data_1P4Y
# 
_entry.id   1P4Y 
# 
_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   1P4Y         pdb_00001p4y 10.2210/pdb1p4y/pdb 
NDB   UD0028       ?            ?                   
RCSB  RCSB019012   ?            ?                   
WWPDB D_1000019012 ?            ?                   
# 
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 2024-02-14 
5 'Structure model' 1 4 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' 'Data collection'           
4 4 'Structure model' 'Database references'       
5 4 'Structure model' 'Derived calculations'      
6 5 '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 4 'Structure model' chem_comp_atom                
2 4 'Structure model' chem_comp_bond                
3 4 'Structure model' database_2                    
4 4 'Structure model' pdbx_struct_conn_angle        
5 4 'Structure model' struct_conn                   
6 4 'Structure model' struct_site                   
7 5 '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  4 'Structure model' '_database_2.pdbx_DOI'                        
2  4 'Structure model' '_database_2.pdbx_database_accession'         
3  4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_comp_id'  
4  4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id'   
5  4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_asym_id' 
6  4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_atom_id' 
7  4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_comp_id' 
8  4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_seq_id'  
9  4 'Structure model' '_pdbx_struct_conn_angle.ptnr2_auth_seq_id'   
10 4 'Structure model' '_pdbx_struct_conn_angle.ptnr2_label_asym_id' 
11 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_comp_id'  
12 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id'   
13 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id' 
14 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_atom_id' 
15 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_comp_id' 
16 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_seq_id'  
17 4 'Structure model' '_pdbx_struct_conn_angle.value'               
18 4 'Structure model' '_struct_conn.pdbx_dist_value'                
19 4 'Structure model' '_struct_conn.ptnr1_auth_asym_id'             
20 4 'Structure model' '_struct_conn.ptnr1_auth_comp_id'             
21 4 'Structure model' '_struct_conn.ptnr1_auth_seq_id'              
22 4 'Structure model' '_struct_conn.ptnr1_label_asym_id'            
23 4 'Structure model' '_struct_conn.ptnr1_label_atom_id'            
24 4 'Structure model' '_struct_conn.ptnr1_label_comp_id'            
25 4 'Structure model' '_struct_conn.ptnr1_label_seq_id'             
26 4 'Structure model' '_struct_conn.ptnr2_auth_asym_id'             
27 4 'Structure model' '_struct_conn.ptnr2_auth_comp_id'             
28 4 'Structure model' '_struct_conn.ptnr2_auth_seq_id'              
29 4 'Structure model' '_struct_conn.ptnr2_label_asym_id'            
30 4 'Structure model' '_struct_conn.ptnr2_label_atom_id'            
31 4 'Structure model' '_struct_conn.ptnr2_label_comp_id'            
32 4 'Structure model' '_struct_conn.ptnr2_label_seq_id'             
33 4 'Structure model' '_struct_site.pdbx_auth_asym_id'              
34 4 'Structure model' '_struct_site.pdbx_auth_comp_id'              
35 4 'Structure model' '_struct_site.pdbx_auth_seq_id'               
# 
_pdbx_database_status.status_code                     REL 
_pdbx_database_status.entry_id                        1P4Y 
_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 1P4Z '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*GP*GP*CP*GP*CP*CP*GP*G)-3'" 3046.980 2   ? ? ? ? 
2 non-polymer syn 'SODIUM ION'                             22.990   4   ? ? ? ? 
3 water       nat water                                    18.015   108 ? ? ? ? 
# 
_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)(DG)(DG)(DC)(DG)(DC)(DC)(DG)(DG)' 
_entity_poly.pdbx_seq_one_letter_code_can   CCGGCGCCGG 
_entity_poly.pdbx_strand_id                 A,B 
_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  DG n 
1 4  DG n 
1 5  DC n 
1 6  DG n 
1 7  DC n 
1 8  DC 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 
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 
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  DG 3  3  3  DG G A . n 
A 1 4  DG 4  4  4  DG G A . n 
A 1 5  DC 5  5  5  DC C A . n 
A 1 6  DG 6  6  6  DG G A . n 
A 1 7  DC 7  7  7  DC C A . n 
A 1 8  DC 8  8  8  DC C A . n 
A 1 9  DG 9  9  9  DG G A . n 
A 1 10 DG 10 10 10 DG G A . n 
B 1 1  DC 1  11 11 DC C B . n 
B 1 2  DC 2  12 12 DC C B . n 
B 1 3  DG 3  13 13 DG G B . n 
B 1 4  DG 4  14 14 DG G B . n 
B 1 5  DC 5  15 15 DC C B . n 
B 1 6  DG 6  16 16 DG G B . n 
B 1 7  DC 7  17 17 DC C B . n 
B 1 8  DC 8  18 18 DC C B . n 
B 1 9  DG 9  19 19 DG G B . n 
B 1 10 DG 10 20 20 DG G B . n 
# 
loop_
_pdbx_nonpoly_scheme.asym_id 
_pdbx_nonpoly_scheme.entity_id 
_pdbx_nonpoly_scheme.mon_id 
_pdbx_nonpoly_scheme.ndb_seq_num 
_pdbx_nonpoly_scheme.pdb_seq_num 
_pdbx_nonpoly_scheme.auth_seq_num 
_pdbx_nonpoly_scheme.pdb_mon_id 
_pdbx_nonpoly_scheme.auth_mon_id 
_pdbx_nonpoly_scheme.pdb_strand_id 
_pdbx_nonpoly_scheme.pdb_ins_code 
C 2 NA  1  21  21  NA  N A . 
D 2 NA  1  36  36  NA  N A . 
E 2 NA  1  49  49  NA  N A . 
F 2 NA  1  55  55  NA  N B . 
G 3 HOH 1  22  22  HOH W A . 
G 3 HOH 2  24  24  HOH W A . 
G 3 HOH 3  25  25  HOH W A . 
G 3 HOH 4  26  26  HOH W A . 
G 3 HOH 5  27  27  HOH W A . 
G 3 HOH 6  32  32  HOH W A . 
G 3 HOH 7  33  33  HOH W A . 
G 3 HOH 8  34  34  HOH W A . 
G 3 HOH 9  37  37  HOH W A . 
G 3 HOH 10 38  38  HOH W A . 
G 3 HOH 11 39  39  HOH W A . 
G 3 HOH 12 41  41  HOH W A . 
G 3 HOH 13 43  43  HOH W A . 
G 3 HOH 14 46  46  HOH W A . 
G 3 HOH 15 47  47  HOH W A . 
G 3 HOH 16 48  48  HOH W A . 
G 3 HOH 17 51  51  HOH W A . 
G 3 HOH 18 54  54  HOH W A . 
G 3 HOH 19 56  56  HOH W A . 
G 3 HOH 20 58  58  HOH W A . 
G 3 HOH 21 59  59  HOH W A . 
G 3 HOH 22 62  62  HOH W A . 
G 3 HOH 23 67  67  HOH W A . 
G 3 HOH 24 70  70  HOH W A . 
G 3 HOH 25 71  71  HOH W A . 
G 3 HOH 26 72  72  HOH W A . 
G 3 HOH 27 78  78  HOH W A . 
G 3 HOH 28 80  80  HOH W A . 
G 3 HOH 29 81  81  HOH W A . 
G 3 HOH 30 82  82  HOH W A . 
G 3 HOH 31 84  84  HOH W A . 
G 3 HOH 32 85  85  HOH W A . 
G 3 HOH 33 86  86  HOH W A . 
G 3 HOH 34 87  87  HOH W A . 
G 3 HOH 35 88  88  HOH W A . 
G 3 HOH 36 90  90  HOH W A . 
G 3 HOH 37 95  95  HOH W A . 
G 3 HOH 38 97  97  HOH W A . 
G 3 HOH 39 98  98  HOH W A . 
G 3 HOH 40 101 101 HOH W A . 
G 3 HOH 41 103 103 HOH W A . 
G 3 HOH 42 105 105 HOH W A . 
G 3 HOH 43 107 107 HOH W A . 
G 3 HOH 44 109 109 HOH W A . 
G 3 HOH 45 110 110 HOH W A . 
G 3 HOH 46 115 115 HOH W A . 
G 3 HOH 47 116 116 HOH W A . 
G 3 HOH 48 119 119 HOH W A . 
G 3 HOH 49 120 120 HOH W A . 
G 3 HOH 50 121 121 HOH W A . 
G 3 HOH 51 122 122 HOH W A . 
G 3 HOH 52 123 123 HOH W A . 
G 3 HOH 53 125 125 HOH W A . 
G 3 HOH 54 127 127 HOH W A . 
G 3 HOH 55 130 130 HOH W A . 
G 3 HOH 56 131 131 HOH W A . 
G 3 HOH 57 132 132 HOH W A . 
H 3 HOH 1  23  23  HOH W B . 
H 3 HOH 2  28  28  HOH W B . 
H 3 HOH 3  29  29  HOH W B . 
H 3 HOH 4  30  30  HOH W B . 
H 3 HOH 5  31  31  HOH W B . 
H 3 HOH 6  35  35  HOH W B . 
H 3 HOH 7  40  40  HOH W B . 
H 3 HOH 8  42  42  HOH W B . 
H 3 HOH 9  44  44  HOH W B . 
H 3 HOH 10 45  45  HOH W B . 
H 3 HOH 11 50  50  HOH W B . 
H 3 HOH 12 52  52  HOH W B . 
H 3 HOH 13 53  53  HOH W B . 
H 3 HOH 14 57  57  HOH W B . 
H 3 HOH 15 60  60  HOH W B . 
H 3 HOH 16 61  61  HOH W B . 
H 3 HOH 17 63  63  HOH W B . 
H 3 HOH 18 64  64  HOH W B . 
H 3 HOH 19 65  65  HOH W B . 
H 3 HOH 20 66  66  HOH W B . 
H 3 HOH 21 68  68  HOH W B . 
H 3 HOH 22 69  69  HOH W B . 
H 3 HOH 23 73  73  HOH W B . 
H 3 HOH 24 74  74  HOH W B . 
H 3 HOH 25 75  75  HOH W B . 
H 3 HOH 26 76  76  HOH W B . 
H 3 HOH 27 77  77  HOH W B . 
H 3 HOH 28 79  79  HOH W B . 
H 3 HOH 29 83  83  HOH W B . 
H 3 HOH 30 89  89  HOH W B . 
H 3 HOH 31 91  91  HOH W B . 
H 3 HOH 32 92  92  HOH W B . 
H 3 HOH 33 93  93  HOH W B . 
H 3 HOH 34 94  94  HOH W B . 
H 3 HOH 35 96  96  HOH W B . 
H 3 HOH 36 99  99  HOH W B . 
H 3 HOH 37 100 100 HOH W B . 
H 3 HOH 38 102 102 HOH W B . 
H 3 HOH 39 104 104 HOH W B . 
H 3 HOH 40 106 106 HOH W B . 
H 3 HOH 41 108 108 HOH W B . 
H 3 HOH 42 111 111 HOH W B . 
H 3 HOH 43 112 112 HOH W B . 
H 3 HOH 44 113 113 HOH W B . 
H 3 HOH 45 114 114 HOH W B . 
H 3 HOH 46 117 117 HOH W B . 
H 3 HOH 47 118 118 HOH W B . 
H 3 HOH 48 124 124 HOH W B . 
H 3 HOH 49 126 126 HOH W B . 
H 3 HOH 50 128 128 HOH W B . 
H 3 HOH 51 129 129 HOH W B . 
# 
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           1P4Y 
_cell.length_a           66.513 
_cell.length_b           24.179 
_cell.length_c           37.004 
_cell.angle_alpha        90.0 
_cell.angle_beta         110.010 
_cell.angle_gamma        90.0 
_cell.pdbx_unique_axis   ? 
_cell.Z_PDB              8 
# 
_symmetry.entry_id                         1P4Y 
_symmetry.space_group_name_H-M             'C 1 2 1' 
_symmetry.pdbx_full_space_group_name_H-M   ? 
_symmetry.Int_Tables_number                5 
_symmetry.cell_setting                     ? 
# 
_exptl.entry_id          1P4Y 
_exptl.method            'X-RAY DIFFRACTION' 
_exptl.crystals_number   1 
# 
_exptl_crystal.id                    1 
_exptl_crystal.density_meas          ? 
_exptl_crystal.density_Matthews      1.94 
_exptl_crystal.density_percent_sol   35.95 
_exptl_crystal.description           ? 
# 
_exptl_crystal_grow.crystal_id      1 
_exptl_crystal_grow.method          ? 
_exptl_crystal_grow.temp            298 
_exptl_crystal_grow.temp_details    ? 
_exptl_crystal_grow.pH              7.00 
_exptl_crystal_grow.pdbx_details    
;0.5mM DNA, 25mM sodium cacodylate, 7.5mM CaCl2, 0.1mM SPERMINE TETRAHYDROCHLORIDE, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K, pH 7.00
;
_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 'sodium cacodylate'           ? ? ? 
1 2 1 CaCl2                         ? ? ? 
1 3 1 'SPERMINE TETRAHYDROCHLORIDE' ? ? ? 
1 4 1 H2O                           ? ? ? 
1 5 2 'sodium cacodylate'           ? ? ? 
1 6 2 CaCl2                         ? ? ? 
1 7 2 'SPERMINE TETRAHYDROCHLORIDE' ? ? ? 
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               'IMAGE PLATE' 
_diffrn_detector.type                   'RIGAKU RAXIS IV' 
_diffrn_detector.pdbx_collection_date   2003-01-24 
_diffrn_detector.details                ? 
# 
_diffrn_radiation.diffrn_id                        1 
_diffrn_radiation.wavelength_id                    1 
_diffrn_radiation.pdbx_monochromatic_or_laue_m_l   M 
_diffrn_radiation.monochromator                    'NI FILTER' 
_diffrn_radiation.pdbx_diffrn_protocol             'SINGLE WAVELENGTH' 
_diffrn_radiation.pdbx_scattering_type             x-ray 
# 
_diffrn_radiation_wavelength.id           1 
_diffrn_radiation_wavelength.wavelength   1.542 
_diffrn_radiation_wavelength.wt           1.0 
# 
_diffrn_source.diffrn_id                   1 
_diffrn_source.source                      'ROTATING ANODE' 
_diffrn_source.type                        'RIGAKU RU300' 
_diffrn_source.pdbx_synchrotron_site       ? 
_diffrn_source.pdbx_synchrotron_beamline   ? 
_diffrn_source.pdbx_wavelength             1.542 
_diffrn_source.pdbx_wavelength_list        ? 
# 
_reflns.entry_id                     1P4Y 
_reflns.observed_criterion_sigma_I   0.000 
_reflns.observed_criterion_sigma_F   ? 
_reflns.d_resolution_low             22.550 
_reflns.d_resolution_high            1.650 
_reflns.number_obs                   4940 
_reflns.number_all                   ? 
_reflns.percent_possible_obs         74.0 
_reflns.pdbx_Rmerge_I_obs            0.048 
_reflns.pdbx_Rsym_value              ? 
_reflns.pdbx_netI_over_sigmaI        ? 
_reflns.B_iso_Wilson_estimate        1.6 
_reflns.pdbx_redundancy              ? 
_reflns.R_free_details               ? 
_reflns.pdbx_diffrn_id               1 
_reflns.pdbx_ordinal                 1 
# 
_reflns_shell.d_res_high             1.65 
_reflns_shell.d_res_low              1.71 
_reflns_shell.percent_possible_all   21.7 
_reflns_shell.Rmerge_I_obs           0.279 
_reflns_shell.pdbx_Rsym_value        ? 
_reflns_shell.meanI_over_sigI_obs    2.140 
_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                                 1P4Y 
_refine.ls_number_reflns_obs                     4436 
_refine.ls_number_reflns_all                     4940 
_refine.pdbx_ls_sigma_I                          ? 
_refine.pdbx_ls_sigma_F                          2.000 
_refine.pdbx_data_cutoff_high_absF               ? 
_refine.pdbx_data_cutoff_low_absF                ? 
_refine.pdbx_data_cutoff_high_rms_absF           ? 
_refine.ls_d_res_low                             22.50 
_refine.ls_d_res_high                            1.70 
_refine.ls_percent_reflns_obs                    77.1 
_refine.ls_R_factor_obs                          0.229 
_refine.ls_R_factor_all                          ? 
_refine.ls_R_factor_R_work                       0.229 
_refine.ls_R_factor_R_free                       0.26 
_refine.ls_R_factor_R_free_error                 0.012 
_refine.ls_R_factor_R_free_error_details         ? 
_refine.ls_percent_reflns_R_free                 10 
_refine.ls_number_reflns_R_free                  490 
_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                               8.7 
_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                      UD0008 
_refine.pdbx_method_to_determine_struct          'MOLECULAR REPLACEMENT' 
_refine.pdbx_isotropic_thermal_model             ? 
_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                        1P4Y 
_refine_analyze.Luzzati_coordinate_error_obs    0.21 
_refine_analyze.Luzzati_sigma_a_obs             0.03 
_refine_analyze.Luzzati_d_res_low_obs           5.00 
_refine_analyze.Luzzati_coordinate_error_free   0.26 
_refine_analyze.Luzzati_sigma_a_free            0.10 
_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   404 
_refine_hist.pdbx_number_atoms_ligand         4 
_refine_hist.number_atoms_solvent             108 
_refine_hist.number_atoms_total               516 
_refine_hist.d_res_high                       1.70 
_refine_hist.d_res_low                        22.50 
# 
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                0.007 ? ? ? '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             1.2   ? ? ? 'X-RAY DIFFRACTION' ? 
c_angle_deg_na          ?     ? ? ? 'X-RAY DIFFRACTION' ? 
c_angle_deg_prot        ?     ? ? ? 'X-RAY DIFFRACTION' ? 
c_dihedral_angle_d      18.5  ? ? ? 'X-RAY DIFFRACTION' ? 
c_dihedral_angle_d_na   ?     ? ? ? 'X-RAY DIFFRACTION' ? 
c_dihedral_angle_d_prot ?     ? ? ? 'X-RAY DIFFRACTION' ? 
c_improper_angle_d      1.57  ? ? ? '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                       1.7 
_refine_ls_shell.d_res_low                        1.81 
_refine_ls_shell.number_reflns_R_work             374 
_refine_ls_shell.R_factor_R_work                  0.209 
_refine_ls_shell.percent_reflns_obs               40.8 
_refine_ls_shell.R_factor_R_free                  0.285 
_refine_ls_shell.R_factor_R_free_error            0.046 
_refine_ls_shell.percent_reflns_R_free            9.4 
_refine_ls_shell.number_reflns_R_free             39 
_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          1P4Y 
_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                  1P4Y 
_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        1P4Y 
_struct_keywords.pdbx_keywords   DNA 
_struct_keywords.text            'Holliday Junction, DNA Four-Way Junction, DNA' 
# 
loop_
_struct_asym.id 
_struct_asym.pdbx_blank_PDB_chainid_flag 
_struct_asym.pdbx_modified 
_struct_asym.entity_id 
_struct_asym.details 
A N N 1 ? 
B N N 1 ? 
C N N 2 ? 
D N N 2 ? 
E N N 2 ? 
F N N 2 ? 
G N N 3 ? 
H N N 3 ? 
# 
_struct_ref.id                         1 
_struct_ref.entity_id                  1 
_struct_ref.db_name                    PDB 
_struct_ref.db_code                    1P4Y 
_struct_ref.pdbx_db_accession          1P4Y 
_struct_ref.pdbx_db_isoform            ? 
_struct_ref.pdbx_seq_one_letter_code   ? 
_struct_ref.pdbx_align_begin           ? 
# 
loop_
_struct_ref_seq.align_id 
_struct_ref_seq.ref_id 
_struct_ref_seq.pdbx_PDB_id_code 
_struct_ref_seq.pdbx_strand_id 
_struct_ref_seq.seq_align_beg 
_struct_ref_seq.pdbx_seq_align_beg_ins_code 
_struct_ref_seq.seq_align_end 
_struct_ref_seq.pdbx_seq_align_end_ins_code 
_struct_ref_seq.pdbx_db_accession 
_struct_ref_seq.db_align_beg 
_struct_ref_seq.pdbx_db_align_beg_ins_code 
_struct_ref_seq.db_align_end 
_struct_ref_seq.pdbx_db_align_end_ins_code 
_struct_ref_seq.pdbx_auth_seq_align_beg 
_struct_ref_seq.pdbx_auth_seq_align_end 
1 1 1P4Y A 1 ? 10 ? 1P4Y 1  ? 10 ? 1  10 
2 1 1P4Y B 1 ? 10 ? 1P4Y 11 ? 20 ? 11 20 
# 
_pdbx_struct_assembly.id                   1 
_pdbx_struct_assembly.details              author_defined_assembly 
_pdbx_struct_assembly.method_details       ? 
_pdbx_struct_assembly.oligomeric_details   tetrameric 
_pdbx_struct_assembly.oligomeric_count     4 
# 
_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,F,G,H 
# 
loop_
_pdbx_struct_oper_list.id 
_pdbx_struct_oper_list.type 
_pdbx_struct_oper_list.name 
_pdbx_struct_oper_list.symmetry_operation 
_pdbx_struct_oper_list.matrix[1][1] 
_pdbx_struct_oper_list.matrix[1][2] 
_pdbx_struct_oper_list.matrix[1][3] 
_pdbx_struct_oper_list.vector[1] 
_pdbx_struct_oper_list.matrix[2][1] 
_pdbx_struct_oper_list.matrix[2][2] 
_pdbx_struct_oper_list.matrix[2][3] 
_pdbx_struct_oper_list.vector[2] 
_pdbx_struct_oper_list.matrix[3][1] 
_pdbx_struct_oper_list.matrix[3][2] 
_pdbx_struct_oper_list.matrix[3][3] 
_pdbx_struct_oper_list.vector[3] 
1 'identity operation'         1_555 x,y,z     1.0000000000  0.0000000000 0.0000000000 0.0000000000   0.0000000000 1.0000000000 
0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000  0.0000000000  
2 'crystal symmetry operation' 2_556 -x,y,-z+1 -1.0000000000 0.0000000000 0.0000000000 -12.6621821170 0.0000000000 1.0000000000 
0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 34.7701763015 
# 
_struct_biol.id                    1 
_struct_biol.details               
;THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF TWO CHAINS A AND B.  THE FULL FOUR STRANDED HOLLIDAY JUNCTION STRUCTURE CAN BE GENERATED BY THE FOLLOWING: 
 
matrix=  
( -1.00000 -0.00046 -0.00015 ) 
( -0.00046  1.00000  0.00072 ) 
(  0.00015  0.00072 -1.00000 ) 
 
translation=  
(-12.65734 -0.02663 34.77174)
;
_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 1  "O5'" ? ? ? 1_555 D NA  .  NA ? ? A DC 1  A NA  36  1_555 ? ? ? ? ? ? ?            2.475 ? ? 
metalc2  metalc ? ? A DG 10 N3    ? ? ? 1_555 E NA  .  NA ? ? A DG 10 A NA  49  1_555 ? ? ? ? ? ? ?            2.945 ? ? 
metalc3  metalc ? ? C NA .  NA    ? ? ? 1_555 G HOH .  O  ? ? A NA 21 A HOH 24  1_555 ? ? ? ? ? ? ?            2.810 ? ? 
metalc4  metalc ? ? C NA .  NA    ? ? ? 1_555 G HOH .  O  ? ? A NA 21 A HOH 25  1_555 ? ? ? ? ? ? ?            2.470 ? ? 
metalc5  metalc ? ? C NA .  NA    ? ? ? 1_555 G HOH .  O  ? ? A NA 21 A HOH 56  1_555 ? ? ? ? ? ? ?            2.716 ? ? 
metalc6  metalc ? ? C NA .  NA    ? ? ? 1_555 G HOH .  O  ? ? A NA 21 A HOH 109 1_555 ? ? ? ? ? ? ?            2.476 ? ? 
metalc7  metalc ? ? D NA .  NA    ? ? ? 1_555 G HOH .  O  ? ? A NA 36 A HOH 82  1_555 ? ? ? ? ? ? ?            2.638 ? ? 
metalc8  metalc ? ? E NA .  NA    ? ? ? 1_555 G HOH .  O  ? ? A NA 49 A HOH 56  1_555 ? ? ? ? ? ? ?            2.560 ? ? 
metalc9  metalc ? ? B DG 9  "O4'" ? ? ? 1_555 F NA  .  NA ? ? B DG 19 B NA  55  1_555 ? ? ? ? ? ? ?            2.634 ? ? 
metalc10 metalc ? ? F NA .  NA    ? ? ? 1_555 H HOH .  O  ? ? B NA 55 B HOH 75  1_555 ? ? ? ? ? ? ?            2.806 ? ? 
hydrog1  hydrog ? ? A DC 1  N3    ? ? ? 1_555 B DG  10 N1 ? ? A DC 1  B DG  20  1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog2  hydrog ? ? A DC 1  N4    ? ? ? 1_555 B DG  10 O6 ? ? A DC 1  B DG  20  1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog3  hydrog ? ? A DC 1  O2    ? ? ? 1_555 B DG  10 N2 ? ? A DC 1  B DG  20  1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog4  hydrog ? ? A DC 2  N3    ? ? ? 1_555 B DG  9  N1 ? ? A DC 2  B DG  19  1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog5  hydrog ? ? A DC 2  N4    ? ? ? 1_555 B DG  9  O6 ? ? A DC 2  B DG  19  1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog6  hydrog ? ? A DC 2  O2    ? ? ? 1_555 B DG  9  N2 ? ? A DC 2  B DG  19  1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog7  hydrog ? ? A DG 3  N1    ? ? ? 1_555 B DC  8  N3 ? ? A DG 3  B DC  18  1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog8  hydrog ? ? A DG 3  N2    ? ? ? 1_555 B DC  8  O2 ? ? A DG 3  B DC  18  1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog9  hydrog ? ? A DG 3  O6    ? ? ? 1_555 B DC  8  N4 ? ? A DG 3  B DC  18  1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog10 hydrog ? ? A DG 4  N1    ? ? ? 1_555 B DC  7  N3 ? ? A DG 4  B DC  17  1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog11 hydrog ? ? A DG 4  N2    ? ? ? 1_555 B DC  7  O2 ? ? A DG 4  B DC  17  1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog12 hydrog ? ? A DG 4  O6    ? ? ? 1_555 B DC  7  N4 ? ? A DG 4  B DC  17  1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog13 hydrog ? ? A DC 5  N3    ? ? ? 1_555 B DG  6  N1 ? ? A DC 5  B DG  16  1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog14 hydrog ? ? A DC 5  N4    ? ? ? 1_555 B DG  6  O6 ? ? A DC 5  B DG  16  1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog15 hydrog ? ? A DC 5  O2    ? ? ? 1_555 B DG  6  N2 ? ? A DC 5  B DG  16  1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog16 hydrog ? ? A DG 6  N1    ? ? ? 1_555 B DC  5  N3 ? ? A DG 6  B DC  15  1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog17 hydrog ? ? A DG 6  N2    ? ? ? 1_555 B DC  5  O2 ? ? A DG 6  B DC  15  1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog18 hydrog ? ? A DG 6  O6    ? ? ? 1_555 B DC  5  N4 ? ? A DG 6  B DC  15  1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
# 
loop_
_struct_conn_type.id 
_struct_conn_type.criteria 
_struct_conn_type.reference 
metalc ? ? 
hydrog ? ? 
# 
loop_
_pdbx_struct_conn_angle.id 
_pdbx_struct_conn_angle.ptnr1_label_atom_id 
_pdbx_struct_conn_angle.ptnr1_label_alt_id 
_pdbx_struct_conn_angle.ptnr1_label_asym_id 
_pdbx_struct_conn_angle.ptnr1_label_comp_id 
_pdbx_struct_conn_angle.ptnr1_label_seq_id 
_pdbx_struct_conn_angle.ptnr1_auth_atom_id 
_pdbx_struct_conn_angle.ptnr1_auth_asym_id 
_pdbx_struct_conn_angle.ptnr1_auth_comp_id 
_pdbx_struct_conn_angle.ptnr1_auth_seq_id 
_pdbx_struct_conn_angle.ptnr1_PDB_ins_code 
_pdbx_struct_conn_angle.ptnr1_symmetry 
_pdbx_struct_conn_angle.ptnr2_label_atom_id 
_pdbx_struct_conn_angle.ptnr2_label_alt_id 
_pdbx_struct_conn_angle.ptnr2_label_asym_id 
_pdbx_struct_conn_angle.ptnr2_label_comp_id 
_pdbx_struct_conn_angle.ptnr2_label_seq_id 
_pdbx_struct_conn_angle.ptnr2_auth_atom_id 
_pdbx_struct_conn_angle.ptnr2_auth_asym_id 
_pdbx_struct_conn_angle.ptnr2_auth_comp_id 
_pdbx_struct_conn_angle.ptnr2_auth_seq_id 
_pdbx_struct_conn_angle.ptnr2_PDB_ins_code 
_pdbx_struct_conn_angle.ptnr2_symmetry 
_pdbx_struct_conn_angle.ptnr3_label_atom_id 
_pdbx_struct_conn_angle.ptnr3_label_alt_id 
_pdbx_struct_conn_angle.ptnr3_label_asym_id 
_pdbx_struct_conn_angle.ptnr3_label_comp_id 
_pdbx_struct_conn_angle.ptnr3_label_seq_id 
_pdbx_struct_conn_angle.ptnr3_auth_atom_id 
_pdbx_struct_conn_angle.ptnr3_auth_asym_id 
_pdbx_struct_conn_angle.ptnr3_auth_comp_id 
_pdbx_struct_conn_angle.ptnr3_auth_seq_id 
_pdbx_struct_conn_angle.ptnr3_PDB_ins_code 
_pdbx_struct_conn_angle.ptnr3_symmetry 
_pdbx_struct_conn_angle.value 
_pdbx_struct_conn_angle.value_esd 
1 "O5'" ? A DC  1  ? A DC  1  ? 1_555 NA ? D NA . ? A NA 36 ? 1_555 O ? G HOH . ? A HOH 82  ? 1_555 121.7 ? 
2 N3    ? A DG  10 ? A DG  10 ? 1_555 NA ? E NA . ? A NA 49 ? 1_555 O ? G HOH . ? A HOH 56  ? 1_555 101.5 ? 
3 O     ? G HOH .  ? A HOH 24 ? 1_555 NA ? C NA . ? A NA 21 ? 1_555 O ? G HOH . ? A HOH 25  ? 1_555 77.2  ? 
4 O     ? G HOH .  ? A HOH 24 ? 1_555 NA ? C NA . ? A NA 21 ? 1_555 O ? G HOH . ? A HOH 56  ? 1_555 83.5  ? 
5 O     ? G HOH .  ? A HOH 25 ? 1_555 NA ? C NA . ? A NA 21 ? 1_555 O ? G HOH . ? A HOH 56  ? 1_555 147.8 ? 
6 O     ? G HOH .  ? A HOH 24 ? 1_555 NA ? C NA . ? A NA 21 ? 1_555 O ? G HOH . ? A HOH 109 ? 1_555 134.8 ? 
7 O     ? G HOH .  ? A HOH 25 ? 1_555 NA ? C NA . ? A NA 21 ? 1_555 O ? G HOH . ? A HOH 109 ? 1_555 143.1 ? 
8 O     ? G HOH .  ? A HOH 56 ? 1_555 NA ? C NA . ? A NA 21 ? 1_555 O ? G HOH . ? A HOH 109 ? 1_555 66.6  ? 
9 "O4'" ? B DG  9  ? B DG  19 ? 1_555 NA ? F NA . ? B NA 55 ? 1_555 O ? H HOH . ? B HOH 75  ? 1_555 57.0  ? 
# 
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 21 ? 6 'BINDING SITE FOR RESIDUE NA A 21' 
AC2 Software A NA 36 ? 4 'BINDING SITE FOR RESIDUE NA A 36' 
AC3 Software A NA 49 ? 3 'BINDING SITE FOR RESIDUE NA A 49' 
AC4 Software B NA 55 ? 2 'BINDING SITE FOR RESIDUE NA B 55' 
# 
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 6 HOH G .  ? HOH A 24  . ? 1_555 ? 
2  AC1 6 HOH G .  ? HOH A 25  . ? 1_555 ? 
3  AC1 6 NA  E .  ? NA  A 49  . ? 1_555 ? 
4  AC1 6 HOH G .  ? HOH A 56  . ? 1_555 ? 
5  AC1 6 HOH G .  ? HOH A 109 . ? 1_555 ? 
6  AC1 6 HOH H .  ? HOH B 76  . ? 2_556 ? 
7  AC2 4 DC  A 1  ? DC  A 1   . ? 1_555 ? 
8  AC2 4 DC  A 2  ? DC  A 2   . ? 1_555 ? 
9  AC2 4 HOH G .  ? HOH A 82  . ? 1_555 ? 
10 AC2 4 DG  B 4  ? DG  B 14  . ? 2_557 ? 
11 AC3 3 DG  A 10 ? DG  A 10  . ? 1_555 ? 
12 AC3 3 NA  C .  ? NA  A 21  . ? 1_555 ? 
13 AC3 3 HOH G .  ? HOH A 56  . ? 1_555 ? 
14 AC4 2 DG  B 9  ? DG  B 19  . ? 1_555 ? 
15 AC4 2 HOH H .  ? HOH B 75  . ? 1_555 ? 
# 
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 
DC  OP3    O  N N 1  
DC  P      P  N N 2  
DC  OP1    O  N N 3  
DC  OP2    O  N N 4  
DC  "O5'"  O  N N 5  
DC  "C5'"  C  N N 6  
DC  "C4'"  C  N R 7  
DC  "O4'"  O  N N 8  
DC  "C3'"  C  N S 9  
DC  "O3'"  O  N N 10 
DC  "C2'"  C  N N 11 
DC  "C1'"  C  N R 12 
DC  N1     N  N N 13 
DC  C2     C  N N 14 
DC  O2     O  N N 15 
DC  N3     N  N N 16 
DC  C4     C  N N 17 
DC  N4     N  N N 18 
DC  C5     C  N N 19 
DC  C6     C  N N 20 
DC  HOP3   H  N N 21 
DC  HOP2   H  N N 22 
DC  "H5'"  H  N N 23 
DC  "H5''" H  N N 24 
DC  "H4'"  H  N N 25 
DC  "H3'"  H  N N 26 
DC  "HO3'" H  N N 27 
DC  "H2'"  H  N N 28 
DC  "H2''" H  N N 29 
DC  "H1'"  H  N N 30 
DC  H41    H  N N 31 
DC  H42    H  N N 32 
DC  H5     H  N N 33 
DC  H6     H  N N 34 
DG  OP3    O  N N 35 
DG  P      P  N N 36 
DG  OP1    O  N N 37 
DG  OP2    O  N N 38 
DG  "O5'"  O  N N 39 
DG  "C5'"  C  N N 40 
DG  "C4'"  C  N R 41 
DG  "O4'"  O  N N 42 
DG  "C3'"  C  N S 43 
DG  "O3'"  O  N N 44 
DG  "C2'"  C  N N 45 
DG  "C1'"  C  N R 46 
DG  N9     N  Y N 47 
DG  C8     C  Y N 48 
DG  N7     N  Y N 49 
DG  C5     C  Y N 50 
DG  C6     C  N N 51 
DG  O6     O  N N 52 
DG  N1     N  N N 53 
DG  C2     C  N N 54 
DG  N2     N  N N 55 
DG  N3     N  N N 56 
DG  C4     C  Y N 57 
DG  HOP3   H  N N 58 
DG  HOP2   H  N N 59 
DG  "H5'"  H  N N 60 
DG  "H5''" H  N N 61 
DG  "H4'"  H  N N 62 
DG  "H3'"  H  N N 63 
DG  "HO3'" H  N N 64 
DG  "H2'"  H  N N 65 
DG  "H2''" H  N N 66 
DG  "H1'"  H  N N 67 
DG  H8     H  N N 68 
DG  H1     H  N N 69 
DG  H21    H  N N 70 
DG  H22    H  N N 71 
HOH O      O  N N 72 
HOH H1     H  N N 73 
HOH H2     H  N N 74 
NA  NA     NA N N 75 
# 
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 
DC  OP3   P      sing N N 1  
DC  OP3   HOP3   sing N N 2  
DC  P     OP1    doub N N 3  
DC  P     OP2    sing N N 4  
DC  P     "O5'"  sing N N 5  
DC  OP2   HOP2   sing N N 6  
DC  "O5'" "C5'"  sing N N 7  
DC  "C5'" "C4'"  sing N N 8  
DC  "C5'" "H5'"  sing N N 9  
DC  "C5'" "H5''" sing N N 10 
DC  "C4'" "O4'"  sing N N 11 
DC  "C4'" "C3'"  sing N N 12 
DC  "C4'" "H4'"  sing N N 13 
DC  "O4'" "C1'"  sing N N 14 
DC  "C3'" "O3'"  sing N N 15 
DC  "C3'" "C2'"  sing N N 16 
DC  "C3'" "H3'"  sing N N 17 
DC  "O3'" "HO3'" sing N N 18 
DC  "C2'" "C1'"  sing N N 19 
DC  "C2'" "H2'"  sing N N 20 
DC  "C2'" "H2''" sing N N 21 
DC  "C1'" N1     sing N N 22 
DC  "C1'" "H1'"  sing N N 23 
DC  N1    C2     sing N N 24 
DC  N1    C6     sing N N 25 
DC  C2    O2     doub N N 26 
DC  C2    N3     sing N N 27 
DC  N3    C4     doub N N 28 
DC  C4    N4     sing N N 29 
DC  C4    C5     sing N N 30 
DC  N4    H41    sing N N 31 
DC  N4    H42    sing N N 32 
DC  C5    C6     doub N N 33 
DC  C5    H5     sing N N 34 
DC  C6    H6     sing N N 35 
DG  OP3   P      sing N N 36 
DG  OP3   HOP3   sing N N 37 
DG  P     OP1    doub N N 38 
DG  P     OP2    sing N N 39 
DG  P     "O5'"  sing N N 40 
DG  OP2   HOP2   sing N N 41 
DG  "O5'" "C5'"  sing N N 42 
DG  "C5'" "C4'"  sing N N 43 
DG  "C5'" "H5'"  sing N N 44 
DG  "C5'" "H5''" sing N N 45 
DG  "C4'" "O4'"  sing N N 46 
DG  "C4'" "C3'"  sing N N 47 
DG  "C4'" "H4'"  sing N N 48 
DG  "O4'" "C1'"  sing N N 49 
DG  "C3'" "O3'"  sing N N 50 
DG  "C3'" "C2'"  sing N N 51 
DG  "C3'" "H3'"  sing N N 52 
DG  "O3'" "HO3'" sing N N 53 
DG  "C2'" "C1'"  sing N N 54 
DG  "C2'" "H2'"  sing N N 55 
DG  "C2'" "H2''" sing N N 56 
DG  "C1'" N9     sing N N 57 
DG  "C1'" "H1'"  sing N N 58 
DG  N9    C8     sing Y N 59 
DG  N9    C4     sing Y N 60 
DG  C8    N7     doub Y N 61 
DG  C8    H8     sing N N 62 
DG  N7    C5     sing Y N 63 
DG  C5    C6     sing N N 64 
DG  C5    C4     doub Y N 65 
DG  C6    O6     doub N N 66 
DG  C6    N1     sing N N 67 
DG  N1    C2     sing N N 68 
DG  N1    H1     sing N N 69 
DG  C2    N2     sing N N 70 
DG  C2    N3     doub N N 71 
DG  N2    H21    sing N N 72 
DG  N2    H22    sing N N 73 
DG  N3    C4     sing N N 74 
HOH O     H1     sing N N 75 
HOH O     H2     sing N N 76 
# 
_ndb_struct_conf_na.entry_id   1P4Y 
_ndb_struct_conf_na.feature    'b-form double 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 DC 1 1_555 B DG 10 1_555 0.293  -0.111 -0.028 -4.913  -7.931  0.007  1 A_DC1:DG20_B A 1 ? B 20 ? 19 1 
1 A DC 2 1_555 B DG 9  1_555 0.116  0.100  -0.281 1.298   -1.726  5.301  2 A_DC2:DG19_B A 2 ? B 19 ? 19 1 
1 A DG 3 1_555 B DC 8  1_555 -0.399 -0.179 0.153  2.223   5.867   -0.414 3 A_DG3:DC18_B A 3 ? B 18 ? 19 1 
1 A DG 4 1_555 B DC 7  1_555 -0.077 -0.140 0.368  -2.849  -25.438 -0.780 4 A_DG4:DC17_B A 4 ? B 17 ? 19 1 
1 A DC 5 1_555 B DG 6  1_555 -0.436 0.049  0.938  -21.163 6.011   -6.733 5 A_DC5:DG16_B A 5 ? B 16 ? 19 1 
1 A DG 6 1_555 B DC 5  1_555 -0.172 -0.138 0.100  -0.618  -11.453 -2.019 6 A_DG6:DC15_B A 6 ? B 15 ? 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 B DG 10 1_555 A DC 2 1_555 B DG 9 1_555 0.397  2.433 3.431 4.588  6.244  37.369 2.842  0.039  3.794 9.619  -7.068 
38.136 1 AA_DC1DC2:DG19DG20_BB A 1 ? B 20 ? A 2 ? B 19 ? 
1 A DC 2 1_555 B DG 9  1_555 A DG 3 1_555 B DC 8 1_555 -0.264 2.728 3.402 -3.669 -0.295 34.907 4.570  -0.135 3.389 -0.491 6.096  
35.095 2 AA_DC2DG3:DC18DG19_BB A 2 ? B 19 ? A 3 ? B 18 ? 
1 A DG 3 1_555 B DC 8  1_555 A DG 4 1_555 B DC 7 1_555 -1.195 1.809 3.664 -3.205 0.345  40.411 2.567  1.319  3.759 0.499  4.631  
40.534 3 AA_DG3DG4:DC17DC18_BB A 3 ? B 18 ? A 4 ? B 17 ? 
1 A DG 4 1_555 B DC 7  1_555 A DC 5 1_555 B DG 6 1_555 0.458  0.520 3.863 -5.310 -1.775 38.393 1.036  -1.447 3.742 -2.682 8.022  
38.783 4 AA_DG4DC5:DG16DC17_BB A 4 ? B 17 ? A 5 ? B 16 ? 
1 A DC 5 1_555 B DG 6  1_555 A DG 6 1_555 B DC 5 1_555 0.017  0.408 3.035 3.273  4.789  29.483 -0.136 0.598  3.045 9.296  -6.354 
30.035 5 AA_DC5DG6:DC15DG16_BB A 5 ? B 16 ? A 6 ? B 15 ? 
# 
_pdbx_initial_refinement_model.accession_code   1DCW 
_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      PDB 
_pdbx_initial_refinement_model.details          UD0008 
# 
_atom_sites.entry_id                    1P4Y 
_atom_sites.fract_transf_matrix[1][1]   0.015035 
_atom_sites.fract_transf_matrix[1][2]   0.000000 
_atom_sites.fract_transf_matrix[1][3]   0.005475 
_atom_sites.fract_transf_matrix[2][1]   0.000000 
_atom_sites.fract_transf_matrix[2][2]   0.041358 
_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]   0.028760 
_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_