data_1O56
#
_entry.id 1O56
#
_audit_conform.dict_name mmcif_pdbx.dic
_audit_conform.dict_version 5.383
_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 1O56 pdb_00001o56 10.2210/pdb1o56/pdb
NDB UD0039 ? ?
RCSB rcsb001816 ? ?
WWPDB D_1000001816 ? ?
#
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 2003-08-26
2 'Structure model' 1 1 2008-04-26
3 'Structure model' 1 2 2011-07-13
4 'Structure model' 1 3 2011-11-16
5 'Structure model' 1 4 2017-10-04
6 'Structure model' 1 5 2023-12-27
#
_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' 'Atomic model'
4 5 'Structure model' 'Refinement description'
5 6 'Structure model' 'Data collection'
6 6 '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 5 'Structure model' software
2 6 'Structure model' chem_comp_atom
3 6 'Structure model' chem_comp_bond
4 6 '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 6 'Structure model' '_database_2.pdbx_DOI'
2 6 'Structure model' '_database_2.pdbx_database_accession'
#
_pdbx_database_PDB_obs_spr.id SPRSDE
_pdbx_database_PDB_obs_spr.pdb_id 1O56
_pdbx_database_PDB_obs_spr.replace_pdb_id 416d
_pdbx_database_PDB_obs_spr.date 2003-08-26
_pdbx_database_PDB_obs_spr.details ?
#
_pdbx_database_status.status_code REL
_pdbx_database_status.entry_id 1O56
_pdbx_database_status.recvd_initial_deposition_date 2003-08-20
_pdbx_database_status.deposit_site RCSB
_pdbx_database_status.process_site RCSB
_pdbx_database_status.status_code_sf ?
_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.methods_development_category ?
_pdbx_database_status.status_code_nmr_data ?
#
loop_
_audit_author.name
_audit_author.pdbx_ordinal
'Gao, Y.G.' 1
'Robinson, H.' 2
'Guan, Y.' 3
'Liaw, Y.C.' 4
'van Boom, J.H.' 5
'van der Marel, G.A.' 6
'Wang, A.H.' 7
#
_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
_citation_author.identifier_ORCID
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 ?
#
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 syn
;DNA (5'-CD(*AP*AP*AP*)-3')
;
894.663 2 ? ? ? ?
2 water nat water 18.015 13 ? ? ? ?
#
_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 '(DA)(DA)(DA)'
_entity_poly.pdbx_seq_one_letter_code_can AAA
_entity_poly.pdbx_strand_id A,B
_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 DA n
1 2 DA n
1 3 DA n
#
_pdbx_entity_src_syn.entity_id 1
_pdbx_entity_src_syn.pdbx_src_id 1
_pdbx_entity_src_syn.pdbx_alt_source_flag sample
_pdbx_entity_src_syn.pdbx_beg_seq_num ?
_pdbx_entity_src_syn.pdbx_end_seq_num ?
_pdbx_entity_src_syn.organism_scientific ?
_pdbx_entity_src_syn.organism_common_name ?
_pdbx_entity_src_syn.ncbi_taxonomy_id ?
_pdbx_entity_src_syn.details Synthetic
#
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
DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222
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 DA 1 1 1 DA A A . n
A 1 2 DA 2 2 ? ? ? A . n
A 1 3 DA 3 3 ? ? ? A . n
B 1 1 DA 1 2 2 DA A B . n
B 1 2 DA 2 3 ? ? ? B . n
B 1 3 DA 3 4 ? ? ? B . 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
C 2 HOH 1 4 3 HOH HOH A .
C 2 HOH 2 5 4 HOH HOH A .
C 2 HOH 3 6 5 HOH HOH A .
C 2 HOH 4 7 6 HOH HOH A .
C 2 HOH 5 8 7 HOH HOH A .
C 2 HOH 6 9 8 HOH HOH A .
C 2 HOH 7 10 10 HOH HOH A .
C 2 HOH 8 11 11 HOH HOH A .
C 2 HOH 9 12 12 HOH HOH A .
C 2 HOH 10 13 13 HOH HOH A .
C 2 HOH 11 14 14 HOH HOH A .
C 2 HOH 12 15 15 HOH HOH A .
D 2 HOH 1 9 9 HOH HOH B .
#
loop_
_software.name
_software.classification
_software.version
_software.citation_id
_software.pdbx_ordinal
SHELXS phasing . ? 1
SHELXL-97 refinement . ? 2
#
_cell.entry_id 1O56
_cell.length_a 23.328
_cell.length_b 23.328
_cell.length_c 9.680
_cell.angle_alpha 90.00
_cell.angle_beta 90.00
_cell.angle_gamma 120.00
_cell.Z_PDB 6
_cell.pdbx_unique_axis ?
_cell.length_a_esd ?
_cell.length_b_esd ?
_cell.length_c_esd ?
_cell.angle_alpha_esd ?
_cell.angle_beta_esd ?
_cell.angle_gamma_esd ?
#
_symmetry.entry_id 1O56
_symmetry.space_group_name_H-M 'P 3'
_symmetry.pdbx_full_space_group_name_H-M ?
_symmetry.cell_setting ?
_symmetry.Int_Tables_number 143
_symmetry.space_group_name_Hall ?
#
_exptl.entry_id 1O56
_exptl.method 'X-RAY DIFFRACTION'
_exptl.crystals_number 1
#
_exptl_crystal.id 1
_exptl_crystal.density_meas ?
_exptl_crystal.density_Matthews 1.41
_exptl_crystal.density_percent_sol 42.0000
_exptl_crystal.description ?
_exptl_crystal.F_000 ?
_exptl_crystal.preparation ?
#
_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 'pH 4.50, VAPOR DIFFUSION, HANGING DROP, temperature 298.00K'
_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 MPD ? ? ?
1 2 1 GLYCINE ? ? ?
1 3 1 MGCL2 ? ? ?
1 4 2 MPD ? ? ?
#
_diffrn.id 1
_diffrn.ambient_temp 298.00
_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 '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 'RIGAKU RU200'
_diffrn_source.pdbx_synchrotron_site ?
_diffrn_source.pdbx_synchrotron_beamline ?
_diffrn_source.pdbx_wavelength ?
_diffrn_source.pdbx_wavelength_list ?
#
_reflns.entry_id 1O56
_reflns.observed_criterion_sigma_I ?
_reflns.observed_criterion_sigma_F 3.000
_reflns.d_resolution_low 10.000
_reflns.d_resolution_high 0.900
_reflns.number_obs 3059
_reflns.number_all ?
_reflns.percent_possible_obs ?
_reflns.pdbx_Rmerge_I_obs ?
_reflns.pdbx_Rsym_value ?
_reflns.pdbx_netI_over_sigmaI ?
_reflns.B_iso_Wilson_estimate ?
_reflns.pdbx_redundancy ?
_reflns.R_free_details ?
_reflns.pdbx_chi_squared ?
_reflns.pdbx_scaling_rejects ?
_reflns.pdbx_diffrn_id 1
_reflns.pdbx_ordinal 1
#
_refine.entry_id 1O56
_refine.ls_number_reflns_obs 3059
_refine.ls_number_reflns_all 3059
_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 10.000
_refine.ls_d_res_high 0.900
_refine.ls_percent_reflns_obs ?
_refine.ls_R_factor_obs ?
_refine.ls_R_factor_all 0.109
_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.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.ls_wR_factor_R_free ?
_refine.ls_wR_factor_R_work ?
_refine.overall_FOM_free_R_set ?
_refine.overall_FOM_work_R_set ?
_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 42
_refine_hist.pdbx_number_atoms_ligand 0
_refine_hist.number_atoms_solvent 13
_refine_hist.number_atoms_total 55
_refine_hist.d_res_high 0.900
_refine_hist.d_res_low 10.000
#
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
s_bond_d 0.032 ? ? ? 'X-RAY DIFFRACTION' ?
s_angle_d ? ? ? ? '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 1O56
_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 0.109
_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.number_reflns_obs_no_cutoff ?
_pdbx_refine.pdbx_refine_id 'X-RAY DIFFRACTION'
_pdbx_refine.free_R_error_no_cutoff ?
#
_database_PDB_matrix.entry_id 1O56
_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 1O56
_struct.title 'MOLECULAR STRUCTURE OF TWO CRYSTAL FORMS OF CYCLIC TRIADENYLIC ACID AT 1 ANGSTROM RESOLUTION'
_struct.pdbx_model_details ?
_struct.pdbx_CASP_flag ?
_struct.pdbx_model_type_details ?
#
_struct_keywords.entry_id 1O56
_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 2 ?
#
_struct_ref.id 1
_struct_ref.entity_id 1
_struct_ref.db_name PDB
_struct_ref.db_code 1O56
_struct_ref.pdbx_db_accession 1O56
_struct_ref.pdbx_db_isoform ?
_struct_ref.pdbx_seq_one_letter_code ?
_struct_ref.pdbx_align_begin ?
#
loop_
_struct_ref_seq.align_id
_struct_ref_seq.ref_id
_struct_ref_seq.pdbx_PDB_id_code
_struct_ref_seq.pdbx_strand_id
_struct_ref_seq.seq_align_beg
_struct_ref_seq.pdbx_seq_align_beg_ins_code
_struct_ref_seq.seq_align_end
_struct_ref_seq.pdbx_seq_align_end_ins_code
_struct_ref_seq.pdbx_db_accession
_struct_ref_seq.db_align_beg
_struct_ref_seq.pdbx_db_align_beg_ins_code
_struct_ref_seq.db_align_end
_struct_ref_seq.pdbx_db_align_end_ins_code
_struct_ref_seq.pdbx_auth_seq_align_beg
_struct_ref_seq.pdbx_auth_seq_align_end
1 1 1O56 A 1 ? 3 ? 1O56 1 ? 3 ? 1 3
2 1 1O56 B 1 ? 3 ? 1O56 2 ? 4 ? 2 4
#
loop_
_pdbx_struct_assembly.id
_pdbx_struct_assembly.details
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
1 author_defined_assembly ? trimeric 3
2 author_defined_assembly ? trimeric 3
#
loop_
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
_pdbx_struct_assembly_gen.asym_id_list
1 1,2,3 A,C
2 1,4,5 B,D
#
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_555 -y,x-y,z -0.5000000000 -0.8660254038 0.0000000000 0.0000000000 0.8660254038
-0.5000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000
3 'crystal symmetry operation' 3_555 -x+y,-x,z -0.5000000000 0.8660254038 0.0000000000 0.0000000000 -0.8660254038
-0.5000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000
4 'crystal symmetry operation' 2_655 -y+1,x-y,z -0.5000000000 -0.8660254038 0.0000000000 23.3280000000 0.8660254038
-0.5000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000
5 'crystal symmetry operation' 3_665 -x+y+1,-x+1,z -0.5000000000 0.8660254038 0.0000000000 11.6640000000 -0.8660254038
-0.5000000000 0.0000000000 20.2026406195 0.0000000000 0.0000000000 1.0000000000 0.0000000000
#
loop_
_struct_biol.id
_struct_biol.pdbx_parent_biol_id
_struct_biol.details
1 ? ?
2 ? ?
#
_pdbx_validate_close_contact.id 1
_pdbx_validate_close_contact.PDB_model_num 1
_pdbx_validate_close_contact.auth_atom_id_1 O
_pdbx_validate_close_contact.auth_asym_id_1 A
_pdbx_validate_close_contact.auth_comp_id_1 HOH
_pdbx_validate_close_contact.auth_seq_id_1 13
_pdbx_validate_close_contact.PDB_ins_code_1 ?
_pdbx_validate_close_contact.label_alt_id_1 ?
_pdbx_validate_close_contact.auth_atom_id_2 O
_pdbx_validate_close_contact.auth_asym_id_2 A
_pdbx_validate_close_contact.auth_comp_id_2 HOH
_pdbx_validate_close_contact.auth_seq_id_2 14
_pdbx_validate_close_contact.PDB_ins_code_2 ?
_pdbx_validate_close_contact.label_alt_id_2 ?
_pdbx_validate_close_contact.dist 2.17
#
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 B DA 2 ? ? 1_555 "O3'" B DA 2 ? ? 3_665 1.59
2 1 P A DA 1 ? ? 1_555 "O3'" A DA 1 ? ? 2_555 1.61
3 1 O A HOH 13 ? ? 1_555 O A HOH 15 ? ? 1_554 2.17
#
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 DA 1 ? ? "C4'" A DA 1 ? ? 1.557 1.512 0.045 0.007 N
2 1 N1 A DA 1 ? ? C2 A DA 1 ? ? 1.259 1.339 -0.080 0.009 N
3 1 C6 A DA 1 ? ? N1 A DA 1 ? ? 1.288 1.351 -0.063 0.007 N
4 1 N1 B DA 2 ? ? C2 B DA 2 ? ? 1.257 1.339 -0.082 0.009 N
5 1 C4 B DA 2 ? ? C5 B DA 2 ? ? 1.313 1.383 -0.070 0.007 N
6 1 C6 B DA 2 ? ? N1 B DA 2 ? ? 1.398 1.351 0.047 0.007 N
7 1 N7 B DA 2 ? ? C8 B DA 2 ? ? 1.359 1.311 0.048 0.007 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 "O4'" B DA 2 ? ? "C1'" B DA 2 ? ? N9 B DA 2 ? ? 110.10 108.30 1.80 0.30 N
2 1 C6 B DA 2 ? ? N1 B DA 2 ? ? C2 B DA 2 ? ? 113.54 118.60 -5.06 0.60 N
3 1 N1 B DA 2 ? ? C2 B DA 2 ? ? N3 B DA 2 ? ? 136.69 129.30 7.39 0.50 N
4 1 C4 B DA 2 ? ? C5 B DA 2 ? ? C6 B DA 2 ? ? 121.01 117.00 4.01 0.50 N
5 1 N9 B DA 2 ? ? C4 B DA 2 ? ? C5 B DA 2 ? ? 110.18 105.80 4.38 0.40 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 4 ? C HOH .
2 1 A HOH 5 ? C HOH .
3 1 A HOH 6 ? C HOH .
4 1 A HOH 12 ? C HOH .
#
_pdbx_database_remark.id 999
_pdbx_database_remark.text
;SEQUENCE
The crystallized entity is 5'-CD(*AP*AP*AP)-3', however,
each of the two independent molecules sits on the
crystallographic 3-fold axis. Remark 350 provides the way
to create cyclic D(*Ap*Ap*Ap) molecule.
;
#
loop_
_pdbx_unobs_or_zero_occ_residues.id
_pdbx_unobs_or_zero_occ_residues.PDB_model_num
_pdbx_unobs_or_zero_occ_residues.polymer_flag
_pdbx_unobs_or_zero_occ_residues.occupancy_flag
_pdbx_unobs_or_zero_occ_residues.auth_asym_id
_pdbx_unobs_or_zero_occ_residues.auth_comp_id
_pdbx_unobs_or_zero_occ_residues.auth_seq_id
_pdbx_unobs_or_zero_occ_residues.PDB_ins_code
_pdbx_unobs_or_zero_occ_residues.label_asym_id
_pdbx_unobs_or_zero_occ_residues.label_comp_id
_pdbx_unobs_or_zero_occ_residues.label_seq_id
1 1 Y 1 A DA 2 ? A DA 2
2 1 Y 1 A DA 3 ? A DA 3
3 1 Y 1 B DA 3 ? B DA 2
4 1 Y 1 B DA 4 ? B DA 3
#
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
DA OP3 O N N 1
DA P P N N 2
DA OP1 O N N 3
DA OP2 O N N 4
DA "O5'" O N N 5
DA "C5'" C N N 6
DA "C4'" C N R 7
DA "O4'" O N N 8
DA "C3'" C N S 9
DA "O3'" O N N 10
DA "C2'" C N N 11
DA "C1'" C N R 12
DA N9 N Y N 13
DA C8 C Y N 14
DA N7 N Y N 15
DA C5 C Y N 16
DA C6 C Y N 17
DA N6 N N N 18
DA N1 N Y N 19
DA C2 C Y N 20
DA N3 N Y N 21
DA C4 C Y N 22
DA HOP3 H N N 23
DA HOP2 H N N 24
DA "H5'" H N N 25
DA "H5''" H N N 26
DA "H4'" H N N 27
DA "H3'" H N N 28
DA "HO3'" H N N 29
DA "H2'" H N N 30
DA "H2''" H N N 31
DA "H1'" H N N 32
DA H8 H N N 33
DA H61 H N N 34
DA H62 H N N 35
DA H2 H N N 36
HOH O O N N 37
HOH H1 H N N 38
HOH H2 H N N 39
#
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
DA OP3 P sing N N 1
DA OP3 HOP3 sing N N 2
DA P OP1 doub N N 3
DA P OP2 sing N N 4
DA P "O5'" sing N N 5
DA OP2 HOP2 sing N N 6
DA "O5'" "C5'" sing N N 7
DA "C5'" "C4'" sing N N 8
DA "C5'" "H5'" sing N N 9
DA "C5'" "H5''" sing N N 10
DA "C4'" "O4'" sing N N 11
DA "C4'" "C3'" sing N N 12
DA "C4'" "H4'" sing N N 13
DA "O4'" "C1'" sing N N 14
DA "C3'" "O3'" sing N N 15
DA "C3'" "C2'" sing N N 16
DA "C3'" "H3'" sing N N 17
DA "O3'" "HO3'" sing N N 18
DA "C2'" "C1'" sing N N 19
DA "C2'" "H2'" sing N N 20
DA "C2'" "H2''" sing N N 21
DA "C1'" N9 sing N N 22
DA "C1'" "H1'" sing N N 23
DA N9 C8 sing Y N 24
DA N9 C4 sing Y N 25
DA C8 N7 doub Y N 26
DA C8 H8 sing N N 27
DA N7 C5 sing Y N 28
DA C5 C6 sing Y N 29
DA C5 C4 doub Y N 30
DA C6 N6 sing N N 31
DA C6 N1 doub Y N 32
DA N6 H61 sing N N 33
DA N6 H62 sing N N 34
DA N1 C2 sing Y N 35
DA C2 N3 doub Y N 36
DA C2 H2 sing N N 37
DA N3 C4 sing Y N 38
HOH O H1 sing N N 39
HOH O H2 sing N N 40
#
_atom_sites.entry_id 1O56
_atom_sites.fract_transf_matrix[1][1] 0.042867
_atom_sites.fract_transf_matrix[1][2] 0.024749
_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] 0.049498
_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] 0.103306
_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 . DA A 1 1 ? 0.421 4.039 -2.933 1.00 0.10 ? 1 DA A P 1
ATOM 2 O OP1 . DA A 1 1 ? 0.818 5.069 -3.901 1.00 0.16 ? 1 DA A OP1 1
ATOM 3 O OP2 . DA A 1 1 ? 0.311 4.338 -1.509 1.00 0.12 ? 1 DA A OP2 1
ATOM 4 O "O5'" . DA A 1 1 ? 1.400 2.800 -2.997 1.00 0.11 ? 1 DA A "O5'" 1
ATOM 5 C "C5'" . DA A 1 1 ? 1.801 2.311 -4.251 1.00 0.13 ? 1 DA A "C5'" 1
ATOM 6 C "C4'" . DA A 1 1 ? 2.995 1.329 -4.062 1.00 0.08 ? 1 DA A "C4'" 1
ATOM 7 O "O4'" . DA A 1 1 ? 4.119 2.107 -3.636 1.00 0.08 ? 1 DA A "O4'" 1
ATOM 8 C "C3'" . DA A 1 1 ? 2.825 0.234 -2.994 1.00 0.07 ? 1 DA A "C3'" 1
ATOM 9 O "O3'" . DA A 1 1 ? 3.486 -0.903 -3.541 1.00 0.09 ? 1 DA A "O3'" 1
ATOM 10 C "C2'" . DA A 1 1 ? 3.512 0.802 -1.757 1.00 0.09 ? 1 DA A "C2'" 1
ATOM 11 C "C1'" . DA A 1 1 ? 4.621 1.636 -2.392 1.00 0.09 ? 1 DA A "C1'" 1
ATOM 12 N N9 . DA A 1 1 ? 5.017 2.794 -1.636 1.00 0.08 ? 1 DA A N9 1
ATOM 13 C C8 . DA A 1 1 ? 4.355 3.964 -1.571 1.00 0.10 ? 1 DA A C8 1
ATOM 14 N N7 . DA A 1 1 ? 4.943 4.873 -0.817 1.00 0.10 ? 1 DA A N7 1
ATOM 15 C C5 . DA A 1 1 ? 6.031 4.196 -0.300 1.00 0.08 ? 1 DA A C5 1
ATOM 16 C C6 . DA A 1 1 ? 7.094 4.570 0.542 1.00 0.07 ? 1 DA A C6 1
ATOM 17 N N6 . DA A 1 1 ? 7.194 5.794 1.058 1.00 0.08 ? 1 DA A N6 1
ATOM 18 N N1 . DA A 1 1 ? 8.004 3.701 0.819 1.00 0.09 ? 1 DA A N1 1
ATOM 19 C C2 . DA A 1 1 ? 7.926 2.564 0.285 1.00 0.10 ? 1 DA A C2 1
ATOM 20 N N3 . DA A 1 1 ? 6.983 2.026 -0.522 1.00 0.10 ? 1 DA A N3 1
ATOM 21 C C4 . DA A 1 1 ? 6.068 2.946 -0.788 1.00 0.07 ? 1 DA A C4 1
ATOM 22 P P . DA B 1 1 ? 14.944 9.099 5.933 1.00 0.09 ? 2 DA B P 1
ATOM 23 O OP1 . DA B 1 1 ? 15.269 9.154 4.483 1.00 0.15 ? 2 DA B OP1 1
ATOM 24 O OP2 . DA B 1 1 ? 15.672 9.976 6.862 1.00 0.13 ? 2 DA B OP2 1
ATOM 25 O "O5'" . DA B 1 1 ? 13.348 9.362 5.980 1.00 0.10 ? 2 DA B "O5'" 1
ATOM 26 C "C5'" . DA B 1 1 ? 12.696 9.433 7.234 1.00 0.12 ? 2 DA B "C5'" 1
ATOM 27 C "C4'" . DA B 1 1 ? 11.318 9.990 7.024 1.00 0.10 ? 2 DA B "C4'" 1
ATOM 28 O "O4'" . DA B 1 1 ? 11.421 11.354 6.614 1.00 0.11 ? 2 DA B "O4'" 1
ATOM 29 C "C3'" . DA B 1 1 ? 10.430 9.273 5.987 1.00 0.10 ? 2 DA B "C3'" 1
ATOM 30 O "O3'" . DA B 1 1 ? 9.132 9.324 6.513 1.00 0.08 ? 2 DA B "O3'" 1
ATOM 31 C "C2'" . DA B 1 1 ? 10.633 10.186 4.785 1.00 0.09 ? 2 DA B "C2'" 1
ATOM 32 C "C1'" . DA B 1 1 ? 10.804 11.562 5.401 1.00 0.09 ? 2 DA B "C1'" 1
ATOM 33 N N9 . DA B 1 1 ? 11.568 12.473 4.612 1.00 0.09 ? 2 DA B N9 1
ATOM 34 C C8 . DA B 1 1 ? 12.900 12.477 4.536 1.00 0.15 ? 2 DA B C8 1
ATOM 35 N N7 . DA B 1 1 ? 13.380 13.505 3.788 1.00 0.12 ? 2 DA B N7 1
ATOM 36 C C5 . DA B 1 1 ? 12.238 14.069 3.280 1.00 0.10 ? 2 DA B C5 1
ATOM 37 C C6 . DA B 1 1 ? 12.104 15.166 2.454 1.00 0.12 ? 2 DA B C6 1
ATOM 38 N N6 . DA B 1 1 ? 13.096 15.851 1.925 1.00 0.14 ? 2 DA B N6 1
ATOM 39 N N1 . DA B 1 1 ? 10.788 15.546 2.175 1.00 0.11 ? 2 DA B N1 1
ATOM 40 C C2 . DA B 1 1 ? 9.927 14.827 2.742 1.00 0.13 ? 2 DA B C2 1
ATOM 41 N N3 . DA B 1 1 ? 9.928 13.794 3.511 1.00 0.11 ? 2 DA B N3 1
ATOM 42 C C4 . DA B 1 1 ? 11.185 13.473 3.789 1.00 0.10 ? 2 DA B C4 1
HETATM 43 O O . HOH C 2 . ? 0.000 0.000 -0.975 0.33 0.17 ? 4 HOH A O 1
HETATM 44 O O . HOH C 2 . ? 11.665 6.734 3.904 0.33 0.18 ? 5 HOH A O 1
HETATM 45 O O . HOH C 2 . ? 0.000 0.000 3.307 0.33 0.19 ? 6 HOH A O 1
HETATM 46 O O . HOH C 2 . ? 0.890 2.325 0.214 1.00 0.11 ? 7 HOH A O 1
HETATM 47 O O . HOH C 2 . ? 9.230 7.154 2.752 1.00 0.10 ? 8 HOH A O 1
HETATM 48 O O . HOH C 2 . ? 0.020 5.012 3.134 1.00 0.22 ? 9 HOH A O 1
HETATM 49 O O . HOH C 2 . ? 10.807 4.273 0.669 1.00 0.13 ? 10 HOH A O 1
HETATM 50 O O . HOH C 2 . ? -0.877 2.489 2.321 1.00 0.14 ? 11 HOH A O 1
HETATM 51 O O . HOH C 2 . ? 11.664 6.735 -0.303 0.33 0.21 ? 12 HOH A O 1
HETATM 52 O O . HOH C 2 . ? 0.146 6.831 1.878 1.00 0.17 ? 13 HOH A O 1
HETATM 53 O O . HOH C 2 . ? 1.701 5.931 0.657 1.00 0.24 ? 14 HOH A O 1
HETATM 54 O O . HOH C 2 . ? -1.182 6.653 9.847 1.00 0.28 ? 15 HOH A O 1
HETATM 55 O O . HOH D 2 . ? 11.619 1.752 9.559 1.00 0.29 ? 9 HOH B O 1
#