data_1P4Z
# 
_entry.id   1P4Z 
# 
_audit_conform.dict_name       mmcif_pdbx.dic 
_audit_conform.dict_version    5.389 
_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   1P4Z         pdb_00001p4z 10.2210/pdb1p4z/pdb 
NDB   UD0029       ?            ?                   
RCSB  RCSB019013   ?            ?                   
WWPDB D_1000019013 ?            ?                   
# 
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 2003-09-02 
2 'Structure model' 1 1 2008-04-29 
3 'Structure model' 1 2 2011-07-13 
4 'Structure model' 1 3 2011-11-16 
5 'Structure model' 1 4 2024-02-14 
6 'Structure model' 1 5 2024-04-03 
# 
_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' 'Data collection'           
5 5 'Structure model' 'Database references'       
6 5 'Structure model' 'Derived calculations'      
7 6 'Structure model' 'Refinement description'    
# 
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' chem_comp_atom                
2 5 'Structure model' chem_comp_bond                
3 5 'Structure model' database_2                    
4 5 'Structure model' struct_site                   
5 6 'Structure model' pdbx_initial_refinement_model 
# 
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 5 'Structure model' '_database_2.pdbx_DOI'                
2 5 'Structure model' '_database_2.pdbx_database_accession' 
3 5 'Structure model' '_struct_site.pdbx_auth_asym_id'      
4 5 'Structure model' '_struct_site.pdbx_auth_comp_id'      
5 5 'Structure model' '_struct_site.pdbx_auth_seq_id'       
# 
_pdbx_database_status.status_code                     REL 
_pdbx_database_status.entry_id                        1P4Z 
_pdbx_database_status.recvd_initial_deposition_date   2003-04-24 
_pdbx_database_status.deposit_site                    RCSB 
_pdbx_database_status.process_site                    RCSB 
_pdbx_database_status.status_code_sf                  REL 
_pdbx_database_status.SG_entry                        . 
_pdbx_database_status.pdb_format_compatible           Y 
_pdbx_database_status.status_code_mr                  ? 
_pdbx_database_status.status_code_cs                  ? 
_pdbx_database_status.status_code_nmr_data            ? 
_pdbx_database_status.methods_development_category    ? 
# 
loop_
_pdbx_database_related.db_name 
_pdbx_database_related.db_id 
_pdbx_database_related.details 
_pdbx_database_related.content_type 
PDB 1P4Y 'Effect of Sequence on the Conformational Geometry of DNA Holliday Junctions' unspecified 
PDB 1P54 'Effect of Sequence on the Conformational Geometry of DNA Holliday Junctions' unspecified 
# 
loop_
_audit_author.name 
_audit_author.pdbx_ordinal 
'Hays, F.A.'     1 
'Vargason, J.M.' 2 
'Ho, P.S.'       3 
# 
_citation.id                        primary 
_citation.title                     'Effect of Sequence on the Conformation of DNA Holliday Junctions' 
_citation.journal_abbrev            Biochemistry 
_citation.journal_volume            42 
_citation.page_first                9586 
_citation.page_last                 9597 
_citation.year                      2003 
_citation.journal_id_ASTM           BICHAW 
_citation.country                   US 
_citation.journal_id_ISSN           0006-2960 
_citation.journal_id_CSD            0033 
_citation.book_publisher            ? 
_citation.pdbx_database_id_PubMed   12911300 
_citation.pdbx_database_id_DOI      10.1021/bi0346603 
# 
loop_
_citation_author.citation_id 
_citation_author.name 
_citation_author.ordinal 
_citation_author.identifier_ORCID 
primary 'Hays, F.A.'     1 ? 
primary 'Vargason, J.M.' 2 ? 
primary 'Ho, P.S.'       3 ? 
# 
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 "5'-D(*CP*CP*AP*GP*TP*AP*CP*TP*GP*G)-3'" 3045.004 1  ? ? ? ? 
2 non-polymer syn 'SODIUM ION'                             22.990   3  ? ? ? ? 
3 water       nat water                                    18.015   64 ? ? ? ? 
# 
_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       '(DC)(DC)(DA)(DG)(DT)(DA)(DC)(DT)(DG)(DG)' 
_entity_poly.pdbx_seq_one_letter_code_can   CCAGTACTGG 
_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 'SODIUM ION' NA  
3 water        HOH 
# 
loop_
_entity_poly_seq.entity_id 
_entity_poly_seq.num 
_entity_poly_seq.mon_id 
_entity_poly_seq.hetero 
1 1  DC n 
1 2  DC n 
1 3  DA n 
1 4  DG n 
1 5  DT n 
1 6  DA n 
1 7  DC n 
1 8  DT n 
1 9  DG n 
1 10 DG 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                
;DNA was synthesized on an Applied Biosystems DNA synthesizer using phosphoramidite chemistry, with the trityl-protecting group left intact at the 5-terminal nucleotide, FOR SUBSEQUENT HPLC PURIFICATION, THEN DEPROTECTED BY TREATMENT WITH 3% ACETIC ACID FOR FIFTEEN MINUTES, NEUTRALIZED WITH AMMONIUM HYDROXIDE, AND DESALTED ON A SIGMA G-25 SEPHADEX COLUMN.
;
# 
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 
DC  'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE"  ? 'C9 H14 N3 O7 P'  307.197 
DG  'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 
DT  'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE"         ? 'C10 H15 N2 O8 P' 322.208 
HOH non-polymer   . WATER                                ? 'H2 O'            18.015  
NA  non-polymer   . 'SODIUM ION'                         ? 'Na 1'            22.990  
# 
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  DC 1  1  1  DC C A . n 
A 1 2  DC 2  2  2  DC C A . n 
A 1 3  DA 3  3  3  DA A A . n 
A 1 4  DG 4  4  4  DG G A . n 
A 1 5  DT 5  5  5  DT T A . n 
A 1 6  DA 6  6  6  DA A A . n 
A 1 7  DC 7  7  7  DC C A . n 
A 1 8  DT 8  8  8  DT T A . n 
A 1 9  DG 9  9  9  DG G A . n 
A 1 10 DG 10 10 10 DG 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 NA  1  12 12 NA  NA  A . 
C 2 NA  1  13 13 NA  NA  A . 
D 2 NA  1  24 24 NA  NA  A . 
E 3 HOH 1  11 11 HOH HOH A . 
E 3 HOH 2  14 14 HOH HOH A . 
E 3 HOH 3  15 15 HOH HOH A . 
E 3 HOH 4  16 16 HOH HOH A . 
E 3 HOH 5  17 17 HOH HOH A . 
E 3 HOH 6  18 18 HOH HOH A . 
E 3 HOH 7  19 19 HOH HOH A . 
E 3 HOH 8  20 20 HOH HOH A . 
E 3 HOH 9  21 21 HOH HOH A . 
E 3 HOH 10 22 22 HOH HOH A . 
E 3 HOH 11 23 23 HOH HOH A . 
E 3 HOH 12 25 25 HOH HOH A . 
E 3 HOH 13 26 26 HOH HOH A . 
E 3 HOH 14 27 27 HOH HOH A . 
E 3 HOH 15 28 28 HOH HOH A . 
E 3 HOH 16 29 29 HOH HOH A . 
E 3 HOH 17 30 30 HOH HOH A . 
E 3 HOH 18 31 31 HOH HOH A . 
E 3 HOH 19 32 32 HOH HOH A . 
E 3 HOH 20 33 33 HOH HOH A . 
E 3 HOH 21 34 34 HOH HOH A . 
E 3 HOH 22 35 35 HOH HOH A . 
E 3 HOH 23 36 36 HOH HOH A . 
E 3 HOH 24 37 37 HOH HOH A . 
E 3 HOH 25 38 38 HOH HOH A . 
E 3 HOH 26 39 39 HOH HOH A . 
E 3 HOH 27 40 40 HOH HOH A . 
E 3 HOH 28 41 41 HOH HOH A . 
E 3 HOH 29 42 42 HOH HOH A . 
E 3 HOH 30 43 43 HOH HOH A . 
E 3 HOH 31 44 44 HOH HOH A . 
E 3 HOH 32 45 45 HOH HOH A . 
E 3 HOH 33 46 46 HOH HOH A . 
E 3 HOH 34 47 47 HOH HOH A . 
E 3 HOH 35 48 48 HOH HOH A . 
E 3 HOH 36 49 49 HOH HOH A . 
E 3 HOH 37 50 50 HOH HOH A . 
E 3 HOH 38 51 51 HOH HOH A . 
E 3 HOH 39 52 52 HOH HOH A . 
E 3 HOH 40 53 53 HOH HOH A . 
E 3 HOH 41 54 54 HOH HOH A . 
E 3 HOH 42 55 55 HOH HOH A . 
E 3 HOH 43 56 56 HOH HOH A . 
E 3 HOH 44 57 57 HOH HOH A . 
E 3 HOH 45 58 58 HOH HOH A . 
E 3 HOH 46 59 59 HOH HOH A . 
E 3 HOH 47 60 60 HOH HOH A . 
E 3 HOH 48 61 61 HOH HOH A . 
E 3 HOH 49 62 62 HOH HOH A . 
E 3 HOH 50 63 63 HOH HOH A . 
E 3 HOH 51 64 64 HOH HOH A . 
E 3 HOH 52 65 65 HOH HOH A . 
E 3 HOH 53 66 66 HOH HOH A . 
E 3 HOH 54 67 67 HOH HOH A . 
E 3 HOH 55 68 68 HOH HOH A . 
E 3 HOH 56 69 69 HOH HOH A . 
E 3 HOH 57 70 70 HOH HOH A . 
E 3 HOH 58 71 71 HOH HOH A . 
E 3 HOH 59 72 72 HOH HOH A . 
E 3 HOH 60 73 73 HOH HOH A . 
E 3 HOH 61 74 74 HOH HOH A . 
E 3 HOH 62 75 75 HOH HOH A . 
E 3 HOH 63 76 76 HOH HOH A . 
E 3 HOH 64 77 77 HOH HOH A . 
# 
loop_
_software.name 
_software.classification 
_software.version 
_software.citation_id 
_software.pdbx_ordinal 
DENZO     'data reduction' .   ? 1 
SCALEPACK 'data scaling'   .   ? 2 
EPMR      phasing          .   ? 3 
CNS       refinement       1.0 ? 4 
# 
_cell.entry_id           1P4Z 
_cell.length_a           33.380 
_cell.length_b           33.380 
_cell.length_c           87.670 
_cell.angle_alpha        90.00 
_cell.angle_beta         90.00 
_cell.angle_gamma        120.00 
_cell.Z_PDB              12 
_cell.pdbx_unique_axis   ? 
# 
_symmetry.entry_id                         1P4Z 
_symmetry.space_group_name_H-M             'P 61 2 2' 
_symmetry.pdbx_full_space_group_name_H-M   ? 
_symmetry.cell_setting                     ? 
_symmetry.Int_Tables_number                178 
# 
_exptl.entry_id          1P4Z 
_exptl.method            'X-RAY DIFFRACTION' 
_exptl.crystals_number   1 
# 
_exptl_crystal.id                    1 
_exptl_crystal.density_meas          ? 
_exptl_crystal.density_Matthews      1.87 
_exptl_crystal.density_percent_sol   33.78 
_exptl_crystal.description           ? 
# 
_exptl_crystal_grow.crystal_id      1 
_exptl_crystal_grow.method          ? 
_exptl_crystal_grow.temp            293 
_exptl_crystal_grow.temp_details    ? 
_exptl_crystal_grow.pH              7.50 
_exptl_crystal_grow.pdbx_details    
'0.6mM DNA, 5mM TRIS(HCl), 25mM Ca-Acetate, 7% MPD, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K, pH 7.50' 
_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 'TRIS(HCl)' ? ? ? 
1 2 1 Ca-Acetate  ? ? ? 
1 3 1 MPD         ? ? ? 
1 4 1 H2O         ? ? ? 
1 5 2 Ca-Acetate  ? ? ? 
1 6 2 MPD         ? ? ? 
1 7 2 'TRIS(HCl)' ? ? ? 
1 8 2 H2O         ? ? ? 
# 
_diffrn.id                     1 
_diffrn.ambient_temp           103.0 
_diffrn.ambient_temp_details   ? 
_diffrn.crystal_id             1 
# 
_diffrn_detector.diffrn_id              1 
_diffrn_detector.detector               CCD 
_diffrn_detector.type                   'ADSC QUANTUM 4' 
_diffrn_detector.pdbx_collection_date   2002-07-18 
_diffrn_detector.details                'BENT CONICAL SI-MIRROR (RH COATING)' 
# 
_diffrn_radiation.diffrn_id                        1 
_diffrn_radiation.wavelength_id                    1 
_diffrn_radiation.pdbx_monochromatic_or_laue_m_l   M 
_diffrn_radiation.monochromator                    'BENT GE(111) MONOCHROMATOR' 
_diffrn_radiation.pdbx_diffrn_protocol             'SINGLE WAVELENGTH' 
_diffrn_radiation.pdbx_scattering_type             x-ray 
# 
_diffrn_radiation_wavelength.id           1 
_diffrn_radiation_wavelength.wavelength   1.0 
_diffrn_radiation_wavelength.wt           1.0 
# 
_diffrn_source.diffrn_id                   1 
_diffrn_source.source                      SYNCHROTRON 
_diffrn_source.type                        'APS BEAMLINE 14-BM-C' 
_diffrn_source.pdbx_synchrotron_site       APS 
_diffrn_source.pdbx_synchrotron_beamline   14-BM-C 
_diffrn_source.pdbx_wavelength             1.0 
_diffrn_source.pdbx_wavelength_list        ? 
# 
_reflns.entry_id                     1P4Z 
_reflns.observed_criterion_sigma_I   0.000 
_reflns.observed_criterion_sigma_F   ? 
_reflns.d_resolution_low             17.470 
_reflns.d_resolution_high            2.000 
_reflns.number_obs                   2143 
_reflns.number_all                   ? 
_reflns.percent_possible_obs         95.1 
_reflns.pdbx_Rmerge_I_obs            0.039 
_reflns.pdbx_Rsym_value              ? 
_reflns.pdbx_netI_over_sigmaI        ? 
_reflns.B_iso_Wilson_estimate        3.6 
_reflns.pdbx_redundancy              ? 
_reflns.R_free_details               ? 
_reflns.pdbx_diffrn_id               1 
_reflns.pdbx_ordinal                 1 
# 
_reflns_shell.d_res_high             2.00 
_reflns_shell.d_res_low              2.13 
_reflns_shell.percent_possible_all   74.6 
_reflns_shell.Rmerge_I_obs           0.124 
_reflns_shell.pdbx_Rsym_value        ? 
_reflns_shell.meanI_over_sigI_obs    2.380 
_reflns_shell.pdbx_redundancy        ? 
_reflns_shell.percent_possible_obs   ? 
_reflns_shell.number_unique_all      ? 
_reflns_shell.pdbx_diffrn_id         ? 
_reflns_shell.pdbx_ordinal           1 
# 
_refine.entry_id                                 1P4Z 
_refine.ls_number_reflns_obs                     2143 
_refine.ls_number_reflns_all                     2143 
_refine.pdbx_ls_sigma_I                          ? 
_refine.pdbx_ls_sigma_F                          0.000 
_refine.pdbx_data_cutoff_high_absF               ? 
_refine.pdbx_data_cutoff_low_absF                ? 
_refine.pdbx_data_cutoff_high_rms_absF           ? 
_refine.ls_d_res_low                             17.47 
_refine.ls_d_res_high                            2.00 
_refine.ls_percent_reflns_obs                    95.1 
_refine.ls_R_factor_obs                          0.236 
_refine.ls_R_factor_all                          ? 
_refine.ls_R_factor_R_work                       0.236 
_refine.ls_R_factor_R_free                       0.268 
_refine.ls_R_factor_R_free_error                 0.019 
_refine.ls_R_factor_R_free_error_details         ? 
_refine.ls_percent_reflns_R_free                 9.1 
_refine.ls_number_reflns_R_free                  195 
_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                               7.80 
_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_solvent_vdw_probe_radii             ? 
_refine.pdbx_solvent_ion_probe_radii             ? 
_refine.pdbx_solvent_shrinkage_radii             ? 
_refine.pdbx_ls_cross_valid_method               THROUGHOUT 
_refine.details                                  ? 
_refine.pdbx_starting_model                      'UNPUBLISHED RESULTS OF STRUCTURE WITH ISOMORPHOUS UNIT CELL DIMENSIONS' 
_refine.pdbx_method_to_determine_struct          'MOLECULAR REPLACEMENT' 
_refine.pdbx_isotropic_thermal_model             RESTRAINED 
_refine.pdbx_stereochemistry_target_values       ? 
_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.overall_SU_R_Cruickshank_DPI             ? 
_refine.overall_SU_R_free                        ? 
_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_analyze.entry_id                        1P4Z 
_refine_analyze.Luzzati_coordinate_error_obs    0.26 
_refine_analyze.Luzzati_sigma_a_obs             0.24 
_refine_analyze.Luzzati_d_res_low_obs           5.00 
_refine_analyze.Luzzati_coordinate_error_free   0.33 
_refine_analyze.Luzzati_sigma_a_free            0.23 
_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_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   202 
_refine_hist.pdbx_number_atoms_ligand         3 
_refine_hist.number_atoms_solvent             64 
_refine_hist.number_atoms_total               269 
_refine_hist.d_res_high                       2.00 
_refine_hist.d_res_low                        17.47 
# 
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                0.015 ? ? ? 'X-RAY DIFFRACTION' ? 
c_bond_d_na             ?     ? ? ? 'X-RAY DIFFRACTION' ? 
c_bond_d_prot           ?     ? ? ? 'X-RAY DIFFRACTION' ? 
c_angle_d               ?     ? ? ? 'X-RAY DIFFRACTION' ? 
c_angle_d_na            ?     ? ? ? 'X-RAY DIFFRACTION' ? 
c_angle_d_prot          ?     ? ? ? 'X-RAY DIFFRACTION' ? 
c_angle_deg             1.7   ? ? ? 'X-RAY DIFFRACTION' ? 
c_angle_deg_na          ?     ? ? ? 'X-RAY DIFFRACTION' ? 
c_angle_deg_prot        ?     ? ? ? 'X-RAY DIFFRACTION' ? 
c_dihedral_angle_d      18.30 ? ? ? 'X-RAY DIFFRACTION' ? 
c_dihedral_angle_d_na   ?     ? ? ? 'X-RAY DIFFRACTION' ? 
c_dihedral_angle_d_prot ?     ? ? ? 'X-RAY DIFFRACTION' ? 
c_improper_angle_d      2.23  ? ? ? 'X-RAY DIFFRACTION' ? 
c_improper_angle_d_na   ?     ? ? ? 'X-RAY DIFFRACTION' ? 
c_improper_angle_d_prot ?     ? ? ? 'X-RAY DIFFRACTION' ? 
c_mcbond_it             ?     ? ? ? 'X-RAY DIFFRACTION' ? 
c_mcangle_it            ?     ? ? ? 'X-RAY DIFFRACTION' ? 
c_scbond_it             ?     ? ? ? 'X-RAY DIFFRACTION' ? 
c_scangle_it            ?     ? ? ? 'X-RAY DIFFRACTION' ? 
# 
_refine_ls_shell.pdbx_total_number_of_bins_used   6 
_refine_ls_shell.d_res_high                       2.00 
_refine_ls_shell.d_res_low                        2.13 
_refine_ls_shell.number_reflns_R_work             244 
_refine_ls_shell.R_factor_R_work                  0.242 
_refine_ls_shell.percent_reflns_obs               74.6 
_refine_ls_shell.R_factor_R_free                  0.251 
_refine_ls_shell.R_factor_R_free_error            0.055 
_refine_ls_shell.percent_reflns_R_free            7.9 
_refine_ls_shell.number_reflns_R_free             21 
_refine_ls_shell.redundancy_reflns_obs            ? 
_refine_ls_shell.pdbx_refine_id                   'X-RAY DIFFRACTION' 
_refine_ls_shell.number_reflns_all                ? 
_refine_ls_shell.R_factor_all                     ? 
# 
_database_PDB_matrix.entry_id          1P4Z 
_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                  1P4Z 
_struct.title                     'Effect of Sequence on the Conformational Geometry of DNA Holliday Junctions' 
_struct.pdbx_model_details        ? 
_struct.pdbx_CASP_flag            ? 
_struct.pdbx_model_type_details   ? 
# 
_struct_keywords.entry_id        1P4Z 
_struct_keywords.pdbx_keywords   DNA 
_struct_keywords.text            'B-DNA, Double Helix, 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 2 ? 
C N N 2 ? 
D N N 2 ? 
E N N 3 ? 
# 
_struct_ref.id                         1 
_struct_ref.entity_id                  1 
_struct_ref.db_name                    PDB 
_struct_ref.db_code                    1P4Z 
_struct_ref.pdbx_db_accession          1P4Z 
_struct_ref.pdbx_db_isoform            ? 
_struct_ref.pdbx_seq_one_letter_code   ? 
_struct_ref.pdbx_align_begin           ? 
# 
_struct_ref_seq.align_id                      1 
_struct_ref_seq.ref_id                        1 
_struct_ref_seq.pdbx_PDB_id_code              1P4Z 
_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                 10 
_struct_ref_seq.pdbx_seq_align_end_ins_code   ? 
_struct_ref_seq.pdbx_db_accession             1P4Z 
_struct_ref_seq.db_align_beg                  1 
_struct_ref_seq.pdbx_db_align_beg_ins_code    ? 
_struct_ref_seq.db_align_end                  10 
_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       10 
# 
_pdbx_struct_assembly.id                   1 
_pdbx_struct_assembly.details              author_defined_assembly 
_pdbx_struct_assembly.method_details       ? 
_pdbx_struct_assembly.oligomeric_details   dimeric 
_pdbx_struct_assembly.oligomeric_count     2 
# 
_pdbx_struct_assembly_gen.assembly_id       1 
_pdbx_struct_assembly_gen.oper_expression   1,2 
_pdbx_struct_assembly_gen.asym_id_list      A,B,C,D,E 
# 
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' 12_545 x,x-y-1,-z+1/6 0.5000000000 0.8660254038 0.0000000000 16.6900000000 0.8660254038 
-0.5000000000 0.0000000000 -28.9079279783 0.0000000000 0.0000000000 -1.0000000000 14.6116666667 
# 
_struct_biol.id                    1 
_struct_biol.details               
;THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF ONE CHAIN.  GENERATION OF THE DOUBLE HELIX CAN BE PERFORMED WITH THE FOLLOWING: 
 
matrix= 
(0.50000  0.86603  0.00000 ) 
(0.86603 -0.50000  0.00000 ) 
(0.00000  0.00000 -1.00000 ) 
 
translation=  
(16.68855 -28.90537 14.61163)
;
_struct_biol.pdbx_parent_biol_id   ? 
# 
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 
metalc1  metalc ? ? A DC 2  OP2 ? ? ? 1_555 B NA  .  NA ? ? A DC 2  A NA  12 1_555  ? ? ? ? ? ? ?            2.825 ? ? 
metalc2  metalc ? ? A DG 4  OP2 ? ? ? 1_555 C NA  .  NA ? ? A DG 4  A NA  13 1_555  ? ? ? ? ? ? ?            2.944 ? ? 
metalc3  metalc ? ? B NA .  NA  ? ? ? 1_555 E HOH .  O  ? ? A NA 12 A HOH 25 1_555  ? ? ? ? ? ? ?            2.713 ? ? 
metalc4  metalc ? ? D NA .  NA  ? ? ? 1_555 E HOH .  O  ? ? A NA 24 A HOH 42 1_555  ? ? ? ? ? ? ?            2.920 ? ? 
hydrog1  hydrog ? ? A DC 1  N3  ? ? ? 1_555 A DG  10 N1 ? ? A DC 1  A DG  10 12_545 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog2  hydrog ? ? A DC 1  N4  ? ? ? 1_555 A DG  10 O6 ? ? A DC 1  A DG  10 12_545 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog3  hydrog ? ? A DC 1  O2  ? ? ? 1_555 A DG  10 N2 ? ? A DC 1  A DG  10 12_545 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog4  hydrog ? ? A DC 2  O2  ? ? ? 1_555 A DG  9  N2 ? ? A DC 2  A DG  9  12_545 ? ? ? ? ? ? 'DC-DG PAIR' ?     ? ? 
hydrog5  hydrog ? ? A DA 3  N1  ? ? ? 1_555 A DT  8  N3 ? ? A DA 3  A DT  8  12_545 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog6  hydrog ? ? A DA 3  N6  ? ? ? 1_555 A DT  8  O4 ? ? A DA 3  A DT  8  12_545 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog7  hydrog ? ? A DG 4  N1  ? ? ? 1_555 A DC  7  N3 ? ? A DG 4  A DC  7  12_545 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog8  hydrog ? ? A DG 4  N2  ? ? ? 1_555 A DC  7  O2 ? ? A DG 4  A DC  7  12_545 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog9  hydrog ? ? A DG 4  O6  ? ? ? 1_555 A DC  7  N4 ? ? A DG 4  A DC  7  12_545 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog10 hydrog ? ? A DC 7  N3  ? ? ? 1_555 A DG  4  N1 ? ? A DC 7  A DG  4  12_545 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog11 hydrog ? ? A DC 7  N4  ? ? ? 1_555 A DG  4  O6 ? ? A DC 7  A DG  4  12_545 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog12 hydrog ? ? A DC 7  O2  ? ? ? 1_555 A DG  4  N2 ? ? A DC 7  A DG  4  12_545 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog13 hydrog ? ? A DT 8  N3  ? ? ? 1_555 A DA  3  N1 ? ? A DT 8  A DA  3  12_545 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog14 hydrog ? ? A DT 8  O4  ? ? ? 1_555 A DA  3  N6 ? ? A DT 8  A DA  3  12_545 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog15 hydrog ? ? A DG 9  N1  ? ? ? 1_555 A DC  2  N3 ? ? A DG 9  A DC  2  12_545 ? ? ? ? ? ? 'DG-DC PAIR' ?     ? ? 
hydrog16 hydrog ? ? A DG 10 N1  ? ? ? 1_555 A DC  1  N3 ? ? A DG 10 A DC  1  12_545 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog17 hydrog ? ? A DG 10 N2  ? ? ? 1_555 A DC  1  O2 ? ? A DG 10 A DC  1  12_545 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog18 hydrog ? ? A DG 10 O6  ? ? ? 1_555 A DC  1  N4 ? ? A DG 10 A DC  1  12_545 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
# 
loop_
_struct_conn_type.id 
_struct_conn_type.criteria 
_struct_conn_type.reference 
metalc ? ? 
hydrog ? ? 
# 
_pdbx_struct_conn_angle.id                    1 
_pdbx_struct_conn_angle.ptnr1_label_atom_id   OP2 
_pdbx_struct_conn_angle.ptnr1_label_alt_id    ? 
_pdbx_struct_conn_angle.ptnr1_label_asym_id   A 
_pdbx_struct_conn_angle.ptnr1_label_comp_id   DC 
_pdbx_struct_conn_angle.ptnr1_label_seq_id    2 
_pdbx_struct_conn_angle.ptnr1_auth_atom_id    ? 
_pdbx_struct_conn_angle.ptnr1_auth_asym_id    A 
_pdbx_struct_conn_angle.ptnr1_auth_comp_id    DC 
_pdbx_struct_conn_angle.ptnr1_auth_seq_id     2 
_pdbx_struct_conn_angle.ptnr1_PDB_ins_code    ? 
_pdbx_struct_conn_angle.ptnr1_symmetry        1_555 
_pdbx_struct_conn_angle.ptnr2_label_atom_id   NA 
_pdbx_struct_conn_angle.ptnr2_label_alt_id    ? 
_pdbx_struct_conn_angle.ptnr2_label_asym_id   B 
_pdbx_struct_conn_angle.ptnr2_label_comp_id   NA 
_pdbx_struct_conn_angle.ptnr2_label_seq_id    . 
_pdbx_struct_conn_angle.ptnr2_auth_atom_id    ? 
_pdbx_struct_conn_angle.ptnr2_auth_asym_id    A 
_pdbx_struct_conn_angle.ptnr2_auth_comp_id    NA 
_pdbx_struct_conn_angle.ptnr2_auth_seq_id     12 
_pdbx_struct_conn_angle.ptnr2_PDB_ins_code    ? 
_pdbx_struct_conn_angle.ptnr2_symmetry        1_555 
_pdbx_struct_conn_angle.ptnr3_label_atom_id   O 
_pdbx_struct_conn_angle.ptnr3_label_alt_id    ? 
_pdbx_struct_conn_angle.ptnr3_label_asym_id   E 
_pdbx_struct_conn_angle.ptnr3_label_comp_id   HOH 
_pdbx_struct_conn_angle.ptnr3_label_seq_id    . 
_pdbx_struct_conn_angle.ptnr3_auth_atom_id    ? 
_pdbx_struct_conn_angle.ptnr3_auth_asym_id    A 
_pdbx_struct_conn_angle.ptnr3_auth_comp_id    HOH 
_pdbx_struct_conn_angle.ptnr3_auth_seq_id     25 
_pdbx_struct_conn_angle.ptnr3_PDB_ins_code    ? 
_pdbx_struct_conn_angle.ptnr3_symmetry        1_555 
_pdbx_struct_conn_angle.value                 127.0 
_pdbx_struct_conn_angle.value_esd             ? 
# 
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 NA 12 ? 2 'BINDING SITE FOR RESIDUE NA A 12' 
AC2 Software A NA 13 ? 1 'BINDING SITE FOR RESIDUE NA A 13' 
AC3 Software A NA 24 ? 2 'BINDING SITE FOR RESIDUE NA A 24' 
# 
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 2 DC  A 2 ? DC  A 2  . ? 1_555 ? 
2 AC1 2 HOH E . ? HOH A 25 . ? 1_555 ? 
3 AC2 1 DG  A 4 ? DG  A 4  . ? 1_555 ? 
4 AC3 2 DC  A 7 ? DC  A 7  . ? 1_555 ? 
5 AC3 2 HOH E . ? HOH A 42 . ? 1_555 ? 
# 
_pdbx_validate_close_contact.id               1 
_pdbx_validate_close_contact.PDB_model_num    1 
_pdbx_validate_close_contact.auth_atom_id_1   OP1 
_pdbx_validate_close_contact.auth_asym_id_1   A 
_pdbx_validate_close_contact.auth_comp_id_1   DT 
_pdbx_validate_close_contact.auth_seq_id_1    8 
_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    16 
_pdbx_validate_close_contact.PDB_ins_code_2   ? 
_pdbx_validate_close_contact.label_alt_id_2   ? 
_pdbx_validate_close_contact.dist             2.04 
# 
_pdbx_validate_rmsd_bond.id                        1 
_pdbx_validate_rmsd_bond.PDB_model_num             1 
_pdbx_validate_rmsd_bond.auth_atom_id_1            "O3'" 
_pdbx_validate_rmsd_bond.auth_asym_id_1            A 
_pdbx_validate_rmsd_bond.auth_comp_id_1            DG 
_pdbx_validate_rmsd_bond.auth_seq_id_1             10 
_pdbx_validate_rmsd_bond.PDB_ins_code_1            ? 
_pdbx_validate_rmsd_bond.label_alt_id_1            ? 
_pdbx_validate_rmsd_bond.auth_atom_id_2            "C3'" 
_pdbx_validate_rmsd_bond.auth_asym_id_2            A 
_pdbx_validate_rmsd_bond.auth_comp_id_2            DG 
_pdbx_validate_rmsd_bond.auth_seq_id_2             10 
_pdbx_validate_rmsd_bond.PDB_ins_code_2            ? 
_pdbx_validate_rmsd_bond.label_alt_id_2            ? 
_pdbx_validate_rmsd_bond.bond_value                1.377 
_pdbx_validate_rmsd_bond.bond_target_value         1.419 
_pdbx_validate_rmsd_bond.bond_deviation            -0.042 
_pdbx_validate_rmsd_bond.bond_standard_deviation   0.006 
_pdbx_validate_rmsd_bond.linker_flag               N 
# 
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 DC A 1 ? ? 0.081 'SIDE CHAIN' 
2 1 DG A 9 ? ? 0.095 'SIDE CHAIN' 
# 
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 11 ? E HOH . 
2 1 A HOH 32 ? E HOH . 
3 1 A HOH 33 ? E HOH . 
4 1 A HOH 43 ? E HOH . 
5 1 A HOH 62 ? E HOH . 
# 
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  
DC  OP3    O  N N 37  
DC  P      P  N N 38  
DC  OP1    O  N N 39  
DC  OP2    O  N N 40  
DC  "O5'"  O  N N 41  
DC  "C5'"  C  N N 42  
DC  "C4'"  C  N R 43  
DC  "O4'"  O  N N 44  
DC  "C3'"  C  N S 45  
DC  "O3'"  O  N N 46  
DC  "C2'"  C  N N 47  
DC  "C1'"  C  N R 48  
DC  N1     N  N N 49  
DC  C2     C  N N 50  
DC  O2     O  N N 51  
DC  N3     N  N N 52  
DC  C4     C  N N 53  
DC  N4     N  N N 54  
DC  C5     C  N N 55  
DC  C6     C  N N 56  
DC  HOP3   H  N N 57  
DC  HOP2   H  N N 58  
DC  "H5'"  H  N N 59  
DC  "H5''" H  N N 60  
DC  "H4'"  H  N N 61  
DC  "H3'"  H  N N 62  
DC  "HO3'" H  N N 63  
DC  "H2'"  H  N N 64  
DC  "H2''" H  N N 65  
DC  "H1'"  H  N N 66  
DC  H41    H  N N 67  
DC  H42    H  N N 68  
DC  H5     H  N N 69  
DC  H6     H  N N 70  
DG  OP3    O  N N 71  
DG  P      P  N N 72  
DG  OP1    O  N N 73  
DG  OP2    O  N N 74  
DG  "O5'"  O  N N 75  
DG  "C5'"  C  N N 76  
DG  "C4'"  C  N R 77  
DG  "O4'"  O  N N 78  
DG  "C3'"  C  N S 79  
DG  "O3'"  O  N N 80  
DG  "C2'"  C  N N 81  
DG  "C1'"  C  N R 82  
DG  N9     N  Y N 83  
DG  C8     C  Y N 84  
DG  N7     N  Y N 85  
DG  C5     C  Y N 86  
DG  C6     C  N N 87  
DG  O6     O  N N 88  
DG  N1     N  N N 89  
DG  C2     C  N N 90  
DG  N2     N  N N 91  
DG  N3     N  N N 92  
DG  C4     C  Y N 93  
DG  HOP3   H  N N 94  
DG  HOP2   H  N N 95  
DG  "H5'"  H  N N 96  
DG  "H5''" H  N N 97  
DG  "H4'"  H  N N 98  
DG  "H3'"  H  N N 99  
DG  "HO3'" H  N N 100 
DG  "H2'"  H  N N 101 
DG  "H2''" H  N N 102 
DG  "H1'"  H  N N 103 
DG  H8     H  N N 104 
DG  H1     H  N N 105 
DG  H21    H  N N 106 
DG  H22    H  N N 107 
DT  OP3    O  N N 108 
DT  P      P  N N 109 
DT  OP1    O  N N 110 
DT  OP2    O  N N 111 
DT  "O5'"  O  N N 112 
DT  "C5'"  C  N N 113 
DT  "C4'"  C  N R 114 
DT  "O4'"  O  N N 115 
DT  "C3'"  C  N S 116 
DT  "O3'"  O  N N 117 
DT  "C2'"  C  N N 118 
DT  "C1'"  C  N R 119 
DT  N1     N  N N 120 
DT  C2     C  N N 121 
DT  O2     O  N N 122 
DT  N3     N  N N 123 
DT  C4     C  N N 124 
DT  O4     O  N N 125 
DT  C5     C  N N 126 
DT  C7     C  N N 127 
DT  C6     C  N N 128 
DT  HOP3   H  N N 129 
DT  HOP2   H  N N 130 
DT  "H5'"  H  N N 131 
DT  "H5''" H  N N 132 
DT  "H4'"  H  N N 133 
DT  "H3'"  H  N N 134 
DT  "HO3'" H  N N 135 
DT  "H2'"  H  N N 136 
DT  "H2''" H  N N 137 
DT  "H1'"  H  N N 138 
DT  H3     H  N N 139 
DT  H71    H  N N 140 
DT  H72    H  N N 141 
DT  H73    H  N N 142 
DT  H6     H  N N 143 
HOH O      O  N N 144 
HOH H1     H  N N 145 
HOH H2     H  N N 146 
NA  NA     NA N N 147 
# 
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  
DC  OP3   P      sing N N 39  
DC  OP3   HOP3   sing N N 40  
DC  P     OP1    doub N N 41  
DC  P     OP2    sing N N 42  
DC  P     "O5'"  sing N N 43  
DC  OP2   HOP2   sing N N 44  
DC  "O5'" "C5'"  sing N N 45  
DC  "C5'" "C4'"  sing N N 46  
DC  "C5'" "H5'"  sing N N 47  
DC  "C5'" "H5''" sing N N 48  
DC  "C4'" "O4'"  sing N N 49  
DC  "C4'" "C3'"  sing N N 50  
DC  "C4'" "H4'"  sing N N 51  
DC  "O4'" "C1'"  sing N N 52  
DC  "C3'" "O3'"  sing N N 53  
DC  "C3'" "C2'"  sing N N 54  
DC  "C3'" "H3'"  sing N N 55  
DC  "O3'" "HO3'" sing N N 56  
DC  "C2'" "C1'"  sing N N 57  
DC  "C2'" "H2'"  sing N N 58  
DC  "C2'" "H2''" sing N N 59  
DC  "C1'" N1     sing N N 60  
DC  "C1'" "H1'"  sing N N 61  
DC  N1    C2     sing N N 62  
DC  N1    C6     sing N N 63  
DC  C2    O2     doub N N 64  
DC  C2    N3     sing N N 65  
DC  N3    C4     doub N N 66  
DC  C4    N4     sing N N 67  
DC  C4    C5     sing N N 68  
DC  N4    H41    sing N N 69  
DC  N4    H42    sing N N 70  
DC  C5    C6     doub N N 71  
DC  C5    H5     sing N N 72  
DC  C6    H6     sing N N 73  
DG  OP3   P      sing N N 74  
DG  OP3   HOP3   sing N N 75  
DG  P     OP1    doub N N 76  
DG  P     OP2    sing N N 77  
DG  P     "O5'"  sing N N 78  
DG  OP2   HOP2   sing N N 79  
DG  "O5'" "C5'"  sing N N 80  
DG  "C5'" "C4'"  sing N N 81  
DG  "C5'" "H5'"  sing N N 82  
DG  "C5'" "H5''" sing N N 83  
DG  "C4'" "O4'"  sing N N 84  
DG  "C4'" "C3'"  sing N N 85  
DG  "C4'" "H4'"  sing N N 86  
DG  "O4'" "C1'"  sing N N 87  
DG  "C3'" "O3'"  sing N N 88  
DG  "C3'" "C2'"  sing N N 89  
DG  "C3'" "H3'"  sing N N 90  
DG  "O3'" "HO3'" sing N N 91  
DG  "C2'" "C1'"  sing N N 92  
DG  "C2'" "H2'"  sing N N 93  
DG  "C2'" "H2''" sing N N 94  
DG  "C1'" N9     sing N N 95  
DG  "C1'" "H1'"  sing N N 96  
DG  N9    C8     sing Y N 97  
DG  N9    C4     sing Y N 98  
DG  C8    N7     doub Y N 99  
DG  C8    H8     sing N N 100 
DG  N7    C5     sing Y N 101 
DG  C5    C6     sing N N 102 
DG  C5    C4     doub Y N 103 
DG  C6    O6     doub N N 104 
DG  C6    N1     sing N N 105 
DG  N1    C2     sing N N 106 
DG  N1    H1     sing N N 107 
DG  C2    N2     sing N N 108 
DG  C2    N3     doub N N 109 
DG  N2    H21    sing N N 110 
DG  N2    H22    sing N N 111 
DG  N3    C4     sing N N 112 
DT  OP3   P      sing N N 113 
DT  OP3   HOP3   sing N N 114 
DT  P     OP1    doub N N 115 
DT  P     OP2    sing N N 116 
DT  P     "O5'"  sing N N 117 
DT  OP2   HOP2   sing N N 118 
DT  "O5'" "C5'"  sing N N 119 
DT  "C5'" "C4'"  sing N N 120 
DT  "C5'" "H5'"  sing N N 121 
DT  "C5'" "H5''" sing N N 122 
DT  "C4'" "O4'"  sing N N 123 
DT  "C4'" "C3'"  sing N N 124 
DT  "C4'" "H4'"  sing N N 125 
DT  "O4'" "C1'"  sing N N 126 
DT  "C3'" "O3'"  sing N N 127 
DT  "C3'" "C2'"  sing N N 128 
DT  "C3'" "H3'"  sing N N 129 
DT  "O3'" "HO3'" sing N N 130 
DT  "C2'" "C1'"  sing N N 131 
DT  "C2'" "H2'"  sing N N 132 
DT  "C2'" "H2''" sing N N 133 
DT  "C1'" N1     sing N N 134 
DT  "C1'" "H1'"  sing N N 135 
DT  N1    C2     sing N N 136 
DT  N1    C6     sing N N 137 
DT  C2    O2     doub N N 138 
DT  C2    N3     sing N N 139 
DT  N3    C4     sing N N 140 
DT  N3    H3     sing N N 141 
DT  C4    O4     doub N N 142 
DT  C4    C5     sing N N 143 
DT  C5    C7     sing N N 144 
DT  C5    C6     doub N N 145 
DT  C7    H71    sing N N 146 
DT  C7    H72    sing N N 147 
DT  C7    H73    sing N N 148 
DT  C6    H6     sing N N 149 
HOH O     H1     sing N N 150 
HOH O     H2     sing N N 151 
# 
loop_
_ndb_struct_conf_na.entry_id 
_ndb_struct_conf_na.feature 
1P4Z 'b-form double helix' 
1P4Z 'internal loop'       
# 
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 DC 1 1_555 A DG 10 12_545 -0.650 0.410  0.611  -13.196 -2.093  0.642  1 A_DC1:DG10_A A 1 ? A 10 ? 19 1 
1 A DC 2 1_555 A DG 9  12_545 -0.624 0.424  -0.315 5.008   -8.075  10.114 2 A_DC2:DG9_A  A 2 ? A 9  ? ?  1 
1 A DA 3 1_555 A DT 8  12_545 -0.077 0.073  0.342  -3.108  -19.925 1.668  3 A_DA3:DT8_A  A 3 ? A 8  ? 20 1 
1 A DG 4 1_555 A DC 7  12_545 -0.869 -0.147 0.356  12.333  -18.762 6.043  4 A_DG4:DC7_A  A 4 ? A 7  ? 19 1 
1 A DC 1 1_555 A DG 10 1_555  -0.650 0.410  0.611  -13.196 -2.093  0.642  5 A_DC1:DG10_A A 1 ? A 10 ? 19 1 
1 A DC 2 1_555 A DG 9  1_555  -0.624 0.424  -0.315 5.008   -8.075  10.114 6 A_DC2:DG9_A  A 2 ? A 9  ? ?  1 
1 A DA 3 1_555 A DT 8  1_555  -0.077 0.073  0.342  -3.108  -19.925 1.668  7 A_DA3:DT8_A  A 3 ? A 8  ? 20 1 
1 A DG 4 1_555 A DC 7  1_555  -0.869 -0.147 0.356  12.333  -18.762 6.043  8 A_DG4:DC7_A  A 4 ? A 7  ? 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 DC 1 1_555 A DG 10 12_545 A DC 2 1_555 A DG 9 12_545 0.392  0.197 2.750 10.499 2.470 24.894 -0.122 1.473  2.697 5.417 -23.024 
27.097 1 AA_DC1DC2:DG9DG10_AA A 1 ? A 10 ? A 2 ? A 9 ? 
1 A DC 2 1_555 A DG 9  12_545 A DA 3 1_555 A DT 8 12_545 -0.279 2.516 3.324 -1.108 4.375 51.684 2.569  0.241  3.516 5.007 1.268   
51.867 2 AA_DC2DA3:DT8DG9_AA  A 2 ? A 9  ? A 3 ? A 8 ? 
1 A DA 3 1_555 A DT 8  12_545 A DG 4 1_555 A DC 7 12_545 0.731  0.249 3.195 -4.526 3.916 26.602 -0.416 -2.643 3.036 8.376 9.682   
27.255 3 AA_DA3DG4:DC7DT8_AA  A 3 ? A 8  ? A 4 ? A 7 ? 
1 A DC 1 1_555 A DG 10 1_555  A DC 2 1_555 A DG 9 1_555  0.392  0.197 2.750 10.499 2.470 24.894 -0.122 1.473  2.697 5.417 -23.024 
27.097 4 AA_DC1DC2:DG9DG10_AA A 1 ? A 10 ? A 2 ? A 9 ? 
1 A DC 2 1_555 A DG 9  1_555  A DA 3 1_555 A DT 8 1_555  -0.279 2.516 3.324 -1.108 4.375 51.684 2.569  0.241  3.516 5.007 1.268   
51.867 5 AA_DC2DA3:DT8DG9_AA  A 2 ? A 9  ? A 3 ? A 8 ? 
1 A DA 3 1_555 A DT 8  1_555  A DG 4 1_555 A DC 7 1_555  0.731  0.249 3.195 -4.526 3.916 26.602 -0.416 -2.643 3.036 8.376 9.682   
27.255 6 AA_DA3DG4:DC7DT8_AA  A 3 ? A 8  ? A 4 ? A 7 ? 
# 
_pdbx_initial_refinement_model.accession_code   ? 
_pdbx_initial_refinement_model.id               1 
_pdbx_initial_refinement_model.entity_id_list   ? 
_pdbx_initial_refinement_model.type             'experimental model' 
_pdbx_initial_refinement_model.source_name      Other 
_pdbx_initial_refinement_model.details          'UNPUBLISHED RESULTS OF STRUCTURE WITH ISOMORPHOUS UNIT CELL DIMENSIONS' 
# 
_atom_sites.entry_id                    1P4Z 
_atom_sites.fract_transf_matrix[1][1]   0.029958 
_atom_sites.fract_transf_matrix[1][2]   0.017296 
_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]   0.034593 
_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]   0.011406 
_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  
NA 
O  
P  
# 
loop_