data_4GRE
# 
_entry.id   4GRE 
# 
_audit_conform.dict_name       mmcif_pdbx.dic 
_audit_conform.dict_version    5.387 
_audit_conform.dict_location   http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 
# 
loop_
_database_2.database_id 
_database_2.database_code 
_database_2.pdbx_database_accession 
_database_2.pdbx_DOI 
PDB   4GRE         pdb_00004gre 10.2210/pdb4gre/pdb 
NDB   NA2015       ?            ?                   
RCSB  RCSB074542   ?            ?                   
WWPDB D_1000074542 ?            ?                   
# 
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 2013-07-31 
2 'Structure model' 1 1 2013-12-18 
3 'Structure model' 1 2 2024-02-28 
# 
_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' 'Database references'  
2 3 'Structure model' 'Data collection'      
3 3 'Structure model' 'Database references'  
4 3 'Structure model' 'Derived calculations' 
# 
loop_
_pdbx_audit_revision_category.ordinal 
_pdbx_audit_revision_category.revision_ordinal 
_pdbx_audit_revision_category.data_content_type 
_pdbx_audit_revision_category.category 
1 3 'Structure model' chem_comp_atom 
2 3 'Structure model' chem_comp_bond 
3 3 'Structure model' database_2     
4 3 'Structure model' struct_conn    
# 
loop_
_pdbx_audit_revision_item.ordinal 
_pdbx_audit_revision_item.revision_ordinal 
_pdbx_audit_revision_item.data_content_type 
_pdbx_audit_revision_item.item 
1 3 'Structure model' '_database_2.pdbx_DOI'                
2 3 'Structure model' '_database_2.pdbx_database_accession' 
3 3 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 
# 
_pdbx_database_status.entry_id                        4GRE 
_pdbx_database_status.status_code                     REL 
_pdbx_database_status.deposit_site                    RCSB 
_pdbx_database_status.process_site                    RCSB 
_pdbx_database_status.recvd_initial_deposition_date   2012-08-24 
_pdbx_database_status.status_code_sf                  REL 
_pdbx_database_status.status_code_mr                  ? 
_pdbx_database_status.SG_entry                        ? 
_pdbx_database_status.status_code_cs                  ? 
_pdbx_database_status.methods_development_category    ? 
_pdbx_database_status.pdb_format_compatible           Y 
_pdbx_database_status.status_code_nmr_data            ? 
# 
loop_
_pdbx_database_related.db_name 
_pdbx_database_related.db_id 
_pdbx_database_related.details 
_pdbx_database_related.content_type 
PDB 2ORG . unspecified 
PDB 2ORF . unspecified 
PDB 2ORH . unspecified 
PDB 3TOK . unspecified 
PDB 4GQD . unspecified 
PDB 4GS2 . unspecified 
PDB 4GSG . unspecified 
PDB 4GSI . unspecified 
# 
loop_
_audit_author.name 
_audit_author.pdbx_ordinal 
'Ho, P.S.'   1 
'Carter, M.' 2 
# 
_citation.id                        primary 
_citation.title                     'Enthalpy-entropy compensation in biomolecular halogen bonds measured in DNA junctions.' 
_citation.journal_abbrev            Biochemistry 
_citation.journal_volume            52 
_citation.page_first                4891 
_citation.page_last                 4903 
_citation.year                      2013 
_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   23789744 
_citation.pdbx_database_id_DOI      10.1021/bi400590h 
# 
loop_
_citation_author.citation_id 
_citation_author.name 
_citation_author.ordinal 
_citation_author.identifier_ORCID 
primary 'Carter, M.'       1 ? 
primary 'Voth, A.R.'       2 ? 
primary 'Scholfield, M.R.' 3 ? 
primary 'Rummel, B.'       4 ? 
primary 'Sowers, L.C.'     5 ? 
primary 'Ho, P.S.'         6 ? 
# 
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 man 
;DNA (5'-D(*CP*CP*GP*GP*TP*AP*(IOU)P*CP*GP*G)-3')
;
3172.874 1  ? ? ? ? 
2 polymer syn 
;DNA (5'-D(*CP*CP*GP*AP*TP*AP*CP*CP*GP*G)-3')
;
3029.994 1  ? ? ? ? 
3 water   nat water                                              18.015   74 ? ? ? ? 
# 
loop_
_entity_poly.entity_id 
_entity_poly.type 
_entity_poly.nstd_linkage 
_entity_poly.nstd_monomer 
_entity_poly.pdbx_seq_one_letter_code 
_entity_poly.pdbx_seq_one_letter_code_can 
_entity_poly.pdbx_strand_id 
_entity_poly.pdbx_target_identifier 
1 polydeoxyribonucleotide no yes '(DC)(DC)(DG)(DG)(DT)(DA)(5IU)(DC)(DG)(DG)' CCGGTAUCGG A ? 
2 polydeoxyribonucleotide no no  '(DC)(DC)(DG)(DA)(DT)(DA)(DC)(DC)(DG)(DG)'  CCGATACCGG B ? 
# 
_pdbx_entity_nonpoly.entity_id   3 
_pdbx_entity_nonpoly.name        water 
_pdbx_entity_nonpoly.comp_id     HOH 
# 
loop_
_entity_poly_seq.entity_id 
_entity_poly_seq.num 
_entity_poly_seq.mon_id 
_entity_poly_seq.hetero 
1 1  DC  n 
1 2  DC  n 
1 3  DG  n 
1 4  DG  n 
1 5  DT  n 
1 6  DA  n 
1 7  5IU n 
1 8  DC  n 
1 9  DG  n 
1 10 DG  n 
2 1  DC  n 
2 2  DC  n 
2 3  DG  n 
2 4  DA  n 
2 5  DT  n 
2 6  DA  n 
2 7  DC  n 
2 8  DC  n 
2 9  DG  n 
2 10 DG  n 
# 
loop_
_pdbx_entity_src_syn.entity_id 
_pdbx_entity_src_syn.pdbx_src_id 
_pdbx_entity_src_syn.pdbx_alt_source_flag 
_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 
1 1 sample ? ? ? ? ? 'synthetically engineered DNA sequence' 
2 1 sample ? ? ? ? ? 'synthetically engineered DNA sequence' 
# 
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 
5IU 'DNA linking' n "5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE" ? 'C9 H12 I N2 O8 P' 434.078 
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  
# 
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  DC  A . n 
A 1 2  DC  2  2  2  DC  DC  A . n 
A 1 3  DG  3  3  3  DG  DG  A . n 
A 1 4  DG  4  4  4  DG  DG  A . n 
A 1 5  DT  5  5  5  DT  DT  A . n 
A 1 6  DA  6  6  6  DA  DA  A . n 
A 1 7  5IU 7  7  7  5IU IOU A . n 
A 1 8  DC  8  8  8  DC  DC  A . n 
A 1 9  DG  9  9  9  DG  DG  A . n 
A 1 10 DG  10 10 10 DG  DG  A . n 
B 2 1  DC  1  11 11 DC  DC  B . n 
B 2 2  DC  2  12 12 DC  DC  B . n 
B 2 3  DG  3  13 13 DG  DG  B . n 
B 2 4  DA  4  14 14 DA  DA  B . n 
B 2 5  DT  5  15 15 DT  DT  B . n 
B 2 6  DA  6  16 16 DA  DA  B . n 
B 2 7  DC  7  17 17 DC  DC  B . n 
B 2 8  DC  8  18 18 DC  DC  B . n 
B 2 9  DG  9  19 19 DG  DG  B . n 
B 2 10 DG  10 20 20 DG  DG  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 3 HOH 1  101 21 HOH HOH A . 
C 3 HOH 2  102 22 HOH HOH A . 
C 3 HOH 3  103 24 HOH HOH A . 
C 3 HOH 4  104 25 HOH HOH A . 
C 3 HOH 5  105 28 HOH HOH A . 
C 3 HOH 6  106 29 HOH HOH A . 
C 3 HOH 7  107 31 HOH HOH A . 
C 3 HOH 8  108 33 HOH HOH A . 
C 3 HOH 9  109 34 HOH HOH A . 
C 3 HOH 10 110 37 HOH HOH A . 
C 3 HOH 11 111 39 HOH HOH A . 
C 3 HOH 12 112 40 HOH HOH A . 
C 3 HOH 13 113 44 HOH HOH A . 
C 3 HOH 14 114 48 HOH HOH A . 
C 3 HOH 15 115 49 HOH HOH A . 
C 3 HOH 16 116 50 HOH HOH A . 
C 3 HOH 17 117 54 HOH HOH A . 
C 3 HOH 18 118 55 HOH HOH A . 
C 3 HOH 19 119 57 HOH HOH A . 
C 3 HOH 20 120 59 HOH HOH A . 
C 3 HOH 21 121 60 HOH HOH A . 
C 3 HOH 22 122 62 HOH HOH A . 
C 3 HOH 23 123 63 HOH HOH A . 
C 3 HOH 24 124 64 HOH HOH A . 
C 3 HOH 25 125 65 HOH HOH A . 
C 3 HOH 26 126 70 HOH HOH A . 
C 3 HOH 27 127 73 HOH HOH A . 
C 3 HOH 28 128 74 HOH HOH A . 
C 3 HOH 29 129 78 HOH HOH A . 
C 3 HOH 30 130 79 HOH HOH A . 
C 3 HOH 31 131 80 HOH HOH A . 
C 3 HOH 32 132 82 HOH HOH A . 
C 3 HOH 33 133 83 HOH HOH A . 
C 3 HOH 34 134 86 HOH HOH A . 
C 3 HOH 35 135 88 HOH HOH A . 
C 3 HOH 36 136 89 HOH HOH A . 
D 3 HOH 1  101 95 HOH HOH B . 
D 3 HOH 2  102 23 HOH HOH B . 
D 3 HOH 3  103 26 HOH HOH B . 
D 3 HOH 4  104 27 HOH HOH B . 
D 3 HOH 5  105 30 HOH HOH B . 
D 3 HOH 6  106 32 HOH HOH B . 
D 3 HOH 7  107 36 HOH HOH B . 
D 3 HOH 8  108 38 HOH HOH B . 
D 3 HOH 9  109 41 HOH HOH B . 
D 3 HOH 10 110 42 HOH HOH B . 
D 3 HOH 11 111 43 HOH HOH B . 
D 3 HOH 12 112 45 HOH HOH B . 
D 3 HOH 13 113 46 HOH HOH B . 
D 3 HOH 14 114 47 HOH HOH B . 
D 3 HOH 15 115 51 HOH HOH B . 
D 3 HOH 16 116 52 HOH HOH B . 
D 3 HOH 17 117 53 HOH HOH B . 
D 3 HOH 18 118 56 HOH HOH B . 
D 3 HOH 19 119 58 HOH HOH B . 
D 3 HOH 20 120 61 HOH HOH B . 
D 3 HOH 21 121 66 HOH HOH B . 
D 3 HOH 22 122 67 HOH HOH B . 
D 3 HOH 23 123 68 HOH HOH B . 
D 3 HOH 24 124 69 HOH HOH B . 
D 3 HOH 25 125 71 HOH HOH B . 
D 3 HOH 26 126 72 HOH HOH B . 
D 3 HOH 27 127 75 HOH HOH B . 
D 3 HOH 28 128 76 HOH HOH B . 
D 3 HOH 29 129 77 HOH HOH B . 
D 3 HOH 30 130 81 HOH HOH B . 
D 3 HOH 31 131 84 HOH HOH B . 
D 3 HOH 32 132 85 HOH HOH B . 
D 3 HOH 33 133 87 HOH HOH B . 
D 3 HOH 34 134 90 HOH HOH B . 
D 3 HOH 35 135 91 HOH HOH B . 
D 3 HOH 36 136 92 HOH HOH B . 
D 3 HOH 37 137 93 HOH HOH B . 
D 3 HOH 38 138 94 HOH HOH B . 
# 
loop_
_software.pdbx_ordinal 
_software.name 
_software.version 
_software.date 
_software.type 
_software.contact_author 
_software.contact_author_email 
_software.classification 
_software.location 
_software.language 
_software.citation_id 
1 CNS         1.2  ?                package 'Axel T. Brunger' axel.brunger@yale.edu    refinement        http://cns-online.org/ 
Fortran_77 ? 
2 PDB_EXTRACT 3.11 'April 22, 2011' package PDB               deposit@deposit.rcsb.org 'data extraction' 
http://sw-tools.pdb.org/apps/PDB_EXTRACT/ C++        ? 
3 HKL-2000    .    ?                ?       ?                 ?                        'data collection' ? ?          ? 
4 HKL-2000    .    ?                ?       ?                 ?                        'data reduction'  ? ?          ? 
5 HKL-2000    .    ?                ?       ?                 ?                        'data scaling'    ? ?          ? 
6 CNS         .    ?                ?       ?                 ?                        phasing           ? ?          ? 
# 
_cell.entry_id           4GRE 
_cell.length_a           64.956 
_cell.length_b           24.773 
_cell.length_c           37.616 
_cell.angle_alpha        90.00 
_cell.angle_beta         111.59 
_cell.angle_gamma        90.00 
_cell.Z_PDB              4 
_cell.pdbx_unique_axis   ? 
_cell.length_a_esd       ? 
_cell.length_b_esd       ? 
_cell.length_c_esd       ? 
_cell.angle_alpha_esd    ? 
_cell.angle_beta_esd     ? 
_cell.angle_gamma_esd    ? 
# 
_symmetry.entry_id                         4GRE 
_symmetry.space_group_name_H-M             'C 1 2 1' 
_symmetry.pdbx_full_space_group_name_H-M   ? 
_symmetry.cell_setting                     ? 
_symmetry.Int_Tables_number                5 
_symmetry.space_group_name_Hall            ? 
# 
_exptl.crystals_number   1 
_exptl.entry_id          4GRE 
_exptl.method            'X-RAY DIFFRACTION' 
# 
_exptl_crystal.id                    1 
_exptl_crystal.density_Matthews      2.44 
_exptl_crystal.density_meas          ? 
_exptl_crystal.density_percent_sol   49.58 
_exptl_crystal.description           ? 
_exptl_crystal.F_000                 ? 
_exptl_crystal.preparation           ? 
# 
_exptl_crystal_grow.crystal_id      1 
_exptl_crystal_grow.method          'hanging drop' 
_exptl_crystal_grow.pH              7 
_exptl_crystal_grow.temp            298 
_exptl_crystal_grow.pdbx_details    
;0.7mM DNA, 25mM sodium cacodylate pH 7.0 buffer, 10-25mM calcium chloride, and 0.8-1.2mM spermine, equilibrated against a reservoir of 30-40% aqueous MPD, hanging drop, temperature 298 K
;
_exptl_crystal_grow.temp_details    ? 
_exptl_crystal_grow.pdbx_pH_range   ? 
# 
_diffrn.id                     1 
_diffrn.ambient_temp           133 
_diffrn.ambient_temp_details   ? 
_diffrn.crystal_id             1 
# 
_diffrn_detector.diffrn_id              1 
_diffrn_detector.detector               CCD 
_diffrn_detector.type                   'ADSC QUANTUM 315' 
_diffrn_detector.pdbx_collection_date   2004-10-31 
_diffrn_detector.details                ? 
# 
_diffrn_radiation.diffrn_id                        1 
_diffrn_radiation.pdbx_diffrn_protocol             'SINGLE WAVELENGTH' 
_diffrn_radiation.monochromator                    ? 
_diffrn_radiation.wavelength_id                    1 
_diffrn_radiation.pdbx_monochromatic_or_laue_m_l   M 
_diffrn_radiation.pdbx_scattering_type             x-ray 
# 
_diffrn_radiation_wavelength.id           1 
_diffrn_radiation_wavelength.wavelength   1 
_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_wavelength_list        1 
_diffrn_source.pdbx_wavelength             ? 
_diffrn_source.pdbx_synchrotron_site       APS 
_diffrn_source.pdbx_synchrotron_beamline   14-BM-C 
# 
_reflns.entry_id                     4GRE 
_reflns.B_iso_Wilson_estimate        9.900 
_reflns.observed_criterion_sigma_F   1.4 
_reflns.observed_criterion_sigma_I   2 
_reflns.d_resolution_high            1.7 
_reflns.d_resolution_low             19.57 
_reflns.number_all                   6266 
_reflns.number_obs                   5772 
_reflns.percent_possible_obs         91.4 
_reflns.pdbx_Rmerge_I_obs            ? 
_reflns.pdbx_Rsym_value              ? 
_reflns.pdbx_netI_over_sigmaI        ? 
_reflns.pdbx_redundancy              ? 
_reflns.R_free_details               ? 
_reflns.limit_h_max                  ? 
_reflns.limit_h_min                  ? 
_reflns.limit_k_max                  ? 
_reflns.limit_k_min                  ? 
_reflns.limit_l_max                  ? 
_reflns.limit_l_min                  ? 
_reflns.observed_criterion_F_max     ? 
_reflns.observed_criterion_F_min     ? 
_reflns.pdbx_chi_squared             ? 
_reflns.pdbx_scaling_rejects         ? 
_reflns.pdbx_ordinal                 1 
_reflns.pdbx_diffrn_id               1 
# 
_reflns_shell.d_res_high             1.7 
_reflns_shell.d_res_low              1.81 
_reflns_shell.percent_possible_obs   ? 
_reflns_shell.percent_possible_all   78.2 
_reflns_shell.Rmerge_I_obs           ? 
_reflns_shell.meanI_over_sigI_obs    ? 
_reflns_shell.pdbx_Rsym_value        ? 
_reflns_shell.pdbx_redundancy        ? 
_reflns_shell.number_unique_all      ? 
_reflns_shell.number_measured_all    ? 
_reflns_shell.number_measured_obs    ? 
_reflns_shell.number_unique_obs      ? 
_reflns_shell.pdbx_chi_squared       ? 
_reflns_shell.pdbx_ordinal           1 
_reflns_shell.pdbx_diffrn_id         1 
# 
_refine.entry_id                                 4GRE 
_refine.ls_d_res_high                            1.7000 
_refine.ls_d_res_low                             19.5700 
_refine.pdbx_ls_sigma_F                          0.000 
_refine.pdbx_data_cutoff_high_absF               49861.0000 
_refine.pdbx_data_cutoff_low_absF                0.0000 
_refine.ls_percent_reflns_obs                    91.4000 
_refine.ls_number_reflns_obs                     5772 
_refine.ls_number_reflns_all                     6319 
_refine.pdbx_ls_cross_valid_method               THROUGHOUT 
_refine.pdbx_R_Free_selection_details            RANDOM 
_refine.details                                  'BULK SOLVENT MODEL USED' 
_refine.ls_R_factor_all                          ? 
_refine.ls_R_factor_obs                          ? 
_refine.ls_R_factor_R_work                       0.2390 
_refine.ls_wR_factor_R_work                      ? 
_refine.ls_R_factor_R_free                       0.2550 
_refine.ls_wR_factor_R_free                      ? 
_refine.ls_percent_reflns_R_free                 10.7000 
_refine.ls_number_reflns_R_free                  619 
_refine.ls_R_factor_R_free_error                 0.0100 
_refine.B_iso_mean                               18.0466 
_refine.solvent_model_param_bsol                 95.1750 
_refine.solvent_model_param_ksol                 0.4500 
_refine.pdbx_isotropic_thermal_model             RESTRAINED 
_refine.aniso_B[1][1]                            -1.7700 
_refine.aniso_B[2][2]                            5.4700 
_refine.aniso_B[3][3]                            -3.7000 
_refine.aniso_B[1][2]                            0.0000 
_refine.aniso_B[1][3]                            -0.5900 
_refine.aniso_B[2][3]                            0.0000 
_refine.correlation_coeff_Fo_to_Fc               ? 
_refine.correlation_coeff_Fo_to_Fc_free          ? 
_refine.overall_SU_R_Cruickshank_DPI             ? 
_refine.overall_SU_R_free                        ? 
_refine.pdbx_overall_ESU_R                       ? 
_refine.pdbx_overall_ESU_R_Free                  ? 
_refine.overall_SU_ML                            ? 
_refine.overall_SU_B                             ? 
_refine.solvent_model_details                    'FLAT MODEL' 
_refine.pdbx_solvent_vdw_probe_radii             ? 
_refine.pdbx_solvent_ion_probe_radii             ? 
_refine.pdbx_solvent_shrinkage_radii             ? 
_refine.ls_number_parameters                     ? 
_refine.ls_number_restraints                     ? 
_refine.pdbx_starting_model                      ? 
_refine.pdbx_method_to_determine_struct          'MOLECULAR REPLACEMENT' 
_refine.pdbx_stereochemistry_target_values       ? 
_refine.pdbx_stereochem_target_val_spec_case     ? 
_refine.overall_FOM_work_R_set                   ? 
_refine.B_iso_max                                42.810 
_refine.B_iso_min                                1.330 
_refine.pdbx_overall_phase_error                 ? 
_refine.occupancy_max                            1.000 
_refine.occupancy_min                            0.500 
_refine.pdbx_ls_sigma_I                          ? 
_refine.ls_redundancy_reflns_obs                 ? 
_refine.ls_R_factor_R_free_error_details         ? 
_refine.pdbx_data_cutoff_high_rms_absF           ? 
_refine.overall_FOM_free_R_set                   ? 
_refine.pdbx_diffrn_id                           1 
_refine.pdbx_refine_id                           'X-RAY DIFFRACTION' 
_refine.pdbx_TLS_residual_ADP_flag               ? 
_refine.pdbx_overall_SU_R_free_Cruickshank_DPI   ? 
_refine.pdbx_overall_SU_R_Blow_DPI               ? 
_refine.pdbx_overall_SU_R_free_Blow_DPI          ? 
# 
_refine_analyze.entry_id                        4GRE 
_refine_analyze.Luzzati_coordinate_error_obs    0.240 
_refine_analyze.Luzzati_sigma_a_obs             0.170 
_refine_analyze.Luzzati_d_res_low_obs           5.000 
_refine_analyze.Luzzati_coordinate_error_free   0.270 
_refine_analyze.Luzzati_sigma_a_free            0.230 
_refine_analyze.Luzzati_d_res_low_free          ? 
_refine_analyze.number_disordered_residues      ? 
_refine_analyze.occupancy_sum_non_hydrogen      ? 
_refine_analyze.occupancy_sum_hydrogen          ? 
_refine_analyze.pdbx_Luzzati_d_res_high_obs     ? 
_refine_analyze.pdbx_refine_id                  'X-RAY DIFFRACTION' 
# 
_refine_hist.pdbx_refine_id                   'X-RAY DIFFRACTION' 
_refine_hist.cycle_id                         LAST 
_refine_hist.pdbx_number_atoms_protein        0 
_refine_hist.pdbx_number_atoms_nucleic_acid   404 
_refine_hist.pdbx_number_atoms_ligand         0 
_refine_hist.number_atoms_solvent             74 
_refine_hist.number_atoms_total               478 
_refine_hist.d_res_high                       1.7000 
_refine_hist.d_res_low                        19.5700 
# 
loop_
_refine_ls_restr.type 
_refine_ls_restr.number 
_refine_ls_restr.dev_ideal 
_refine_ls_restr.dev_ideal_target 
_refine_ls_restr.weight 
_refine_ls_restr.pdbx_restraint_function 
_refine_ls_restr.pdbx_refine_id 
c_bond_d           ? 0.007  ? ? ? 'X-RAY DIFFRACTION' 
c_angle_deg        ? 1.100  ? ? ? 'X-RAY DIFFRACTION' 
c_dihedral_angle_d ? 18.600 ? ? ? 'X-RAY DIFFRACTION' 
c_improper_angle_d ? 1.730  ? ? ? '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.d_res_high                       1.7000 
_refine_ls_shell.d_res_low                        1.8100 
_refine_ls_shell.pdbx_total_number_of_bins_used   6 
_refine_ls_shell.percent_reflns_obs               78.2000 
_refine_ls_shell.number_reflns_R_work             724 
_refine_ls_shell.R_factor_all                     ? 
_refine_ls_shell.R_factor_R_work                  0.2660 
_refine_ls_shell.R_factor_R_free                  0.3090 
_refine_ls_shell.percent_reflns_R_free            11.9000 
_refine_ls_shell.number_reflns_R_free             98 
_refine_ls_shell.R_factor_R_free_error            0.0310 
_refine_ls_shell.number_reflns_all                822 
_refine_ls_shell.number_reflns_obs                ? 
_refine_ls_shell.redundancy_reflns_obs            ? 
_refine_ls_shell.pdbx_refine_id                   'X-RAY DIFFRACTION' 
# 
loop_
_pdbx_xplor_file.serial_no 
_pdbx_xplor_file.param_file 
_pdbx_xplor_file.topol_file 
_pdbx_xplor_file.pdbx_refine_id 
1 dna-rna_rep.param dna-rna.top 'X-RAY DIFFRACTION' 
2 ion.param         ?           'X-RAY DIFFRACTION' 
3 water_rep.param   ?           'X-RAY DIFFRACTION' 
# 
_database_PDB_matrix.entry_id          4GRE 
_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]   0.000000 
_database_PDB_matrix.origx_vector[2]   0.000000 
_database_PDB_matrix.origx_vector[3]   0.000000 
# 
_struct.entry_id                  4GRE 
_struct.title                     'DNA holliday junction stabilized by iodine halogen bond. I2J Construct of related reference' 
_struct.pdbx_model_details        ? 
_struct.pdbx_CASP_flag            ? 
_struct.pdbx_model_type_details   ? 
# 
_struct_keywords.entry_id        4GRE 
_struct_keywords.text            'DNA Holliday junction, halogen bond, DNA' 
_struct_keywords.pdbx_keywords   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 3 ? 
D N N 3 ? 
# 
loop_
_struct_ref.id 
_struct_ref.db_name 
_struct_ref.db_code 
_struct_ref.pdbx_db_accession 
_struct_ref.entity_id 
_struct_ref.pdbx_align_begin 
_struct_ref.pdbx_seq_one_letter_code 
_struct_ref.pdbx_db_isoform 
1 PDB 4GRE 4GRE 1 ? CCGGTAXCGG ? 
2 PDB 4GRE 4GRE 2 ? CCGATACCGG ? 
# 
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 4GRE A 1 ? 10 ? 4GRE 1  ? 10 ? 1  10 
2 2 4GRE B 1 ? 10 ? 4GRE 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 
# 
loop_
_pdbx_struct_assembly_prop.biol_id 
_pdbx_struct_assembly_prop.type 
_pdbx_struct_assembly_prop.value 
_pdbx_struct_assembly_prop.details 
1 'ABSA (A^2)' 620  ? 
1 MORE         -3   ? 
1 'SSA (A^2)'  4210 ? 
# 
_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 
# 
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_657 -x+1,y,-z+2 -1.0000000000 0.0000000000 0.0000000000 37.2734624681 0.0000000000 1.0000000000 
0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 69.9537771660 
# 
_struct_biol.id        1 
_struct_biol.details   ? 
# 
loop_
_struct_conn.id 
_struct_conn.conn_type_id 
_struct_conn.pdbx_leaving_atom_flag 
_struct_conn.pdbx_PDB_id 
_struct_conn.ptnr1_label_asym_id 
_struct_conn.ptnr1_label_comp_id 
_struct_conn.ptnr1_label_seq_id 
_struct_conn.ptnr1_label_atom_id 
_struct_conn.pdbx_ptnr1_label_alt_id 
_struct_conn.pdbx_ptnr1_PDB_ins_code 
_struct_conn.pdbx_ptnr1_standard_comp_id 
_struct_conn.ptnr1_symmetry 
_struct_conn.ptnr2_label_asym_id 
_struct_conn.ptnr2_label_comp_id 
_struct_conn.ptnr2_label_seq_id 
_struct_conn.ptnr2_label_atom_id 
_struct_conn.pdbx_ptnr2_label_alt_id 
_struct_conn.pdbx_ptnr2_PDB_ins_code 
_struct_conn.ptnr1_auth_asym_id 
_struct_conn.ptnr1_auth_comp_id 
_struct_conn.ptnr1_auth_seq_id 
_struct_conn.ptnr2_auth_asym_id 
_struct_conn.ptnr2_auth_comp_id 
_struct_conn.ptnr2_auth_seq_id 
_struct_conn.ptnr2_symmetry 
_struct_conn.pdbx_ptnr3_label_atom_id 
_struct_conn.pdbx_ptnr3_label_seq_id 
_struct_conn.pdbx_ptnr3_label_comp_id 
_struct_conn.pdbx_ptnr3_label_asym_id 
_struct_conn.pdbx_ptnr3_label_alt_id 
_struct_conn.pdbx_ptnr3_PDB_ins_code 
_struct_conn.details 
_struct_conn.pdbx_dist_value 
_struct_conn.pdbx_value_order 
_struct_conn.pdbx_role 
covale1  covale both ? A DA  6 "O3'" ? ? ? 1_555 A 5IU 7  P  ? ? A DA  6 A 5IU 7  1_555 ? ? ? ? ? ? ?            1.613 ? ? 
covale2  covale both ? A 5IU 7 "O3'" ? ? ? 1_555 A DC  8  P  ? ? A 5IU 7 A DC  8  1_555 ? ? ? ? ? ? ?            1.588 ? ? 
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 DT  5 N3    ? ? ? 1_555 B DA  6  N1 ? ? A DT  5 B DA  16 1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog14 hydrog ?    ? A DT  5 O4    ? ? ? 1_555 B DA  6  N6 ? ? A DT  5 B DA  16 1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog15 hydrog ?    ? A DA  6 N1    ? ? ? 1_555 B DT  5  N3 ? ? A DA  6 B DT  15 1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog16 hydrog ?    ? A DA  6 N6    ? ? ? 1_555 B DT  5  O4 ? ? A DA  6 B DT  15 1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
# 
loop_
_struct_conn_type.id 
_struct_conn_type.criteria 
_struct_conn_type.reference 
covale ? ? 
hydrog ? ? 
# 
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 8  ? ? 0.060 'SIDE CHAIN' 
2 1 DG B 13 ? ? 0.058 'SIDE CHAIN' 
# 
_pdbx_struct_mod_residue.id               1 
_pdbx_struct_mod_residue.label_asym_id    A 
_pdbx_struct_mod_residue.label_comp_id    5IU 
_pdbx_struct_mod_residue.label_seq_id     7 
_pdbx_struct_mod_residue.auth_asym_id     A 
_pdbx_struct_mod_residue.auth_comp_id     5IU 
_pdbx_struct_mod_residue.auth_seq_id      7 
_pdbx_struct_mod_residue.PDB_ins_code     ? 
_pdbx_struct_mod_residue.parent_comp_id   DU 
_pdbx_struct_mod_residue.details          "5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE" 
# 
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 134 ? C HOH . 
2 1 B HOH 114 ? D HOH . 
3 1 B HOH 132 ? D 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 
5IU N1     N N N 1   
5IU C2     C N N 2   
5IU N3     N N N 3   
5IU C4     C N N 4   
5IU C5     C N N 5   
5IU C6     C N N 6   
5IU O2     O N N 7   
5IU O4     O N N 8   
5IU I5     I N N 9   
5IU "C1'"  C N R 10  
5IU "C2'"  C N N 11  
5IU "C3'"  C N S 12  
5IU "C4'"  C N R 13  
5IU "O3'"  O N N 14  
5IU "O4'"  O N N 15  
5IU "C5'"  C N N 16  
5IU "O5'"  O N N 17  
5IU P      P N N 18  
5IU OP1    O N N 19  
5IU OP2    O N N 20  
5IU OP3    O N N 21  
5IU HN3    H N N 22  
5IU H6     H N N 23  
5IU "H1'"  H N N 24  
5IU "H2'"  H N N 25  
5IU "H2''" H N N 26  
5IU "H3'"  H N N 27  
5IU "H4'"  H N N 28  
5IU "HO3'" H N N 29  
5IU "H5'"  H N N 30  
5IU "H5''" H N N 31  
5IU HOP2   H N N 32  
5IU HOP3   H N N 33  
DA  OP3    O N N 34  
DA  P      P N N 35  
DA  OP1    O N N 36  
DA  OP2    O N N 37  
DA  "O5'"  O N N 38  
DA  "C5'"  C N N 39  
DA  "C4'"  C N R 40  
DA  "O4'"  O N N 41  
DA  "C3'"  C N S 42  
DA  "O3'"  O N N 43  
DA  "C2'"  C N N 44  
DA  "C1'"  C N R 45  
DA  N9     N Y N 46  
DA  C8     C Y N 47  
DA  N7     N Y N 48  
DA  C5     C Y N 49  
DA  C6     C Y N 50  
DA  N6     N N N 51  
DA  N1     N Y N 52  
DA  C2     C Y N 53  
DA  N3     N Y N 54  
DA  C4     C Y N 55  
DA  HOP3   H N N 56  
DA  HOP2   H N N 57  
DA  "H5'"  H N N 58  
DA  "H5''" H N N 59  
DA  "H4'"  H N N 60  
DA  "H3'"  H N N 61  
DA  "HO3'" H N N 62  
DA  "H2'"  H N N 63  
DA  "H2''" H N N 64  
DA  "H1'"  H N N 65  
DA  H8     H N N 66  
DA  H61    H N N 67  
DA  H62    H N N 68  
DA  H2     H N N 69  
DC  OP3    O N N 70  
DC  P      P N N 71  
DC  OP1    O N N 72  
DC  OP2    O N N 73  
DC  "O5'"  O N N 74  
DC  "C5'"  C N N 75  
DC  "C4'"  C N R 76  
DC  "O4'"  O N N 77  
DC  "C3'"  C N S 78  
DC  "O3'"  O N N 79  
DC  "C2'"  C N N 80  
DC  "C1'"  C N R 81  
DC  N1     N N N 82  
DC  C2     C N N 83  
DC  O2     O N N 84  
DC  N3     N N N 85  
DC  C4     C N N 86  
DC  N4     N N N 87  
DC  C5     C N N 88  
DC  C6     C N N 89  
DC  HOP3   H N N 90  
DC  HOP2   H N N 91  
DC  "H5'"  H N N 92  
DC  "H5''" H N N 93  
DC  "H4'"  H N N 94  
DC  "H3'"  H N N 95  
DC  "HO3'" H N N 96  
DC  "H2'"  H N N 97  
DC  "H2''" H N N 98  
DC  "H1'"  H N N 99  
DC  H41    H N N 100 
DC  H42    H N N 101 
DC  H5     H N N 102 
DC  H6     H N N 103 
DG  OP3    O N N 104 
DG  P      P N N 105 
DG  OP1    O N N 106 
DG  OP2    O N N 107 
DG  "O5'"  O N N 108 
DG  "C5'"  C N N 109 
DG  "C4'"  C N R 110 
DG  "O4'"  O N N 111 
DG  "C3'"  C N S 112 
DG  "O3'"  O N N 113 
DG  "C2'"  C N N 114 
DG  "C1'"  C N R 115 
DG  N9     N Y N 116 
DG  C8     C Y N 117 
DG  N7     N Y N 118 
DG  C5     C Y N 119 
DG  C6     C N N 120 
DG  O6     O N N 121 
DG  N1     N N N 122 
DG  C2     C N N 123 
DG  N2     N N N 124 
DG  N3     N N N 125 
DG  C4     C Y N 126 
DG  HOP3   H N N 127 
DG  HOP2   H N N 128 
DG  "H5'"  H N N 129 
DG  "H5''" H N N 130 
DG  "H4'"  H N N 131 
DG  "H3'"  H N N 132 
DG  "HO3'" H N N 133 
DG  "H2'"  H N N 134 
DG  "H2''" H N N 135 
DG  "H1'"  H N N 136 
DG  H8     H N N 137 
DG  H1     H N N 138 
DG  H21    H N N 139 
DG  H22    H N N 140 
DT  OP3    O N N 141 
DT  P      P N N 142 
DT  OP1    O N N 143 
DT  OP2    O N N 144 
DT  "O5'"  O N N 145 
DT  "C5'"  C N N 146 
DT  "C4'"  C N R 147 
DT  "O4'"  O N N 148 
DT  "C3'"  C N S 149 
DT  "O3'"  O N N 150 
DT  "C2'"  C N N 151 
DT  "C1'"  C N R 152 
DT  N1     N N N 153 
DT  C2     C N N 154 
DT  O2     O N N 155 
DT  N3     N N N 156 
DT  C4     C N N 157 
DT  O4     O N N 158 
DT  C5     C N N 159 
DT  C7     C N N 160 
DT  C6     C N N 161 
DT  HOP3   H N N 162 
DT  HOP2   H N N 163 
DT  "H5'"  H N N 164 
DT  "H5''" H N N 165 
DT  "H4'"  H N N 166 
DT  "H3'"  H N N 167 
DT  "HO3'" H N N 168 
DT  "H2'"  H N N 169 
DT  "H2''" H N N 170 
DT  "H1'"  H N N 171 
DT  H3     H N N 172 
DT  H71    H N N 173 
DT  H72    H N N 174 
DT  H73    H N N 175 
DT  H6     H N N 176 
HOH O      O N N 177 
HOH H1     H N N 178 
HOH H2     H N N 179 
# 
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 
5IU N1    C2     sing N N 1   
5IU N1    C6     sing N N 2   
5IU N1    "C1'"  sing N N 3   
5IU C2    N3     sing N N 4   
5IU C2    O2     doub N N 5   
5IU N3    C4     sing N N 6   
5IU N3    HN3    sing N N 7   
5IU C4    C5     sing N N 8   
5IU C4    O4     doub N N 9   
5IU C5    C6     doub N N 10  
5IU C5    I5     sing N N 11  
5IU C6    H6     sing N N 12  
5IU "C1'" "C2'"  sing N N 13  
5IU "C1'" "O4'"  sing N N 14  
5IU "C1'" "H1'"  sing N N 15  
5IU "C2'" "C3'"  sing N N 16  
5IU "C2'" "H2'"  sing N N 17  
5IU "C2'" "H2''" sing N N 18  
5IU "C3'" "C4'"  sing N N 19  
5IU "C3'" "O3'"  sing N N 20  
5IU "C3'" "H3'"  sing N N 21  
5IU "C4'" "O4'"  sing N N 22  
5IU "C4'" "C5'"  sing N N 23  
5IU "C4'" "H4'"  sing N N 24  
5IU "O3'" "HO3'" sing N N 25  
5IU "C5'" "O5'"  sing N N 26  
5IU "C5'" "H5'"  sing N N 27  
5IU "C5'" "H5''" sing N N 28  
5IU "O5'" P      sing N N 29  
5IU P     OP1    doub N N 30  
5IU P     OP2    sing N N 31  
5IU P     OP3    sing N N 32  
5IU OP2   HOP2   sing N N 33  
5IU OP3   HOP3   sing N N 34  
DA  OP3   P      sing N N 35  
DA  OP3   HOP3   sing N N 36  
DA  P     OP1    doub N N 37  
DA  P     OP2    sing N N 38  
DA  P     "O5'"  sing N N 39  
DA  OP2   HOP2   sing N N 40  
DA  "O5'" "C5'"  sing N N 41  
DA  "C5'" "C4'"  sing N N 42  
DA  "C5'" "H5'"  sing N N 43  
DA  "C5'" "H5''" sing N N 44  
DA  "C4'" "O4'"  sing N N 45  
DA  "C4'" "C3'"  sing N N 46  
DA  "C4'" "H4'"  sing N N 47  
DA  "O4'" "C1'"  sing N N 48  
DA  "C3'" "O3'"  sing N N 49  
DA  "C3'" "C2'"  sing N N 50  
DA  "C3'" "H3'"  sing N N 51  
DA  "O3'" "HO3'" sing N N 52  
DA  "C2'" "C1'"  sing N N 53  
DA  "C2'" "H2'"  sing N N 54  
DA  "C2'" "H2''" sing N N 55  
DA  "C1'" N9     sing N N 56  
DA  "C1'" "H1'"  sing N N 57  
DA  N9    C8     sing Y N 58  
DA  N9    C4     sing Y N 59  
DA  C8    N7     doub Y N 60  
DA  C8    H8     sing N N 61  
DA  N7    C5     sing Y N 62  
DA  C5    C6     sing Y N 63  
DA  C5    C4     doub Y N 64  
DA  C6    N6     sing N N 65  
DA  C6    N1     doub Y N 66  
DA  N6    H61    sing N N 67  
DA  N6    H62    sing N N 68  
DA  N1    C2     sing Y N 69  
DA  C2    N3     doub Y N 70  
DA  C2    H2     sing N N 71  
DA  N3    C4     sing Y N 72  
DC  OP3   P      sing N N 73  
DC  OP3   HOP3   sing N N 74  
DC  P     OP1    doub N N 75  
DC  P     OP2    sing N N 76  
DC  P     "O5'"  sing N N 77  
DC  OP2   HOP2   sing N N 78  
DC  "O5'" "C5'"  sing N N 79  
DC  "C5'" "C4'"  sing N N 80  
DC  "C5'" "H5'"  sing N N 81  
DC  "C5'" "H5''" sing N N 82  
DC  "C4'" "O4'"  sing N N 83  
DC  "C4'" "C3'"  sing N N 84  
DC  "C4'" "H4'"  sing N N 85  
DC  "O4'" "C1'"  sing N N 86  
DC  "C3'" "O3'"  sing N N 87  
DC  "C3'" "C2'"  sing N N 88  
DC  "C3'" "H3'"  sing N N 89  
DC  "O3'" "HO3'" sing N N 90  
DC  "C2'" "C1'"  sing N N 91  
DC  "C2'" "H2'"  sing N N 92  
DC  "C2'" "H2''" sing N N 93  
DC  "C1'" N1     sing N N 94  
DC  "C1'" "H1'"  sing N N 95  
DC  N1    C2     sing N N 96  
DC  N1    C6     sing N N 97  
DC  C2    O2     doub N N 98  
DC  C2    N3     sing N N 99  
DC  N3    C4     doub N N 100 
DC  C4    N4     sing N N 101 
DC  C4    C5     sing N N 102 
DC  N4    H41    sing N N 103 
DC  N4    H42    sing N N 104 
DC  C5    C6     doub N N 105 
DC  C5    H5     sing N N 106 
DC  C6    H6     sing N N 107 
DG  OP3   P      sing N N 108 
DG  OP3   HOP3   sing N N 109 
DG  P     OP1    doub N N 110 
DG  P     OP2    sing N N 111 
DG  P     "O5'"  sing N N 112 
DG  OP2   HOP2   sing N N 113 
DG  "O5'" "C5'"  sing N N 114 
DG  "C5'" "C4'"  sing N N 115 
DG  "C5'" "H5'"  sing N N 116 
DG  "C5'" "H5''" sing N N 117 
DG  "C4'" "O4'"  sing N N 118 
DG  "C4'" "C3'"  sing N N 119 
DG  "C4'" "H4'"  sing N N 120 
DG  "O4'" "C1'"  sing N N 121 
DG  "C3'" "O3'"  sing N N 122 
DG  "C3'" "C2'"  sing N N 123 
DG  "C3'" "H3'"  sing N N 124 
DG  "O3'" "HO3'" sing N N 125 
DG  "C2'" "C1'"  sing N N 126 
DG  "C2'" "H2'"  sing N N 127 
DG  "C2'" "H2''" sing N N 128 
DG  "C1'" N9     sing N N 129 
DG  "C1'" "H1'"  sing N N 130 
DG  N9    C8     sing Y N 131 
DG  N9    C4     sing Y N 132 
DG  C8    N7     doub Y N 133 
DG  C8    H8     sing N N 134 
DG  N7    C5     sing Y N 135 
DG  C5    C6     sing N N 136 
DG  C5    C4     doub Y N 137 
DG  C6    O6     doub N N 138 
DG  C6    N1     sing N N 139 
DG  N1    C2     sing N N 140 
DG  N1    H1     sing N N 141 
DG  C2    N2     sing N N 142 
DG  C2    N3     doub N N 143 
DG  N2    H21    sing N N 144 
DG  N2    H22    sing N N 145 
DG  N3    C4     sing N N 146 
DT  OP3   P      sing N N 147 
DT  OP3   HOP3   sing N N 148 
DT  P     OP1    doub N N 149 
DT  P     OP2    sing N N 150 
DT  P     "O5'"  sing N N 151 
DT  OP2   HOP2   sing N N 152 
DT  "O5'" "C5'"  sing N N 153 
DT  "C5'" "C4'"  sing N N 154 
DT  "C5'" "H5'"  sing N N 155 
DT  "C5'" "H5''" sing N N 156 
DT  "C4'" "O4'"  sing N N 157 
DT  "C4'" "C3'"  sing N N 158 
DT  "C4'" "H4'"  sing N N 159 
DT  "O4'" "C1'"  sing N N 160 
DT  "C3'" "O3'"  sing N N 161 
DT  "C3'" "C2'"  sing N N 162 
DT  "C3'" "H3'"  sing N N 163 
DT  "O3'" "HO3'" sing N N 164 
DT  "C2'" "C1'"  sing N N 165 
DT  "C2'" "H2'"  sing N N 166 
DT  "C2'" "H2''" sing N N 167 
DT  "C1'" N1     sing N N 168 
DT  "C1'" "H1'"  sing N N 169 
DT  N1    C2     sing N N 170 
DT  N1    C6     sing N N 171 
DT  C2    O2     doub N N 172 
DT  C2    N3     sing N N 173 
DT  N3    C4     sing N N 174 
DT  N3    H3     sing N N 175 
DT  C4    O4     doub N N 176 
DT  C4    C5     sing N N 177 
DT  C5    C7     sing N N 178 
DT  C5    C6     doub N N 179 
DT  C7    H71    sing N N 180 
DT  C7    H72    sing N N 181 
DT  C7    H73    sing N N 182 
DT  C6    H6     sing N N 183 
HOH O     H1     sing N N 184 
HOH O     H2     sing N N 185 
# 
_ndb_struct_conf_na.entry_id   4GRE 
_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 1.021  -0.123 0.202  -0.400  -18.100 4.626  1 A_DC1:DG20_B A 1 ? B 20 ? 19 1 
1 A DC 2 1_555 B DG 9  1_555 0.230  -0.133 -0.114 -2.925  -11.469 0.097  2 A_DC2:DG19_B A 2 ? B 19 ? 19 1 
1 A DG 3 1_555 B DC 8  1_555 -0.521 -0.210 0.291  5.781   -2.075  3.764  3 A_DG3:DC18_B A 3 ? B 18 ? 19 1 
1 A DG 4 1_555 B DC 7  1_555 -0.691 -0.146 -0.422 -7.594  -28.057 -2.014 4 A_DG4:DC17_B A 4 ? B 17 ? 19 1 
1 A DT 5 1_555 B DA 6  1_555 -0.205 -0.287 -0.273 -15.311 -19.717 0.284  5 A_DT5:DA16_B A 5 ? B 16 ? 20 1 
1 A DA 6 1_555 B DT 5  1_555 0.133  -0.143 -0.163 -1.557  -11.778 1.164  6 A_DA6:DT15_B A 6 ? B 15 ? 20 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 0.348  2.448 3.378 9.558  7.093  38.658 2.658 0.693  3.732 10.417 -14.038 
40.382 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 0.350  2.730 2.979 -3.907 -4.663 34.763 5.094 -1.071 2.550 -7.730 6.477   
35.275 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 -0.974 1.273 3.883 1.219  9.644  37.357 0.458 1.661  4.044 14.753 -1.865  
38.558 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 DT 5 1_555 B DA 6 1_555 0.188  0.294 3.379 -0.045 1.233  38.125 0.289 -0.294 3.386 1.887  0.069   
38.145 4 AA_DG4DT5:DA16DC17_BB A 4 ? B 17 ? A 5 ? B 16 ? 
1 A DT 5 1_555 B DA 6  1_555 A DA 6 1_555 B DT 5 1_555 -0.091 1.711 3.037 -2.497 5.960  38.872 1.855 -0.152 3.253 8.881  3.720   
39.385 5 AA_DT5DA6:DT15DA16_BB A 5 ? B 16 ? A 6 ? B 15 ? 
# 
_atom_sites.entry_id                    4GRE 
_atom_sites.fract_transf_matrix[1][1]   0.015395 
_atom_sites.fract_transf_matrix[1][2]   0.000000 
_atom_sites.fract_transf_matrix[1][3]   0.006092 
_atom_sites.fract_transf_matrix[2][1]   0.000000 
_atom_sites.fract_transf_matrix[2][2]   0.040367 
_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]   0.028590 
_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 
I 
N 
O 
P 
# 
loop_