data_3GCA
# 
_entry.id   3GCA 
# 
_audit_conform.dict_name       mmcif_pdbx.dic 
_audit_conform.dict_version    5.387 
_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   3GCA         pdb_00003gca 10.2210/pdb3gca/pdb 
NDB   UR0186       ?            ?                   
RCSB  RCSB051685   ?            ?                   
WWPDB D_1000051685 ?            ?                   
# 
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 2009-03-03 
2 'Structure model' 1 1 2011-07-13 
3 'Structure model' 1 2 2024-02-21 
# 
_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' 'Data collection'           
3 3 'Structure model' 'Database references'       
4 3 'Structure model' 'Derived calculations'      
# 
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 3 'Structure model' chem_comp_atom 
2 3 'Structure model' chem_comp_bond 
3 3 'Structure model' database_2     
4 3 'Structure model' struct_site    
# 
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 3 'Structure model' '_database_2.pdbx_DOI'                
2 3 'Structure model' '_database_2.pdbx_database_accession' 
3 3 'Structure model' '_struct_site.pdbx_auth_asym_id'      
4 3 'Structure model' '_struct_site.pdbx_auth_comp_id'      
5 3 'Structure model' '_struct_site.pdbx_auth_seq_id'       
# 
_pdbx_database_status.status_code                     REL 
_pdbx_database_status.entry_id                        3GCA 
_pdbx_database_status.recvd_initial_deposition_date   2009-02-21 
_pdbx_database_status.deposit_site                    RCSB 
_pdbx_database_status.process_site                    RCSB 
_pdbx_database_status.status_code_sf                  REL 
_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.status_code_nmr_data            ? 
_pdbx_database_status.methods_development_category    ? 
# 
loop_
_audit_author.name 
_audit_author.pdbx_ordinal 
'Spitale, R.C.'  1 
'Wedekind, J.E.' 2 
# 
_citation.id                        primary 
_citation.title                     
'The Structural Basis for Recognition of the PreQ0 Metabolite by an Unusually Small Riboswitch Aptamer Domain.' 
_citation.journal_abbrev            J.Biol.Chem. 
_citation.journal_volume            284 
_citation.page_first                11012 
_citation.page_last                 11016 
_citation.year                      2009 
_citation.journal_id_ASTM           JBCHA3 
_citation.country                   US 
_citation.journal_id_ISSN           0021-9258 
_citation.journal_id_CSD            0071 
_citation.book_publisher            ? 
_citation.pdbx_database_id_PubMed   19261617 
_citation.pdbx_database_id_DOI      10.1074/jbc.C900024200 
# 
loop_
_citation_author.citation_id 
_citation_author.name 
_citation_author.ordinal 
_citation_author.identifier_ORCID 
primary 'Spitale, R.C.'  1 ? 
primary 'Torelli, A.T.'  2 ? 
primary 'Krucinska, J.'  3 ? 
primary 'Bandarian, V.'  4 ? 
primary 'Wedekind, J.E.' 5 ? 
# 
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 'PreQ1 riboswitch'                                                     10599.417 1 ? ? ? ? 
2 non-polymer syn '2-AMINO-4-OXO-4,7-DIHYDRO-3H-PYRROLO[2,3-D]PYRIMIDINE-5-CARBONITRILE' 175.147   1 ? ? ? ? 
3 non-polymer syn 'SULFATE ION'                                                          96.063    2 ? ? ? ? 
# 
_entity_poly.entity_id                      1 
_entity_poly.type                           polyribonucleotide 
_entity_poly.nstd_linkage                   no 
_entity_poly.nstd_monomer                   no 
_entity_poly.pdbx_seq_one_letter_code       CUGGGUCGCAGUAACCCCAGUUAACAAAACAAG 
_entity_poly.pdbx_seq_one_letter_code_can   CUGGGUCGCAGUAACCCCAGUUAACAAAACAAG 
_entity_poly.pdbx_strand_id                 A 
_entity_poly.pdbx_target_identifier         ? 
# 
loop_
_pdbx_entity_nonpoly.entity_id 
_pdbx_entity_nonpoly.name 
_pdbx_entity_nonpoly.comp_id 
2 '2-AMINO-4-OXO-4,7-DIHYDRO-3H-PYRROLO[2,3-D]PYRIMIDINE-5-CARBONITRILE' PQ0 
3 'SULFATE ION'                                                          SO4 
# 
loop_
_entity_poly_seq.entity_id 
_entity_poly_seq.num 
_entity_poly_seq.mon_id 
_entity_poly_seq.hetero 
1 1  C n 
1 2  U n 
1 3  G n 
1 4  G n 
1 5  G n 
1 6  U n 
1 7  C n 
1 8  G n 
1 9  C n 
1 10 A n 
1 11 G n 
1 12 U n 
1 13 A n 
1 14 A n 
1 15 C n 
1 16 C n 
1 17 C n 
1 18 C n 
1 19 A n 
1 20 G n 
1 21 U n 
1 22 U n 
1 23 A n 
1 24 A n 
1 25 C n 
1 26 A n 
1 27 A n 
1 28 A n 
1 29 A n 
1 30 C n 
1 31 A n 
1 32 A n 
1 33 G 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                
;The RNA strand was chemically synthesized based on the sequence of Class I, Type I PreQ1 riboswitch aptamer domain from T. tengcongensis
;
# 
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 
C   'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE"                                            ?                       
'C9 H14 N3 O8 P'  323.197 
G   'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE"                                           ?                       
'C10 H14 N5 O8 P' 363.221 
PQ0 non-polymer   . '2-AMINO-4-OXO-4,7-DIHYDRO-3H-PYRROLO[2,3-D]PYRIMIDINE-5-CARBONITRILE' 7-DEAZA-7-CYANO-GUANINE 'C7 H5 N5 O' 
175.147 
SO4 non-polymer   . 'SULFATE ION'                                                          ?                       'O4 S -2' 
96.063  
U   'RNA linking' y "URIDINE-5'-MONOPHOSPHATE"                                             ?                       
'C9 H13 N2 O9 P'  324.181 
# 
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  C 1  1  1  C C A . n 
A 1 2  U 2  2  2  U U A . n 
A 1 3  G 3  3  3  G G A . n 
A 1 4  G 4  4  4  G G A . n 
A 1 5  G 5  5  5  G G A . n 
A 1 6  U 6  6  6  U U A . n 
A 1 7  C 7  7  7  C C A . n 
A 1 8  G 8  8  8  G G A . n 
A 1 9  C 9  9  9  C C A . n 
A 1 10 A 10 10 10 A A A . n 
A 1 11 G 11 11 11 G G A . n 
A 1 12 U 12 12 12 U U A . n 
A 1 13 A 13 13 13 A A A . n 
A 1 14 A 14 14 14 A A A . n 
A 1 15 C 15 15 15 C C A . n 
A 1 16 C 16 16 16 C C A . n 
A 1 17 C 17 17 17 C C A . n 
A 1 18 C 18 18 18 C C A . n 
A 1 19 A 19 19 19 A A A . n 
A 1 20 G 20 20 20 G G A . n 
A 1 21 U 21 21 21 U U A . n 
A 1 22 U 22 22 22 U U A . n 
A 1 23 A 23 23 23 A A A . n 
A 1 24 A 24 24 24 A A A . n 
A 1 25 C 25 25 25 C C A . n 
A 1 26 A 26 26 26 A A A . n 
A 1 27 A 27 27 27 A A A . n 
A 1 28 A 28 28 28 A A A . n 
A 1 29 A 29 29 29 A A A . n 
A 1 30 C 30 30 30 C C A . n 
A 1 31 A 31 31 31 A A A . n 
A 1 32 A 32 32 32 A A A . n 
A 1 33 G 33 33 33 G G A . 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 
B 2 PQ0 1 34  1   PQ0 PQ0 A . 
C 3 SO4 1 102 102 SO4 SO4 A . 
D 3 SO4 1 103 103 SO4 SO4 A . 
# 
loop_
_software.name 
_software.classification 
_software.version 
_software.citation_id 
_software.pdbx_ordinal 
HKL-2000  'data collection' .   ? 1 
PHENIX    'model building'  .   ? 2 
CNS       refinement        1.2 ? 3 
DENZO     'data reduction'  .   ? 4 
SCALEPACK 'data scaling'    .   ? 5 
PHENIX    phasing           .   ? 6 
# 
_cell.entry_id           3GCA 
_cell.length_a           110.5 
_cell.length_b           110.5 
_cell.length_c           59.31 
_cell.angle_alpha        90.00 
_cell.angle_beta         90.00 
_cell.angle_gamma        120.00 
_cell.Z_PDB              12 
_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                         3GCA 
_symmetry.space_group_name_H-M             'P 63 2 2' 
_symmetry.pdbx_full_space_group_name_H-M   ? 
_symmetry.cell_setting                     ? 
_symmetry.Int_Tables_number                182 
_symmetry.space_group_name_Hall            ? 
# 
_exptl.entry_id          3GCA 
_exptl.method            'X-RAY DIFFRACTION' 
_exptl.crystals_number   1 
# 
_exptl_crystal.id                    1 
_exptl_crystal.density_meas          ? 
_exptl_crystal.density_Matthews      4.93 
_exptl_crystal.density_percent_sol   75.05 
_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            293 
_exptl_crystal_grow.temp_details    ? 
_exptl_crystal_grow.pH              6.0 
_exptl_crystal_grow.pdbx_details    
;1.8 M Li2SO4, 0.10 M Na-cacodylate pH 6.0, 0.01 M Mg(SO4)2-, 5% (v/v) 1,3-propanediol and 2 mM spermine., VAPOR DIFFUSION, HANGING DROP, temperature 293K
;
_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 Li2SO4          ? ? ? 
1 2 1 Na-cacodylate   ? ? ? 
1 3 1 'Mg(SO4)2'      ? ? ? 
1 4 1 1,3-Propanediol ? ? ? 
1 5 1 Spermine        ? ? ? 
1 6 2 Li2SO4          ? ? ? 
1 7 2 Na-cacodylate   ? ? ? 
1 8 2 'Mg(SO4)2'      ? ? ? 
1 9 2 1,3-Propanediol ? ? ? 
# 
_diffrn.id                     1 
_diffrn.ambient_temp           100 
_diffrn.ambient_temp_details   ? 
_diffrn.crystal_id             1 
# 
_diffrn_detector.diffrn_id              1 
_diffrn_detector.detector               CCD 
_diffrn_detector.type                   'Quantum 315 CCD detector' 
_diffrn_detector.pdbx_collection_date   2009-01-29 
_diffrn_detector.details                
'Vertical focusing mirror; single crystal (Si111) bent monochromator (horizontal focusing).' 
# 
_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             MAD 
_diffrn_radiation.pdbx_scattering_type             x-ray 
# 
loop_
_diffrn_radiation_wavelength.id 
_diffrn_radiation_wavelength.wavelength 
_diffrn_radiation_wavelength.wt 
1 1.1395  1.0 
2 1.1407  1.0 
3 0.97622 1.0 
# 
_diffrn_source.diffrn_id                   1 
_diffrn_source.source                      SYNCHROTRON 
_diffrn_source.type                        'SSRL BEAMLINE BL7-1' 
_diffrn_source.pdbx_synchrotron_site       SSRL 
_diffrn_source.pdbx_synchrotron_beamline   BL7-1 
_diffrn_source.pdbx_wavelength             ? 
_diffrn_source.pdbx_wavelength_list        '1.1395, 1.1407, 0.97622, 1.1395' 
# 
_reflns.entry_id                     3GCA 
_reflns.observed_criterion_sigma_I   -3 
_reflns.observed_criterion_sigma_F   0 
_reflns.d_resolution_low             50.00 
_reflns.d_resolution_high            2.75 
_reflns.number_obs                   5990 
_reflns.number_all                   ? 
_reflns.percent_possible_obs         97.6 
_reflns.pdbx_Rmerge_I_obs            ? 
_reflns.pdbx_Rsym_value              0.056 
_reflns.pdbx_netI_over_sigmaI        36.47 
_reflns.B_iso_Wilson_estimate        75 
_reflns.pdbx_redundancy              16.6 
_reflns.R_free_details               ? 
_reflns.limit_h_max                  ? 
_reflns.limit_h_min                  ? 
_reflns.limit_k_max                  ? 
_reflns.limit_k_min                  ? 
_reflns.limit_l_max                  ? 
_reflns.limit_l_min                  ? 
_reflns.observed_criterion_F_max     ? 
_reflns.observed_criterion_F_min     ? 
_reflns.pdbx_chi_squared             ? 
_reflns.pdbx_scaling_rejects         ? 
_reflns.pdbx_diffrn_id               1 
_reflns.pdbx_ordinal                 1 
# 
_reflns_shell.d_res_high             2.75 
_reflns_shell.d_res_low              2.85 
_reflns_shell.percent_possible_all   98.5 
_reflns_shell.Rmerge_I_obs           ? 
_reflns_shell.pdbx_Rsym_value        0.36 
_reflns_shell.meanI_over_sigI_obs    6.5 
_reflns_shell.pdbx_redundancy        15.8 
_reflns_shell.percent_possible_obs   ? 
_reflns_shell.number_unique_all      579 
_reflns_shell.number_measured_all    ? 
_reflns_shell.number_measured_obs    ? 
_reflns_shell.number_unique_obs      ? 
_reflns_shell.pdbx_chi_squared       ? 
_reflns_shell.pdbx_diffrn_id         ? 
_reflns_shell.pdbx_ordinal           1 
# 
_refine.entry_id                                 3GCA 
_refine.ls_number_reflns_obs                     5990 
_refine.ls_number_reflns_all                     ? 
_refine.pdbx_ls_sigma_I                          ? 
_refine.pdbx_ls_sigma_F                          0.0 
_refine.pdbx_data_cutoff_high_absF               303382.60 
_refine.pdbx_data_cutoff_low_absF                0.000000 
_refine.pdbx_data_cutoff_high_rms_absF           ? 
_refine.ls_d_res_low                             28.33 
_refine.ls_d_res_high                            2.75 
_refine.ls_percent_reflns_obs                    93.4 
_refine.ls_R_factor_obs                          ? 
_refine.ls_R_factor_all                          ? 
_refine.ls_R_factor_R_work                       0.245 
_refine.ls_R_factor_R_free                       0.272 
_refine.ls_R_factor_R_free_error                 0.013 
_refine.ls_R_factor_R_free_error_details         ? 
_refine.ls_percent_reflns_R_free                 8.0 
_refine.ls_number_reflns_R_free                  441 
_refine.ls_number_parameters                     ? 
_refine.ls_number_restraints                     ? 
_refine.occupancy_min                            ? 
_refine.occupancy_max                            ? 
_refine.correlation_coeff_Fo_to_Fc               ? 
_refine.correlation_coeff_Fo_to_Fc_free          ? 
_refine.B_iso_mean                               76 
_refine.aniso_B[1][1]                            -21 
_refine.aniso_B[2][2]                            -21 
_refine.aniso_B[3][3]                            42 
_refine.aniso_B[1][2]                            ? 
_refine.aniso_B[1][3]                            ? 
_refine.aniso_B[2][3]                            ? 
_refine.solvent_model_details                    'FLAT MODEL' 
_refine.solvent_model_param_ksol                 0.2 
_refine.solvent_model_param_bsol                 51.0924 
_refine.pdbx_solvent_vdw_probe_radii             ? 
_refine.pdbx_solvent_ion_probe_radii             ? 
_refine.pdbx_solvent_shrinkage_radii             ? 
_refine.pdbx_ls_cross_valid_method               THROUGHOUT 
_refine.details                                  'BULK SOLVENT MODEL USED' 
_refine.pdbx_starting_model                      ? 
_refine.pdbx_method_to_determine_struct          MAD 
_refine.pdbx_isotropic_thermal_model             RESTRAINED 
_refine.pdbx_stereochemistry_target_values       'CNS 1.2' 
_refine.pdbx_stereochem_target_val_spec_case     ? 
_refine.pdbx_R_Free_selection_details            RANDOM 
_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.B_iso_min                                ? 
_refine.B_iso_max                                ? 
_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_overall_phase_error                 ? 
_refine.pdbx_refine_id                           'X-RAY DIFFRACTION' 
_refine.pdbx_diffrn_id                           1 
_refine.pdbx_TLS_residual_ADP_flag               ? 
_refine.pdbx_overall_SU_R_free_Cruickshank_DPI   ? 
_refine.pdbx_overall_SU_R_Blow_DPI               ? 
_refine.pdbx_overall_SU_R_free_Blow_DPI          ? 
# 
_refine_analyze.entry_id                        3GCA 
_refine_analyze.Luzzati_coordinate_error_obs    0.44 
_refine_analyze.Luzzati_sigma_a_obs             0.52 
_refine_analyze.Luzzati_d_res_low_obs           5.00 
_refine_analyze.Luzzati_coordinate_error_free   0.49 
_refine_analyze.Luzzati_sigma_a_free            0.53 
_refine_analyze.Luzzati_d_res_low_free          ? 
_refine_analyze.number_disordered_residues      ? 
_refine_analyze.occupancy_sum_hydrogen          ? 
_refine_analyze.occupancy_sum_non_hydrogen      ? 
_refine_analyze.pdbx_Luzzati_d_res_high_obs     ? 
_refine_analyze.pdbx_refine_id                  'X-RAY DIFFRACTION' 
# 
_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   702 
_refine_hist.pdbx_number_atoms_ligand         23 
_refine_hist.number_atoms_solvent             0 
_refine_hist.number_atoms_total               725 
_refine_hist.d_res_high                       2.75 
_refine_hist.d_res_low                        28.33 
# 
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 
c_bond_d           0.008 ? ? ? 'X-RAY DIFFRACTION' ? 
c_angle_deg        1.5   ? ? ? 'X-RAY DIFFRACTION' ? 
c_dihedral_angle_d 20.3  ? ? ? 'X-RAY DIFFRACTION' ? 
c_improper_angle_d 1.99  ? ? ? 'X-RAY DIFFRACTION' ? 
# 
_refine_ls_shell.pdbx_total_number_of_bins_used   6 
_refine_ls_shell.d_res_high                       2.75 
_refine_ls_shell.d_res_low                        2.92 
_refine_ls_shell.number_reflns_R_work             728 
_refine_ls_shell.R_factor_R_work                  0.438 
_refine_ls_shell.percent_reflns_obs               83.0 
_refine_ls_shell.R_factor_R_free                  0.487 
_refine_ls_shell.R_factor_R_free_error            0.060 
_refine_ls_shell.percent_reflns_R_free            8.2 
_refine_ls_shell.number_reflns_R_free             65 
_refine_ls_shell.number_reflns_all                ? 
_refine_ls_shell.R_factor_all                     ? 
_refine_ls_shell.number_reflns_obs                ? 
_refine_ls_shell.redundancy_reflns_obs            ? 
_refine_ls_shell.pdbx_refine_id                   'X-RAY DIFFRACTION' 
# 
loop_
_pdbx_xplor_file.serial_no 
_pdbx_xplor_file.param_file 
_pdbx_xplor_file.topol_file 
_pdbx_xplor_file.pdbx_refine_id 
1 dna-rnaATT dna-rnaATT 'X-RAY DIFFRACTION' 
2 pq         pq         'X-RAY DIFFRACTION' 
4 to         ?          'X-RAY DIFFRACTION' 
3 ?          ion.top    'X-RAY DIFFRACTION' 
# 
_database_PDB_matrix.entry_id          3GCA 
_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                  3GCA 
_struct.title                     
'The structural basis for recognition of the preQ0 metabolite by an unusually small riboswitch aptamer domain' 
_struct.pdbx_model_details        ? 
_struct.pdbx_CASP_flag            ? 
_struct.pdbx_model_type_details   ? 
# 
_struct_keywords.entry_id        3GCA 
_struct_keywords.pdbx_keywords   RNA 
_struct_keywords.text            'PreQ1, PreQ0, riboswitch, RNA, ribosomal binding site, amptamer, metabolite' 
# 
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 2 ? 
C N N 3 ? 
D N N 3 ? 
# 
_struct_ref.id                         1 
_struct_ref.db_name                    PDB 
_struct_ref.db_code                    3GCA 
_struct_ref.pdbx_db_accession          3GCA 
_struct_ref.entity_id                  1 
_struct_ref.pdbx_align_begin           ? 
_struct_ref.pdbx_seq_one_letter_code   CUGGGUCGCAGUAACCCCAGUUAACAAAACAAG 
_struct_ref.pdbx_db_isoform            ? 
# 
_struct_ref_seq.align_id                      1 
_struct_ref_seq.ref_id                        1 
_struct_ref_seq.pdbx_PDB_id_code              3GCA 
_struct_ref_seq.pdbx_strand_id                A 
_struct_ref_seq.seq_align_beg                 1 
_struct_ref_seq.pdbx_seq_align_beg_ins_code   ? 
_struct_ref_seq.seq_align_end                 33 
_struct_ref_seq.pdbx_seq_align_end_ins_code   ? 
_struct_ref_seq.pdbx_db_accession             3GCA 
_struct_ref_seq.db_align_beg                  1 
_struct_ref_seq.pdbx_db_align_beg_ins_code    ? 
_struct_ref_seq.db_align_end                  33 
_struct_ref_seq.pdbx_db_align_end_ins_code    ? 
_struct_ref_seq.pdbx_auth_seq_align_beg       1 
_struct_ref_seq.pdbx_auth_seq_align_end       33 
# 
_pdbx_struct_assembly.id                   1 
_pdbx_struct_assembly.details              author_and_software_defined_assembly 
_pdbx_struct_assembly.method_details       PISA 
_pdbx_struct_assembly.oligomeric_details   monomeric 
_pdbx_struct_assembly.oligomeric_count     1 
# 
_pdbx_struct_assembly_gen.assembly_id       1 
_pdbx_struct_assembly_gen.oper_expression   1 
_pdbx_struct_assembly_gen.asym_id_list      A,B,C,D 
# 
_pdbx_struct_oper_list.id                   1 
_pdbx_struct_oper_list.type                 'identity operation' 
_pdbx_struct_oper_list.name                 1_555 
_pdbx_struct_oper_list.symmetry_operation   x,y,z 
_pdbx_struct_oper_list.matrix[1][1]         1.0000000000 
_pdbx_struct_oper_list.matrix[1][2]         0.0000000000 
_pdbx_struct_oper_list.matrix[1][3]         0.0000000000 
_pdbx_struct_oper_list.vector[1]            0.0000000000 
_pdbx_struct_oper_list.matrix[2][1]         0.0000000000 
_pdbx_struct_oper_list.matrix[2][2]         1.0000000000 
_pdbx_struct_oper_list.matrix[2][3]         0.0000000000 
_pdbx_struct_oper_list.vector[2]            0.0000000000 
_pdbx_struct_oper_list.matrix[3][1]         0.0000000000 
_pdbx_struct_oper_list.matrix[3][2]         0.0000000000 
_pdbx_struct_oper_list.matrix[3][3]         1.0000000000 
_pdbx_struct_oper_list.vector[3]            0.0000000000 
# 
_struct_biol.id        1 
_struct_biol.details   ? 
# 
loop_
_struct_conn.id 
_struct_conn.conn_type_id 
_struct_conn.pdbx_leaving_atom_flag 
_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 
_struct_conn.pdbx_dist_value 
_struct_conn.pdbx_value_order 
_struct_conn.pdbx_role 
hydrog1  hydrog ? ? A C 1  N3 ? ? ? 1_555 A G 20 N1 ? ? A C 1  A G 20 1_555 ? ? ? ? ? ? WATSON-CRICK  ? ? ? 
hydrog2  hydrog ? ? A C 1  N4 ? ? ? 1_555 A G 20 O6 ? ? A C 1  A G 20 1_555 ? ? ? ? ? ? WATSON-CRICK  ? ? ? 
hydrog3  hydrog ? ? A C 1  O2 ? ? ? 1_555 A G 20 N2 ? ? A C 1  A G 20 1_555 ? ? ? ? ? ? WATSON-CRICK  ? ? ? 
hydrog4  hydrog ? ? A U 2  N3 ? ? ? 1_555 A A 19 N1 ? ? A U 2  A A 19 1_555 ? ? ? ? ? ? WATSON-CRICK  ? ? ? 
hydrog5  hydrog ? ? A U 2  O4 ? ? ? 1_555 A A 19 N6 ? ? A U 2  A A 19 1_555 ? ? ? ? ? ? WATSON-CRICK  ? ? ? 
hydrog6  hydrog ? ? A G 3  N1 ? ? ? 1_555 A C 18 N3 ? ? A G 3  A C 18 1_555 ? ? ? ? ? ? WATSON-CRICK  ? ? ? 
hydrog7  hydrog ? ? A G 3  N2 ? ? ? 1_555 A C 18 O2 ? ? A G 3  A C 18 1_555 ? ? ? ? ? ? WATSON-CRICK  ? ? ? 
hydrog8  hydrog ? ? A G 3  O6 ? ? ? 1_555 A C 18 N4 ? ? A G 3  A C 18 1_555 ? ? ? ? ? ? WATSON-CRICK  ? ? ? 
hydrog9  hydrog ? ? A G 4  N1 ? ? ? 1_555 A C 17 N3 ? ? A G 4  A C 17 1_555 ? ? ? ? ? ? WATSON-CRICK  ? ? ? 
hydrog10 hydrog ? ? A G 4  N2 ? ? ? 1_555 A C 17 O2 ? ? A G 4  A C 17 1_555 ? ? ? ? ? ? WATSON-CRICK  ? ? ? 
hydrog11 hydrog ? ? A G 4  O6 ? ? ? 1_555 A C 17 N4 ? ? A G 4  A C 17 1_555 ? ? ? ? ? ? WATSON-CRICK  ? ? ? 
hydrog12 hydrog ? ? A G 5  N1 ? ? ? 1_555 A C 16 N3 ? ? A G 5  A C 16 1_555 ? ? ? ? ? ? WATSON-CRICK  ? ? ? 
hydrog13 hydrog ? ? A G 5  N2 ? ? ? 1_555 A C 16 O2 ? ? A G 5  A C 16 1_555 ? ? ? ? ? ? WATSON-CRICK  ? ? ? 
hydrog14 hydrog ? ? A G 5  O6 ? ? ? 1_555 A C 16 N4 ? ? A G 5  A C 16 1_555 ? ? ? ? ? ? WATSON-CRICK  ? ? ? 
hydrog15 hydrog ? ? A G 5  N2 ? ? ? 1_555 A A 27 N1 ? ? A G 5  A A 27 1_555 ? ? ? ? ? ? TYPE_10_PAIR  ? ? ? 
hydrog16 hydrog ? ? A G 5  N3 ? ? ? 1_555 A A 27 N6 ? ? A G 5  A A 27 1_555 ? ? ? ? ? ? TYPE_10_PAIR  ? ? ? 
hydrog17 hydrog ? ? A U 6  N3 ? ? ? 1_555 A A 28 N7 ? ? A U 6  A A 28 1_555 ? ? ? ? ? ? HOOGSTEEN     ? ? ? 
hydrog18 hydrog ? ? A U 6  O4 ? ? ? 1_555 A A 28 N6 ? ? A U 6  A A 28 1_555 ? ? ? ? ? ? HOOGSTEEN     ? ? ? 
hydrog19 hydrog ? ? A U 6  O4 ? ? ? 1_555 A A 29 N6 ? ? A U 6  A A 29 1_555 ? ? ? ? ? ? 'U-A PAIR'    ? ? ? 
hydrog20 hydrog ? ? A C 7  N4 ? ? ? 1_555 A G 11 N7 ? ? A C 7  A G 11 1_555 ? ? ? ? ? ? 'C-G PAIR'    ? ? ? 
hydrog21 hydrog ? ? A C 7  O2 ? ? ? 1_555 A C 30 N4 ? ? A C 7  A C 30 1_555 ? ? ? ? ? ? 'C-C MISPAIR' ? ? ? 
hydrog22 hydrog ? ? A G 8  N2 ? ? ? 1_555 A A 31 N1 ? ? A G 8  A A 31 1_555 ? ? ? ? ? ? TYPE_10_PAIR  ? ? ? 
hydrog23 hydrog ? ? A G 8  N3 ? ? ? 1_555 A A 31 N6 ? ? A G 8  A A 31 1_555 ? ? ? ? ? ? TYPE_10_PAIR  ? ? ? 
hydrog24 hydrog ? ? A C 9  N3 ? ? ? 1_555 A G 33 N1 ? ? A C 9  A G 33 1_555 ? ? ? ? ? ? WATSON-CRICK  ? ? ? 
hydrog25 hydrog ? ? A C 9  N4 ? ? ? 1_555 A G 33 O6 ? ? A C 9  A G 33 1_555 ? ? ? ? ? ? WATSON-CRICK  ? ? ? 
hydrog26 hydrog ? ? A C 9  O2 ? ? ? 1_555 A G 33 N2 ? ? A C 9  A G 33 1_555 ? ? ? ? ? ? WATSON-CRICK  ? ? ? 
hydrog27 hydrog ? ? A A 10 N3 ? ? ? 1_555 A A 32 N6 ? ? A A 10 A A 32 1_555 ? ? ? ? ? ? 'A-A MISPAIR' ? ? ? 
hydrog28 hydrog ? ? A G 11 N2 ? ? ? 1_555 A A 14 N1 ? ? A G 11 A A 14 1_555 ? ? ? ? ? ? TYPE_10_PAIR  ? ? ? 
hydrog29 hydrog ? ? A G 11 N3 ? ? ? 1_555 A A 14 N6 ? ? A G 11 A A 14 1_555 ? ? ? ? ? ? TYPE_10_PAIR  ? ? ? 
hydrog30 hydrog ? ? A G 11 N2 ? ? ? 1_555 A C 15 O2 ? ? A G 11 A C 15 1_555 ? ? ? ? ? ? 'G-C PAIR'    ? ? ? 
hydrog31 hydrog ? ? A G 11 N1 ? ? ? 1_555 A C 30 N3 ? ? A G 11 A C 30 1_555 ? ? ? ? ? ? WATSON-CRICK  ? ? ? 
hydrog32 hydrog ? ? A G 11 N2 ? ? ? 1_555 A C 30 O2 ? ? A G 11 A C 30 1_555 ? ? ? ? ? ? WATSON-CRICK  ? ? ? 
hydrog33 hydrog ? ? A G 11 O6 ? ? ? 1_555 A C 30 N4 ? ? A G 11 A C 30 1_555 ? ? ? ? ? ? WATSON-CRICK  ? ? ? 
hydrog34 hydrog ? ? A A 13 N6 ? ? ? 1_555 A A 31 N3 ? ? A A 13 A A 31 1_555 ? ? ? ? ? ? 'A-A MISPAIR' ? ? ? 
hydrog35 hydrog ? ? A C 17 O2 ? ? ? 1_555 A A 26 N6 ? ? A C 17 A A 26 1_555 ? ? ? ? ? ? 'C-A MISPAIR' ? ? ? 
hydrog36 hydrog ? ? A G 20 N2 ? ? ? 1_555 A U 21 O4 ? ? A G 20 A U 21 1_555 ? ? ? ? ? ? 'G-U MISPAIR' ? ? ? 
# 
_struct_conn_type.id          hydrog 
_struct_conn_type.criteria    ? 
_struct_conn_type.reference   ? 
# 
loop_
_struct_site.id 
_struct_site.pdbx_evidence_code 
_struct_site.pdbx_auth_asym_id 
_struct_site.pdbx_auth_comp_id 
_struct_site.pdbx_auth_seq_id 
_struct_site.pdbx_auth_ins_code 
_struct_site.pdbx_num_residues 
_struct_site.details 
AC1 Software A PQ0 34  ? 7 'BINDING SITE FOR RESIDUE PQ0 A 34'  
AC2 Software A SO4 102 ? 3 'BINDING SITE FOR RESIDUE SO4 A 102' 
AC3 Software A SO4 103 ? 3 'BINDING SITE FOR RESIDUE SO4 A 103' 
# 
loop_
_struct_site_gen.id 
_struct_site_gen.site_id 
_struct_site_gen.pdbx_num_res 
_struct_site_gen.label_comp_id 
_struct_site_gen.label_asym_id 
_struct_site_gen.label_seq_id 
_struct_site_gen.pdbx_auth_ins_code 
_struct_site_gen.auth_comp_id 
_struct_site_gen.auth_asym_id 
_struct_site_gen.auth_seq_id 
_struct_site_gen.label_atom_id 
_struct_site_gen.label_alt_id 
_struct_site_gen.symmetry 
_struct_site_gen.details 
1  AC1 7 G A 5  ? G A 5  . ? 1_555 ? 
2  AC1 7 U A 6  ? U A 6  . ? 1_555 ? 
3  AC1 7 C A 7  ? C A 7  . ? 1_555 ? 
4  AC1 7 G A 11 ? G A 11 . ? 1_555 ? 
5  AC1 7 C A 15 ? C A 15 . ? 1_555 ? 
6  AC1 7 C A 16 ? C A 16 . ? 1_555 ? 
7  AC1 7 A A 29 ? A A 29 . ? 1_555 ? 
8  AC2 3 C A 15 ? C A 15 . ? 1_555 ? 
9  AC2 3 C A 16 ? C A 16 . ? 1_555 ? 
10 AC2 3 C A 17 ? C A 17 . ? 1_555 ? 
11 AC3 3 U A 2  ? U A 2  . ? 1_555 ? 
12 AC3 3 C A 18 ? C A 18 . ? 1_555 ? 
13 AC3 3 A A 19 ? A A 19 . ? 1_555 ? 
# 
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 "C2'" A G 8  ? ? "C3'" A G 8  ? ? "O3'" A G 8  ? ? 126.52 113.70 12.82 1.60 N 
2 1 "C4'" A G 8  ? ? "C3'" A G 8  ? ? "C2'" A G 8  ? ? 109.26 102.60 6.66  1.00 N 
3 1 N9    A G 8  ? ? "C1'" A G 8  ? ? "C2'" A G 8  ? ? 104.94 112.00 -7.06 1.10 N 
4 1 "O4'" A G 20 ? ? "C1'" A G 20 ? ? N9    A G 20 ? ? 113.46 108.50 4.96  0.70 N 
# 
_pdbx_validate_chiral.id              1 
_pdbx_validate_chiral.PDB_model_num   1 
_pdbx_validate_chiral.auth_atom_id    "C3'" 
_pdbx_validate_chiral.label_alt_id    ? 
_pdbx_validate_chiral.auth_asym_id    A 
_pdbx_validate_chiral.auth_comp_id    G 
_pdbx_validate_chiral.auth_seq_id     8 
_pdbx_validate_chiral.PDB_ins_code    ? 
_pdbx_validate_chiral.details         PLANAR 
_pdbx_validate_chiral.omega           . 
# 
loop_
_pdbx_validate_planes.id 
_pdbx_validate_planes.PDB_model_num 
_pdbx_validate_planes.auth_comp_id 
_pdbx_validate_planes.auth_asym_id 
_pdbx_validate_planes.auth_seq_id 
_pdbx_validate_planes.PDB_ins_code 
_pdbx_validate_planes.label_alt_id 
_pdbx_validate_planes.rmsd 
_pdbx_validate_planes.type 
1 1 U A 22 ? ? 0.090 'SIDE CHAIN' 
2 1 A A 31 ? ? 0.065 'SIDE CHAIN' 
# 
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 
A   OP3    O N N 1   
A   P      P N N 2   
A   OP1    O N N 3   
A   OP2    O N N 4   
A   "O5'"  O N N 5   
A   "C5'"  C N N 6   
A   "C4'"  C N R 7   
A   "O4'"  O N N 8   
A   "C3'"  C N S 9   
A   "O3'"  O N N 10  
A   "C2'"  C N R 11  
A   "O2'"  O N N 12  
A   "C1'"  C N R 13  
A   N9     N Y N 14  
A   C8     C Y N 15  
A   N7     N Y N 16  
A   C5     C Y N 17  
A   C6     C Y N 18  
A   N6     N N N 19  
A   N1     N Y N 20  
A   C2     C Y N 21  
A   N3     N Y N 22  
A   C4     C Y N 23  
A   HOP3   H N N 24  
A   HOP2   H N N 25  
A   "H5'"  H N N 26  
A   "H5''" H N N 27  
A   "H4'"  H N N 28  
A   "H3'"  H N N 29  
A   "HO3'" H N N 30  
A   "H2'"  H N N 31  
A   "HO2'" H N N 32  
A   "H1'"  H N N 33  
A   H8     H N N 34  
A   H61    H N N 35  
A   H62    H N N 36  
A   H2     H N N 37  
C   OP3    O N N 38  
C   P      P N N 39  
C   OP1    O N N 40  
C   OP2    O N N 41  
C   "O5'"  O N N 42  
C   "C5'"  C N N 43  
C   "C4'"  C N R 44  
C   "O4'"  O N N 45  
C   "C3'"  C N S 46  
C   "O3'"  O N N 47  
C   "C2'"  C N R 48  
C   "O2'"  O N N 49  
C   "C1'"  C N R 50  
C   N1     N N N 51  
C   C2     C N N 52  
C   O2     O N N 53  
C   N3     N N N 54  
C   C4     C N N 55  
C   N4     N N N 56  
C   C5     C N N 57  
C   C6     C N N 58  
C   HOP3   H N N 59  
C   HOP2   H N N 60  
C   "H5'"  H N N 61  
C   "H5''" H N N 62  
C   "H4'"  H N N 63  
C   "H3'"  H N N 64  
C   "HO3'" H N N 65  
C   "H2'"  H N N 66  
C   "HO2'" H N N 67  
C   "H1'"  H N N 68  
C   H41    H N N 69  
C   H42    H N N 70  
C   H5     H N N 71  
C   H6     H N N 72  
G   OP3    O N N 73  
G   P      P N N 74  
G   OP1    O N N 75  
G   OP2    O N N 76  
G   "O5'"  O N N 77  
G   "C5'"  C N N 78  
G   "C4'"  C N R 79  
G   "O4'"  O N N 80  
G   "C3'"  C N S 81  
G   "O3'"  O N N 82  
G   "C2'"  C N R 83  
G   "O2'"  O N N 84  
G   "C1'"  C N R 85  
G   N9     N Y N 86  
G   C8     C Y N 87  
G   N7     N Y N 88  
G   C5     C Y N 89  
G   C6     C N N 90  
G   O6     O N N 91  
G   N1     N N N 92  
G   C2     C N N 93  
G   N2     N N N 94  
G   N3     N N N 95  
G   C4     C Y N 96  
G   HOP3   H N N 97  
G   HOP2   H N N 98  
G   "H5'"  H N N 99  
G   "H5''" H N N 100 
G   "H4'"  H N N 101 
G   "H3'"  H N N 102 
G   "HO3'" H N N 103 
G   "H2'"  H N N 104 
G   "HO2'" H N N 105 
G   "H1'"  H N N 106 
G   H8     H N N 107 
G   H1     H N N 108 
G   H21    H N N 109 
G   H22    H N N 110 
PQ0 N1     N Y N 111 
PQ0 C2     C Y N 112 
PQ0 N3     N Y N 113 
PQ0 C4     C Y N 114 
PQ0 C5     C Y N 115 
PQ0 C6     C Y N 116 
PQ0 O6     O N N 117 
PQ0 C7     C Y N 118 
PQ0 C10    C N N 119 
PQ0 N11    N N N 120 
PQ0 C8     C Y N 121 
PQ0 N9     N Y N 122 
PQ0 N2     N N N 123 
PQ0 HN1    H N N 124 
PQ0 H8     H N N 125 
PQ0 HN9    H N N 126 
PQ0 HN21   H N N 127 
PQ0 HN22   H N N 128 
SO4 S      S N N 129 
SO4 O1     O N N 130 
SO4 O2     O N N 131 
SO4 O3     O N N 132 
SO4 O4     O N N 133 
U   OP3    O N N 134 
U   P      P N N 135 
U   OP1    O N N 136 
U   OP2    O N N 137 
U   "O5'"  O N N 138 
U   "C5'"  C N N 139 
U   "C4'"  C N R 140 
U   "O4'"  O N N 141 
U   "C3'"  C N S 142 
U   "O3'"  O N N 143 
U   "C2'"  C N R 144 
U   "O2'"  O N N 145 
U   "C1'"  C N R 146 
U   N1     N N N 147 
U   C2     C N N 148 
U   O2     O N N 149 
U   N3     N N N 150 
U   C4     C N N 151 
U   O4     O N N 152 
U   C5     C N N 153 
U   C6     C N N 154 
U   HOP3   H N N 155 
U   HOP2   H N N 156 
U   "H5'"  H N N 157 
U   "H5''" H N N 158 
U   "H4'"  H N N 159 
U   "H3'"  H N N 160 
U   "HO3'" H N N 161 
U   "H2'"  H N N 162 
U   "HO2'" H N N 163 
U   "H1'"  H N N 164 
U   H3     H N N 165 
U   H5     H N N 166 
U   H6     H N N 167 
# 
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 
A   OP3   P      sing N N 1   
A   OP3   HOP3   sing N N 2   
A   P     OP1    doub N N 3   
A   P     OP2    sing N N 4   
A   P     "O5'"  sing N N 5   
A   OP2   HOP2   sing N N 6   
A   "O5'" "C5'"  sing N N 7   
A   "C5'" "C4'"  sing N N 8   
A   "C5'" "H5'"  sing N N 9   
A   "C5'" "H5''" sing N N 10  
A   "C4'" "O4'"  sing N N 11  
A   "C4'" "C3'"  sing N N 12  
A   "C4'" "H4'"  sing N N 13  
A   "O4'" "C1'"  sing N N 14  
A   "C3'" "O3'"  sing N N 15  
A   "C3'" "C2'"  sing N N 16  
A   "C3'" "H3'"  sing N N 17  
A   "O3'" "HO3'" sing N N 18  
A   "C2'" "O2'"  sing N N 19  
A   "C2'" "C1'"  sing N N 20  
A   "C2'" "H2'"  sing N N 21  
A   "O2'" "HO2'" sing N N 22  
A   "C1'" N9     sing N N 23  
A   "C1'" "H1'"  sing N N 24  
A   N9    C8     sing Y N 25  
A   N9    C4     sing Y N 26  
A   C8    N7     doub Y N 27  
A   C8    H8     sing N N 28  
A   N7    C5     sing Y N 29  
A   C5    C6     sing Y N 30  
A   C5    C4     doub Y N 31  
A   C6    N6     sing N N 32  
A   C6    N1     doub Y N 33  
A   N6    H61    sing N N 34  
A   N6    H62    sing N N 35  
A   N1    C2     sing Y N 36  
A   C2    N3     doub Y N 37  
A   C2    H2     sing N N 38  
A   N3    C4     sing Y N 39  
C   OP3   P      sing N N 40  
C   OP3   HOP3   sing N N 41  
C   P     OP1    doub N N 42  
C   P     OP2    sing N N 43  
C   P     "O5'"  sing N N 44  
C   OP2   HOP2   sing N N 45  
C   "O5'" "C5'"  sing N N 46  
C   "C5'" "C4'"  sing N N 47  
C   "C5'" "H5'"  sing N N 48  
C   "C5'" "H5''" sing N N 49  
C   "C4'" "O4'"  sing N N 50  
C   "C4'" "C3'"  sing N N 51  
C   "C4'" "H4'"  sing N N 52  
C   "O4'" "C1'"  sing N N 53  
C   "C3'" "O3'"  sing N N 54  
C   "C3'" "C2'"  sing N N 55  
C   "C3'" "H3'"  sing N N 56  
C   "O3'" "HO3'" sing N N 57  
C   "C2'" "O2'"  sing N N 58  
C   "C2'" "C1'"  sing N N 59  
C   "C2'" "H2'"  sing N N 60  
C   "O2'" "HO2'" sing N N 61  
C   "C1'" N1     sing N N 62  
C   "C1'" "H1'"  sing N N 63  
C   N1    C2     sing N N 64  
C   N1    C6     sing N N 65  
C   C2    O2     doub N N 66  
C   C2    N3     sing N N 67  
C   N3    C4     doub N N 68  
C   C4    N4     sing N N 69  
C   C4    C5     sing N N 70  
C   N4    H41    sing N N 71  
C   N4    H42    sing N N 72  
C   C5    C6     doub N N 73  
C   C5    H5     sing N N 74  
C   C6    H6     sing N N 75  
G   OP3   P      sing N N 76  
G   OP3   HOP3   sing N N 77  
G   P     OP1    doub N N 78  
G   P     OP2    sing N N 79  
G   P     "O5'"  sing N N 80  
G   OP2   HOP2   sing N N 81  
G   "O5'" "C5'"  sing N N 82  
G   "C5'" "C4'"  sing N N 83  
G   "C5'" "H5'"  sing N N 84  
G   "C5'" "H5''" sing N N 85  
G   "C4'" "O4'"  sing N N 86  
G   "C4'" "C3'"  sing N N 87  
G   "C4'" "H4'"  sing N N 88  
G   "O4'" "C1'"  sing N N 89  
G   "C3'" "O3'"  sing N N 90  
G   "C3'" "C2'"  sing N N 91  
G   "C3'" "H3'"  sing N N 92  
G   "O3'" "HO3'" sing N N 93  
G   "C2'" "O2'"  sing N N 94  
G   "C2'" "C1'"  sing N N 95  
G   "C2'" "H2'"  sing N N 96  
G   "O2'" "HO2'" sing N N 97  
G   "C1'" N9     sing N N 98  
G   "C1'" "H1'"  sing N N 99  
G   N9    C8     sing Y N 100 
G   N9    C4     sing Y N 101 
G   C8    N7     doub Y N 102 
G   C8    H8     sing N N 103 
G   N7    C5     sing Y N 104 
G   C5    C6     sing N N 105 
G   C5    C4     doub Y N 106 
G   C6    O6     doub N N 107 
G   C6    N1     sing N N 108 
G   N1    C2     sing N N 109 
G   N1    H1     sing N N 110 
G   C2    N2     sing N N 111 
G   C2    N3     doub N N 112 
G   N2    H21    sing N N 113 
G   N2    H22    sing N N 114 
G   N3    C4     sing N N 115 
PQ0 N1    C2     sing Y N 116 
PQ0 N1    C6     sing Y N 117 
PQ0 N1    HN1    sing N N 118 
PQ0 C2    N3     doub Y N 119 
PQ0 C2    N2     sing N N 120 
PQ0 N3    C4     sing Y N 121 
PQ0 C4    C5     doub Y N 122 
PQ0 C4    N9     sing Y N 123 
PQ0 C5    C6     sing Y N 124 
PQ0 C5    C7     sing Y N 125 
PQ0 C6    O6     doub N N 126 
PQ0 C7    C10    sing N N 127 
PQ0 C7    C8     doub Y N 128 
PQ0 C10   N11    trip N N 129 
PQ0 C8    N9     sing Y N 130 
PQ0 C8    H8     sing N N 131 
PQ0 N9    HN9    sing N N 132 
PQ0 N2    HN21   sing N N 133 
PQ0 N2    HN22   sing N N 134 
SO4 S     O1     doub N N 135 
SO4 S     O2     doub N N 136 
SO4 S     O3     sing N N 137 
SO4 S     O4     sing N N 138 
U   OP3   P      sing N N 139 
U   OP3   HOP3   sing N N 140 
U   P     OP1    doub N N 141 
U   P     OP2    sing N N 142 
U   P     "O5'"  sing N N 143 
U   OP2   HOP2   sing N N 144 
U   "O5'" "C5'"  sing N N 145 
U   "C5'" "C4'"  sing N N 146 
U   "C5'" "H5'"  sing N N 147 
U   "C5'" "H5''" sing N N 148 
U   "C4'" "O4'"  sing N N 149 
U   "C4'" "C3'"  sing N N 150 
U   "C4'" "H4'"  sing N N 151 
U   "O4'" "C1'"  sing N N 152 
U   "C3'" "O3'"  sing N N 153 
U   "C3'" "C2'"  sing N N 154 
U   "C3'" "H3'"  sing N N 155 
U   "O3'" "HO3'" sing N N 156 
U   "C2'" "O2'"  sing N N 157 
U   "C2'" "C1'"  sing N N 158 
U   "C2'" "H2'"  sing N N 159 
U   "O2'" "HO2'" sing N N 160 
U   "C1'" N1     sing N N 161 
U   "C1'" "H1'"  sing N N 162 
U   N1    C2     sing N N 163 
U   N1    C6     sing N N 164 
U   C2    O2     doub N N 165 
U   C2    N3     sing N N 166 
U   N3    C4     sing N N 167 
U   N3    H3     sing N N 168 
U   C4    O4     doub N N 169 
U   C4    C5     sing N N 170 
U   C5    C6     doub N N 171 
U   C5    H5     sing N N 172 
U   C6    H6     sing N N 173 
# 
loop_
_ndb_struct_conf_na.entry_id 
_ndb_struct_conf_na.feature 
3GCA 'double helix'        
3GCA 'a-form double helix' 
3GCA 'bulge loop'          
3GCA 'quadruple helix'     
# 
loop_
_ndb_struct_na_base_pair.model_number 
_ndb_struct_na_base_pair.i_label_asym_id 
_ndb_struct_na_base_pair.i_label_comp_id 
_ndb_struct_na_base_pair.i_label_seq_id 
_ndb_struct_na_base_pair.i_symmetry 
_ndb_struct_na_base_pair.j_label_asym_id 
_ndb_struct_na_base_pair.j_label_comp_id 
_ndb_struct_na_base_pair.j_label_seq_id 
_ndb_struct_na_base_pair.j_symmetry 
_ndb_struct_na_base_pair.shear 
_ndb_struct_na_base_pair.stretch 
_ndb_struct_na_base_pair.stagger 
_ndb_struct_na_base_pair.buckle 
_ndb_struct_na_base_pair.propeller 
_ndb_struct_na_base_pair.opening 
_ndb_struct_na_base_pair.pair_number 
_ndb_struct_na_base_pair.pair_name 
_ndb_struct_na_base_pair.i_auth_asym_id 
_ndb_struct_na_base_pair.i_auth_seq_id 
_ndb_struct_na_base_pair.i_PDB_ins_code 
_ndb_struct_na_base_pair.j_auth_asym_id 
_ndb_struct_na_base_pair.j_auth_seq_id 
_ndb_struct_na_base_pair.j_PDB_ins_code 
_ndb_struct_na_base_pair.hbond_type_28 
_ndb_struct_na_base_pair.hbond_type_12 
1 A C 1  1_555 A G 20 1_555 0.313  -0.317 -0.186 -1.009  -1.016  -2.852  1  A_C1:G20_A  A 1  ? A 20 ? 19 1 
1 A U 2  1_555 A A 19 1_555 0.327  -0.403 0.079  -3.776  -9.379  -1.038  2  A_U2:A19_A  A 2  ? A 19 ? 20 1 
1 A G 3  1_555 A C 18 1_555 0.049  -0.502 0.318  -3.814  -10.619 -2.756  3  A_G3:C18_A  A 3  ? A 18 ? 19 1 
1 A G 4  1_555 A C 17 1_555 -0.025 -0.302 0.345  -4.583  -11.931 -1.807  4  A_G4:C17_A  A 4  ? A 17 ? 19 1 
1 A G 5  1_555 A C 16 1_555 0.166  -0.147 -0.032 -9.634  -11.244 -2.467  5  A_G5:C16_A  A 5  ? A 16 ? 19 1 
1 A U 6  1_555 A A 28 1_555 -0.223 2.393  1.135  -31.696 -1.751  -78.965 6  A_U6:A28_A  A 6  ? A 28 ? 23 3 
1 A C 30 1_555 A G 11 1_555 0.075  -0.473 0.418  10.403  -16.977 -1.457  7  A_C30:G11_A A 30 ? A 11 ? 19 1 
1 A A 31 1_555 A G 8  1_555 -3.402 3.409  0.609  -14.812 -9.930  74.796  8  A_A31:G8_A  A 31 ? A 8  ? 10 6 
1 A A 32 1_555 A A 10 1_555 -6.474 -3.193 -0.051 10.932  -28.024 -12.131 9  A_A32:A10_A A 32 ? A 10 ? ?  6 
1 A G 33 1_555 A C 9  1_555 0.379  -0.415 0.087  -5.870  -3.632  -10.372 10 A_G33:C9_A  A 33 ? A 9  ? 19 1 
# 
loop_
_ndb_struct_na_base_pair_step.model_number 
_ndb_struct_na_base_pair_step.i_label_asym_id_1 
_ndb_struct_na_base_pair_step.i_label_comp_id_1 
_ndb_struct_na_base_pair_step.i_label_seq_id_1 
_ndb_struct_na_base_pair_step.i_symmetry_1 
_ndb_struct_na_base_pair_step.j_label_asym_id_1 
_ndb_struct_na_base_pair_step.j_label_comp_id_1 
_ndb_struct_na_base_pair_step.j_label_seq_id_1 
_ndb_struct_na_base_pair_step.j_symmetry_1 
_ndb_struct_na_base_pair_step.i_label_asym_id_2 
_ndb_struct_na_base_pair_step.i_label_comp_id_2 
_ndb_struct_na_base_pair_step.i_label_seq_id_2 
_ndb_struct_na_base_pair_step.i_symmetry_2 
_ndb_struct_na_base_pair_step.j_label_asym_id_2 
_ndb_struct_na_base_pair_step.j_label_comp_id_2 
_ndb_struct_na_base_pair_step.j_label_seq_id_2 
_ndb_struct_na_base_pair_step.j_symmetry_2 
_ndb_struct_na_base_pair_step.shift 
_ndb_struct_na_base_pair_step.slide 
_ndb_struct_na_base_pair_step.rise 
_ndb_struct_na_base_pair_step.tilt 
_ndb_struct_na_base_pair_step.roll 
_ndb_struct_na_base_pair_step.twist 
_ndb_struct_na_base_pair_step.x_displacement 
_ndb_struct_na_base_pair_step.y_displacement 
_ndb_struct_na_base_pair_step.helical_rise 
_ndb_struct_na_base_pair_step.inclination 
_ndb_struct_na_base_pair_step.tip 
_ndb_struct_na_base_pair_step.helical_twist 
_ndb_struct_na_base_pair_step.step_number 
_ndb_struct_na_base_pair_step.step_name 
_ndb_struct_na_base_pair_step.i_auth_asym_id_1 
_ndb_struct_na_base_pair_step.i_auth_seq_id_1 
_ndb_struct_na_base_pair_step.i_PDB_ins_code_1 
_ndb_struct_na_base_pair_step.j_auth_asym_id_1 
_ndb_struct_na_base_pair_step.j_auth_seq_id_1 
_ndb_struct_na_base_pair_step.j_PDB_ins_code_1 
_ndb_struct_na_base_pair_step.i_auth_asym_id_2 
_ndb_struct_na_base_pair_step.i_auth_seq_id_2 
_ndb_struct_na_base_pair_step.i_PDB_ins_code_2 
_ndb_struct_na_base_pair_step.j_auth_asym_id_2 
_ndb_struct_na_base_pair_step.j_auth_seq_id_2 
_ndb_struct_na_base_pair_step.j_PDB_ins_code_2 
1 A C 1  1_555 A G 20 1_555 A U 2  1_555 A A 19 1_555 0.557  -1.810 3.118 0.483  8.492  33.297  -4.246 -0.876 2.599  14.526  
-0.826  34.337  1 AA_C1U2:A19G20_AA  A 1  ? A 20 ? A 2  ? A 19 ? 
1 A U 2  1_555 A A 19 1_555 A G 3  1_555 A C 18 1_555 -0.405 -1.732 2.905 1.722  8.666  30.633  -4.443 0.994  2.315  15.990  
-3.177  31.853  2 AA_U2G3:C18A19_AA  A 2  ? A 19 ? A 3  ? A 18 ? 
1 A G 3  1_555 A C 18 1_555 A G 4  1_555 A C 17 1_555 0.760  -1.716 3.012 1.809  7.005  28.150  -4.754 -1.171 2.562  14.110  
-3.645  29.047  3 AA_G3G4:C17C18_AA  A 3  ? A 18 ? A 4  ? A 17 ? 
1 A G 4  1_555 A C 17 1_555 A G 5  1_555 A C 16 1_555 0.248  -1.828 3.303 5.388  6.598  36.115  -3.730 0.309  2.941  10.464  
-8.546  37.073  4 AA_G4G5:C16C17_AA  A 4  ? A 17 ? A 5  ? A 16 ? 
1 A G 5  1_555 A C 16 1_555 A U 6  1_555 A A 28 1_555 -6.107 0.007  1.831 11.386 -0.225 32.544  0.021  10.764 -0.231 -0.387  
-19.585 34.428  5 AA_G5U6:A28C16_AA  A 5  ? A 16 ? A 6  ? A 28 ? 
1 A U 6  1_555 A A 28 1_555 A C 30 1_555 A G 11 1_555 0.337  -3.293 4.990 5.694  4.485  103.755 -2.187 -0.092 4.896  2.848   
-3.616  103.935 6 AA_U6C30:G11A28_AA A 6  ? A 28 ? A 30 ? A 11 ? 
1 A C 30 1_555 A G 11 1_555 A A 31 1_555 A G 8  1_555 1.174  -3.578 3.192 3.857  8.805  -6.411  0.025  13.611 4.107  -51.641 
22.618  -11.550 7 AA_C30A31:G8G11_AA A 30 ? A 11 ? A 31 ? A 8  ? 
1 A A 31 1_555 A G 8  1_555 A A 32 1_555 A A 10 1_555 -3.766 3.074  3.102 -7.270 -3.028 42.937  4.431  4.363  3.450  -4.095  9.833 
43.620  8 AA_A31A32:A10G8_AA A 31 ? A 8  ? A 32 ? A 10 ? 
1 A A 32 1_555 A A 10 1_555 A G 33 1_555 A C 9  1_555 1.135  -1.181 3.996 -4.052 9.905  57.532  -1.824 -1.414 3.685  10.194  4.170 
58.435  9 AA_A32G33:C9A10_AA A 32 ? A 10 ? A 33 ? A 9  ? 
# 
_atom_sites.entry_id                    3GCA 
_atom_sites.fract_transf_matrix[1][1]   0.009050 
_atom_sites.fract_transf_matrix[1][2]   0.005225 
_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]   0.010450 
_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]   0.016861 
_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 
S 
# 
loop_