptl_crystal_grow_comp.sol_id 2 _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 'OSCILLATION CAMERA' _diffrn_detector.type WEISSENBERG _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 1.5400 # _diffrn_source.diffrn_id 1 _diffrn_source.source ? _diffrn_source.type ? _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? # _computing.entry_id URB020 _computing.data_collection ? _computing.data_reduction ? _computing.structure_solution ? _computing.structure_refinement ? _computing.pdbx_structure_refinement_method 'LEAST SQUARES' # _refine.entry_id URB020 _refine.ls_number_reflns_obs 1781 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _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 0.0600000 _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 39 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 3 _refine_hist.number_atoms_total 42 _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 URB020 _struct.title ;THE CRYSTAL AND MOLECULAR STRUCTURE OF A DINUCLEOSIDE PHOSPHATE: BETA-ADENOSINE-2'-BETA-URIDINE-5'-PHOSPHORIC ACI ; _struct.pdbx_model_details ? # _struct_keywords.entry_id URB020 _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'U-RNA, SINGLE STRAND, OPEN' # 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 URB020 _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 URB020 _atom_sites.Cartn_transform_axes ? _atom_sites.fract_transf_matrix[1][1] 0.102218 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.001409 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.062449 _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] 0.114716 _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* . A A 1 1 ? 0.637 3.456 5.458 1.00 10.00 ? ? ? ? ? 1 A A O5* 1 ATOM 2 C C5* . A A 1 1 ? 0.370 2.743 6.677 1.00 10.00 ? ? ? ? ? 1 A A C5* 1 ATOM 3 C C4* . A A 1 1 ? -0.238 1.400 6.407 1.00 10.00 ? ? ? ? ? 1 A A C4* 1 ATOM 4 O O4* . A A 1 1 ? -1.612 1.614 5.974 1.00 10.00 ? ? ? ? ? 1 A A O4* 1 ATOM 5 C C3* . A A 1 1 ? 0.448 0.568 5.270 1.00 10.00 ? ? ? ? ? 1 A A C3* 1 ATOM 6 O O3* . A A 1 1 ? 0.323 -0.826 5.590 1.00 10.00 ? ? ? ? ? 1 A A O3* 1 ATOM 7 C C2* . A A 1 1 ? -0.493 0.868 4.124 1.00 10.00 ? ? ? ? ? 1 A A C2* 1 ATOM 8 O O2* . A A 1 1 ? -0.477 -0.167 3.136 1.00 10.00 ? ? ? ? ? 1 A A O2* 1 ATOM 9 C C1* . A A 1 1 ? -1.839 0.884 4.786 1.00 10.00 ? ? ? ? ? 1 A A C1* 1 ATOM 10 N N9 . A A 1 1 ? -2.923 1.512 4.065 1.00 10.00 ? ? ? ? ? 1 A A N9 1 ATOM 11 C C8 . A A 1 1 ? -3.052 2.839 3.654 1.00 10.00 ? ? ? ? ? 1 A A C8 1 ATOM 12 N N7 . A A 1 1 ? -4.179 3.047 3.013 1.00 10.00 ? ? ? ? ? 1 A A N7 1 ATOM 13 C C5 . A A 1 1 ? -4.793 1.803 2.962 1.00 10.00 ? ? ? ? ? 1 A A C5 1 ATOM 14 C C6 . A A 1 1 ? -6.005 1.396 2.389 1.00 10.00 ? ? ? ? ? 1 A A C6 1 ATOM 15 N N6 . A A 1 1 ? -6.829 2.165 1.701 1.00 10.00 ? ? ? ? ? 1 A A N6 1 ATOM 16 N N1 . A A 1 1 ? -6.284 0.070 2.588 1.00 10.00 ? ? ? ? ? 1 A A N1 1 ATOM 17 C C2 . A A 1 1 ? -5.469 -0.773 3.255 1.00 10.00 ? ? ? ? ? 1 A A C2 1 ATOM 18 N N3 . A A 1 1 ? -4.332 -0.444 3.806 1.00 10.00 ? ? ? ? ? 1 A A N3 1 ATOM 19 C C4 . A A 1 1 ? -4.023 0.857 3.611 1.00 10.00 ? ? ? ? ? 1 A A C4 1 ATOM 20 P P . U A 1 2 ? 0.012 0.035 1.633 1.00 10.00 ? ? ? ? ? 2 U A P 1 ATOM 21 O O1P . U A 1 2 ? 1.207 -0.889 1.486 1.00 10.00 ? ? ? ? ? 2 U A O1P 1 ATOM 22 O O2P . U A 1 2 ? 0.198 1.459 1.281 1.00 10.00 ? ? ? ? ? 2 U A O2P 1 ATOM 23 O O5* . U A 1 2 ? -1.207 -0.527 0.788 1.00 10.00 ? ? ? ? ? 2 U A O5* 1 ATOM 24 C C5* . U A 1 2 ? -1.846 -1.809 1.115 1.00 10.00 ? ? ? ? ? 2 U A C5* 1 ATOM 25 C C4* . U A 1 2 ? -3.102 -1.925 0.297 1.00 10.00 ? ? ? ? ? 2 U A C4* 1 ATOM 26 O O4* . U A 1 2 ? -4.004 -0.847 0.658 1.00 10.00 ? ? ? ? ? 2 U A O4* 1 ATOM 27 C C3* . U A 1 2 ? -2.998 -1.825 -1.216 1.00 10.00 ? ? ? ? ? 2 U A C3* 1 ATOM 28 O O3* . U A 1 2 ? -2.660 -3.026 -1.861 1.00 10.00 ? ? ? ? ? 2 U A O3* 1 ATOM 29 C C2* . U A 1 2 ? -4.413 -1.392 -1.614 1.00 10.00 ? ? ? ? ? 2 U A C2* 1 ATOM 30 O O2* . U A 1 2 ? -5.330 -2.474 -1.489 1.00 10.00 ? ? ? ? ? 2 U A O2* 1 ATOM 31 C C1* . U A 1 2 ? -4.729 -0.431 -0.472 1.00 10.00 ? ? ? ? ? 2 U A C1* 1 ATOM 32 N N1 . U A 1 2 ? -4.361 0.980 -0.811 1.00 10.00 ? ? ? ? ? 2 U A N1 1 ATOM 33 C C2 . U A 1 2 ? -5.133 1.619 -1.726 1.00 10.00 ? ? ? ? ? 2 U A C2 1 ATOM 34 O O2 . U A 1 2 ? -6.065 1.068 -2.321 1.00 10.00 ? ? ? ? ? 2 U A O2 1 ATOM 35 N N3 . U A 1 2 ? -4.764 2.921 -2.005 1.00 10.00 ? ? ? ? ? 2 U A N3 1 ATOM 36 C C4 . U A 1 2 ? -3.726 3.640 -1.378 1.00 10.00 ? ? ? ? ? 2 U A C4 1 ATOM 37 O O4 . U A 1 2 ? -3.480 4.773 -1.761 1.00 10.00 ? ? ? ? ? 2 U A O4 1 ATOM 38 C C5 . U A 1 2 ? -3.047 2.908 -0.342 1.00 10.00 ? ? ? ? ? 2 U A C5 1 ATOM 39 C C6 . U A 1 2 ? -3.352 1.637 -0.110 1.00 10.00 ? ? ? ? ? 2 U A C6 1 HETATM 40 O O . HOH B 2 . ? 3.297 4.287 -3.781 1.00 10.00 ? ? ? ? ? 3 HOH ? O 1 HETATM 41 O O . HOH B 2 . ? -1.759 6.008 1.017 1.00 10.00 ? ? ? ? ? 4 HOH ? O 1 HETATM 42 O O . HOH B 2 . ? -1.215 5.223 -3.748 1.00 10.00 ? ? ? ? ? 5 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 A 1 1 1 A A A A 1 2 U 2 2 2 U U A #