data_3GBI
# 
_entry.id   3GBI 
# 
_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   3GBI         pdb_00003gbi 10.2210/pdb3gbi/pdb 
NDB   BD0116       ?            ?                   
RCSB  RCSB051659   ?            ?                   
WWPDB D_1000051659 ?            ?                   
# 
loop_
_pdbx_audit_revision_history.ordinal 
_pdbx_audit_revision_history.data_content_type 
_pdbx_audit_revision_history.major_revision 
_pdbx_audit_revision_history.minor_revision 
_pdbx_audit_revision_history.revision_date 
1 'Structure model' 1 0 2009-09-01 
2 'Structure model' 1 1 2011-07-13 
3 'Structure model' 1 2 2017-11-01 
4 'Structure model' 1 3 2024-02-21 
# 
_pdbx_audit_revision_details.ordinal             1 
_pdbx_audit_revision_details.revision_ordinal    1 
_pdbx_audit_revision_details.data_content_type   'Structure model' 
_pdbx_audit_revision_details.provider            repository 
_pdbx_audit_revision_details.type                'Initial release' 
_pdbx_audit_revision_details.description         ? 
_pdbx_audit_revision_details.details             ? 
# 
loop_
_pdbx_audit_revision_group.ordinal 
_pdbx_audit_revision_group.revision_ordinal 
_pdbx_audit_revision_group.data_content_type 
_pdbx_audit_revision_group.group 
1 2 'Structure model' 'Version format compliance' 
2 3 'Structure model' 'Refinement description'    
3 4 'Structure model' 'Data collection'           
4 4 'Structure model' 'Database references'       
5 4 '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' software       
2 4 'Structure model' chem_comp_atom 
3 4 'Structure model' chem_comp_bond 
4 4 'Structure model' database_2     
5 4 'Structure model' struct_conn    
6 4 'Structure model' struct_ref_seq 
# 
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' '_software.name'                      
2  4 'Structure model' '_database_2.pdbx_DOI'                
3  4 'Structure model' '_database_2.pdbx_database_accession' 
4  4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 
5  4 'Structure model' '_struct_conn.ptnr1_auth_asym_id'     
6  4 'Structure model' '_struct_conn.ptnr1_auth_comp_id'     
7  4 'Structure model' '_struct_conn.ptnr1_auth_seq_id'      
8  4 'Structure model' '_struct_conn.ptnr1_label_asym_id'    
9  4 'Structure model' '_struct_conn.ptnr1_label_atom_id'    
10 4 'Structure model' '_struct_conn.ptnr1_label_comp_id'    
11 4 'Structure model' '_struct_conn.ptnr1_label_seq_id'     
12 4 'Structure model' '_struct_conn.ptnr1_symmetry'         
13 4 'Structure model' '_struct_conn.ptnr2_auth_asym_id'     
14 4 'Structure model' '_struct_conn.ptnr2_auth_comp_id'     
15 4 'Structure model' '_struct_conn.ptnr2_auth_seq_id'      
16 4 'Structure model' '_struct_conn.ptnr2_label_asym_id'    
17 4 'Structure model' '_struct_conn.ptnr2_label_atom_id'    
18 4 'Structure model' '_struct_conn.ptnr2_label_comp_id'    
19 4 'Structure model' '_struct_conn.ptnr2_label_seq_id'     
20 4 'Structure model' '_struct_conn.ptnr2_symmetry'         
21 4 'Structure model' '_struct_ref_seq.db_align_beg'        
22 4 'Structure model' '_struct_ref_seq.db_align_end'        
# 
_pdbx_database_status.entry_id                        3GBI 
_pdbx_database_status.deposit_site                    RCSB 
_pdbx_database_status.process_site                    RCSB 
_pdbx_database_status.recvd_initial_deposition_date   2009-02-19 
_pdbx_database_status.status_code                     REL 
_pdbx_database_status.status_code_sf                  REL 
_pdbx_database_status.status_code_mr                  ? 
_pdbx_database_status.SG_entry                        ? 
_pdbx_database_status.pdb_format_compatible           Y 
_pdbx_database_status.status_code_cs                  ? 
_pdbx_database_status.methods_development_category    ? 
_pdbx_database_status.status_code_nmr_data            ? 
# 
loop_
_audit_author.name 
_audit_author.pdbx_ordinal 
'Birktoft, J.J.' 1 
'Zheng, J.'      2 
'Seeman, N.C.'   3 
# 
_citation.id                        primary 
_citation.title                     'From molecular to macroscopic via the rational design of a self-assembled 3D DNA crystal.' 
_citation.journal_abbrev            Nature 
_citation.journal_volume            461 
_citation.page_first                74 
_citation.page_last                 77 
_citation.year                      2009 
_citation.journal_id_ASTM           NATUAS 
_citation.country                   UK 
_citation.journal_id_ISSN           0028-0836 
_citation.journal_id_CSD            0006 
_citation.book_publisher            ? 
_citation.pdbx_database_id_PubMed   19727196 
_citation.pdbx_database_id_DOI      10.1038/nature08274 
# 
loop_
_citation_author.citation_id 
_citation_author.name 
_citation_author.ordinal 
_citation_author.identifier_ORCID 
primary 'Zheng, J.'          1 ? 
primary 'Birktoft, J.J.'     2 ? 
primary 'Chen, Y.'           3 ? 
primary 'Wang, T.'           4 ? 
primary 'Sha, R.'            5 ? 
primary 'Constantinou, P.E.' 6 ? 
primary 'Ginell, S.L.'       7 ? 
primary 'Mao, C.'            8 ? 
primary 'Seeman, N.C.'       9 ? 
# 
loop_
_entity.id 
_entity.type 
_entity.src_method 
_entity.pdbx_description 
_entity.formula_weight 
_entity.pdbx_number_of_molecules 
_entity.pdbx_ec 
_entity.pdbx_mutation 
_entity.pdbx_fragment 
_entity.details 
1 polymer syn 
;DNA (5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*AP*CP*GP*GP*AP*CP*AP*TP*CP*A)-3')
;
6457.188 1 ? ? ?                                                                                                         ? 
2 polymer syn 
;DNA (5'-D(P*CP*CP*GP*TP*AP*CP*A)-3')
;
2082.400 1 ? ? 'symmetrically- and sequentially repeating unit of a circular DNA molecules, see remark 400 for details.' ? 
3 polymer syn 
;DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')
;
1825.216 1 ? ? 'last 6 residues of a DNA molecule used in experiment, see remark 400 for details.'                       ? 
4 polymer syn 
;DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*T)-3')
;
2432.614 1 ? ? 'first 8 residues of a DNA molecule used in experiment, see remark 400 for details.'                      ? 
# 
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 no 
;(DG)(DA)(DG)(DC)(DA)(DG)(DC)(DC)(DT)(DG)(DT)(DA)(DC)(DG)(DG)(DA)(DC)(DA)(DT)(DC)
(DA)
;
GAGCAGCCTGTACGGACATCA A ? 
2 polydeoxyribonucleotide no no '(DC)(DC)(DG)(DT)(DA)(DC)(DA)'                                                          CCGTACA B 
? 
3 polydeoxyribonucleotide no no '(DG)(DG)(DC)(DT)(DG)(DC)'                                                              GGCTGC C ? 
4 polydeoxyribonucleotide no no '(DT)(DC)(DT)(DG)(DA)(DT)(DG)(DT)'                                                      TCTGATGT D 
? 
# 
loop_
_entity_poly_seq.entity_id 
_entity_poly_seq.num 
_entity_poly_seq.mon_id 
_entity_poly_seq.hetero 
1 1  DG n 
1 2  DA n 
1 3  DG n 
1 4  DC n 
1 5  DA n 
1 6  DG n 
1 7  DC n 
1 8  DC n 
1 9  DT n 
1 10 DG n 
1 11 DT n 
1 12 DA n 
1 13 DC n 
1 14 DG n 
1 15 DG n 
1 16 DA n 
1 17 DC n 
1 18 DA n 
1 19 DT n 
1 20 DC n 
1 21 DA n 
2 1  DC n 
2 2  DC n 
2 3  DG n 
2 4  DT n 
2 5  DA n 
2 6  DC n 
2 7  DA n 
3 1  DG n 
3 2  DG n 
3 3  DC n 
3 4  DT n 
3 5  DG n 
3 6  DC n 
4 1  DT n 
4 2  DC n 
4 3  DT n 
4 4  DG n 
4 5  DA n 
4 6  DT n 
4 7  DG n 
4 8  DT 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 ? ? ? ? ? 
;DNA strands were synthesized by standard phosphoramidite techniques on an Applied Biosystems 394 DNA synthesizer using trityl-on mode.
;
2 1 sample ? ? ? ? ? 
'DNA strands were synthesized by standard phosphoramidite techniques on an Applied Biosystems 394 DNA synthesizer using trityl-on' 
3 1 sample ? ? ? ? ? 
'DNA strands were synthesized by standard phosphoramidite techniques on an Applied Biosystems 394 DNA synthesizer using trityl-on' 
4 1 sample ? ? ? ? ? 
'DNA strands were synthesized by standard phosphoramidite techniques on an Applied Biosystems 394 DNA synthesizer using trityl-on' 
# 
loop_
_chem_comp.id 
_chem_comp.type 
_chem_comp.mon_nstd_flag 
_chem_comp.name 
_chem_comp.pdbx_synonyms 
_chem_comp.formula 
_chem_comp.formula_weight 
DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 
DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE"  ? 'C9 H14 N3 O7 P'  307.197 
DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 
DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE"         ? 'C10 H15 N2 O8 P' 322.208 
# 
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  DG 1  101 101 DG DG A . n 
A 1 2  DA 2  102 102 DA DA A . n 
A 1 3  DG 3  103 103 DG DG A . n 
A 1 4  DC 4  104 104 DC DC A . n 
A 1 5  DA 5  105 105 DA DA A . n 
A 1 6  DG 6  106 106 DG DG A . n 
A 1 7  DC 7  107 107 DC DC A . n 
A 1 8  DC 8  108 108 DC DC A . n 
A 1 9  DT 9  109 109 DT DT A . n 
A 1 10 DG 10 110 110 DG DG A . n 
A 1 11 DT 11 111 111 DT DT A . n 
A 1 12 DA 12 112 112 DA DA A . n 
A 1 13 DC 13 113 113 DC DC A . n 
A 1 14 DG 14 114 114 DG DG A . n 
A 1 15 DG 15 115 115 DG DG A . n 
A 1 16 DA 16 116 116 DA DA A . n 
A 1 17 DC 17 117 117 DC DC A . n 
A 1 18 DA 18 118 118 DA DA A . n 
A 1 19 DT 19 119 119 DT DT A . n 
A 1 20 DC 20 120 120 DC DC A . n 
A 1 21 DA 21 121 121 DA DA A . n 
B 2 1  DC 1  119 119 DC DC B . n 
B 2 2  DC 2  120 120 DC DC B . n 
B 2 3  DG 3  121 121 DG DG B . n 
B 2 4  DT 4  122 122 DT DT B . n 
B 2 5  DA 5  123 123 DA DA B . n 
B 2 6  DC 6  124 124 DC DC B . n 
B 2 7  DA 7  125 125 DA DA B . n 
C 3 1  DG 1  209 209 DG DG C . n 
C 3 2  DG 2  210 210 DG DG C . n 
C 3 3  DC 3  211 211 DC DC C . n 
C 3 4  DT 4  212 212 DT DT C . n 
C 3 5  DG 5  213 213 DG DG C . n 
C 3 6  DC 6  214 214 DC DC C . n 
D 4 1  DT 1  101 101 DT DT D . n 
D 4 2  DC 2  102 102 DC DC D . n 
D 4 3  DT 3  103 103 DT DT D . n 
D 4 4  DG 4  104 104 DG DG D . n 
D 4 5  DA 5  105 105 DA DA D . n 
D 4 6  DT 6  106 106 DT DT D . n 
D 4 7  DG 7  107 107 DG DG D . n 
D 4 8  DT 8  108 108 DT DT D . n 
# 
loop_
_software.name 
_software.version 
_software.date 
_software.type 
_software.contact_author 
_software.contact_author_email 
_software.classification 
_software.location 
_software.language 
_software.citation_id 
_software.pdbx_ordinal 
PHENIX      .     ?               package 'Paul D. Adams' PDAdams@lbl.gov       refinement        http://www.phenix-online.org/ 
C++ ? 1 
PDB_EXTRACT 3.006 'June 11, 2008' package PDB             help@deposit.rcsb.org 'data extraction' 
http://sw-tools.pdb.org/apps/PDB_EXTRACT/ C++ ? 2 
HKL-3000    .     ?               ?       ?               ?                     'data collection' ? ?   ? 3 
HKL-3000    .     ?               ?       ?               ?                     'data reduction'  ? ?   ? 4 
HKL-3000    .     ?               ?       ?               ?                     'data scaling'    ? ?   ? 5 
HKL2Map     .     ?               ?       ?               ?                     phasing           ? ?   ? 6 
# 
_cell.entry_id           3GBI 
_cell.length_a           107.161 
_cell.length_b           107.161 
_cell.length_c           93.144 
_cell.angle_alpha        90.00 
_cell.angle_beta         90.00 
_cell.angle_gamma        120.00 
_cell.Z_PDB              9 
_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                         3GBI 
_symmetry.space_group_name_H-M             'H 3' 
_symmetry.pdbx_full_space_group_name_H-M   ? 
_symmetry.cell_setting                     ? 
_symmetry.Int_Tables_number                146 
_symmetry.space_group_name_Hall            ? 
# 
_exptl.entry_id          3GBI 
_exptl.method            'X-RAY DIFFRACTION' 
_exptl.crystals_number   1 
# 
_exptl_crystal.id                    1 
_exptl_crystal.density_meas          ? 
_exptl_crystal.density_Matthews      ? 
_exptl_crystal.density_percent_sol   ? 
_exptl_crystal.description           ? 
_exptl_crystal.F_000                 ? 
_exptl_crystal.preparation           ? 
# 
_exptl_crystal_grow.crystal_id      1 
_exptl_crystal_grow.method          'VAPOR DIFFUSION, SITTING DROP' 
_exptl_crystal_grow.temp            293 
_exptl_crystal_grow.temp_details    ? 
_exptl_crystal_grow.pH              8.5 
_exptl_crystal_grow.pdbx_pH_range   ? 
_exptl_crystal_grow.pdbx_details    
;Grown by vapor diffusion while treated with a controlled temperature gradient from 333 degs to 293 degs., pH 8.5, VAPOR DIFFUSION, SITTING DROP
;
# 
_diffrn.id                     1 
_diffrn.ambient_temp           ? 
_diffrn.ambient_temp_details   ? 
_diffrn.crystal_id             1 
# 
_diffrn_detector.diffrn_id              1 
_diffrn_detector.detector               CCD 
_diffrn_detector.type                   'ADSC QUANTUM 315r' 
_diffrn_detector.pdbx_collection_date   2008-06-17 
_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                    Graphite 
_diffrn_radiation.pdbx_diffrn_protocol             'SINGLE WAVELENGTH' 
_diffrn_radiation.pdbx_scattering_type             x-ray 
# 
_diffrn_radiation_wavelength.id           1 
_diffrn_radiation_wavelength.wavelength   1.0 
_diffrn_radiation_wavelength.wt           1.0 
# 
_diffrn_source.diffrn_id                   1 
_diffrn_source.source                      SYNCHROTRON 
_diffrn_source.type                        'APS BEAMLINE 19-ID' 
_diffrn_source.pdbx_synchrotron_site       APS 
_diffrn_source.pdbx_synchrotron_beamline   19-ID 
_diffrn_source.pdbx_wavelength             ? 
_diffrn_source.pdbx_wavelength_list        1.0 
# 
_reflns.entry_id                     3GBI 
_reflns.observed_criterion_sigma_I   0 
_reflns.observed_criterion_sigma_F   0 
_reflns.d_resolution_low             17.3 
_reflns.d_resolution_high            4.01 
_reflns.number_obs                   3211 
_reflns.number_all                   3341 
_reflns.percent_possible_obs         96.1 
_reflns.pdbx_Rmerge_I_obs            0.067 
_reflns.pdbx_Rsym_value              ? 
_reflns.pdbx_netI_over_sigmaI        10.9 
_reflns.B_iso_Wilson_estimate        199.880 
_reflns.pdbx_redundancy              7.3 
_reflns.R_free_details               ? 
_reflns.pdbx_chi_squared             ? 
_reflns.pdbx_scaling_rejects         ? 
_reflns.pdbx_diffrn_id               1 
_reflns.pdbx_ordinal                 1 
# 
_reflns_shell.d_res_high             4.00 
_reflns_shell.d_res_low              4.07 
_reflns_shell.percent_possible_all   100 
_reflns_shell.Rmerge_I_obs           ? 
_reflns_shell.pdbx_Rsym_value        ? 
_reflns_shell.meanI_over_sigI_obs    ? 
_reflns_shell.pdbx_redundancy        ? 
_reflns_shell.percent_possible_obs   ? 
_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_diffrn_id         ? 
_reflns_shell.pdbx_ordinal           1 
# 
_refine.pdbx_refine_id                           'X-RAY DIFFRACTION' 
_refine.entry_id                                 3GBI 
_refine.ls_number_reflns_obs                     2022 
_refine.ls_number_reflns_all                     3211 
_refine.pdbx_ls_sigma_I                          ? 
_refine.pdbx_ls_sigma_F                          0.14 
_refine.pdbx_data_cutoff_high_absF               ? 
_refine.pdbx_data_cutoff_low_absF                ? 
_refine.pdbx_data_cutoff_high_rms_absF           ? 
_refine.ls_d_res_low                             17.288 
_refine.ls_d_res_high                            4.018 
_refine.ls_percent_reflns_obs                    61.140 
_refine.ls_R_factor_obs                          0.246 
_refine.ls_R_factor_all                          0.246 
_refine.ls_R_factor_R_work                       0.240 
_refine.ls_R_factor_R_free                       0.309 
_refine.ls_R_factor_R_free_error                 ? 
_refine.ls_R_factor_R_free_error_details         ? 
_refine.ls_percent_reflns_R_free                 10.040 
_refine.ls_number_reflns_R_free                  203 
_refine.ls_number_parameters                     ? 
_refine.ls_number_restraints                     ? 
_refine.occupancy_min                            1.00 
_refine.occupancy_max                            1.00 
_refine.correlation_coeff_Fo_to_Fc               ? 
_refine.correlation_coeff_Fo_to_Fc_free          ? 
_refine.B_iso_mean                               80.000 
_refine.aniso_B[1][1]                            63.252 
_refine.aniso_B[2][2]                            63.252 
_refine.aniso_B[3][3]                            227.851 
_refine.aniso_B[1][2]                            0.000 
_refine.aniso_B[1][3]                            0.000 
_refine.aniso_B[2][3]                            0.000 
_refine.solvent_model_details                    'FLAT BULK SOLVENT MODEL' 
_refine.solvent_model_param_ksol                 0.090 
_refine.solvent_model_param_bsol                 20.001 
_refine.pdbx_solvent_vdw_probe_radii             ? 
_refine.pdbx_solvent_ion_probe_radii             ? 
_refine.pdbx_solvent_shrinkage_radii             ? 
_refine.pdbx_ls_cross_valid_method               ? 
_refine.details                                  
;In reality all 3211 measured reflections were used in the refinement (using PHENIX). Of these only 2022 had FOBS/SIGMA_FOBS >/=  0.140.
;
_refine.pdbx_starting_model                      ? 
_refine.pdbx_method_to_determine_struct          ? 
_refine.pdbx_isotropic_thermal_model             ? 
_refine.pdbx_stereochemistry_target_values       ML 
_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                            0.830 
_refine.pdbx_overall_phase_error                 ? 
_refine.overall_SU_B                             ? 
_refine.ls_redundancy_reflns_obs                 ? 
_refine.overall_SU_R_Cruickshank_DPI             ? 
_refine.overall_SU_R_free                        ? 
_refine.ls_wR_factor_R_free                      ? 
_refine.ls_wR_factor_R_work                      ? 
_refine.overall_FOM_free_R_set                   ? 
_refine.overall_FOM_work_R_set                   ? 
_refine.pdbx_diffrn_id                           1 
_refine.pdbx_TLS_residual_ADP_flag               ? 
_refine.pdbx_overall_SU_R_free_Cruickshank_DPI   ? 
_refine.pdbx_overall_SU_R_Blow_DPI               ? 
_refine.pdbx_overall_SU_R_free_Blow_DPI          ? 
# 
_refine_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   855 
_refine_hist.pdbx_number_atoms_ligand         0 
_refine_hist.number_atoms_solvent             0 
_refine_hist.number_atoms_total               855 
_refine_hist.d_res_high                       4.018 
_refine_hist.d_res_low                        17.288 
# 
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 
f_bond_d           0.016  ? ? 1052 'X-RAY DIFFRACTION' ? 
f_angle_d          1.364  ? ? 1465 'X-RAY DIFFRACTION' ? 
f_dihedral_angle_d 31.823 ? ? 406  'X-RAY DIFFRACTION' ? 
f_chiral_restr     0.058  ? ? 166  'X-RAY DIFFRACTION' ? 
f_plane_restr      0.002  ? ? 42   'X-RAY DIFFRACTION' ? 
# 
_refine_ls_shell.pdbx_refine_id                   'X-RAY DIFFRACTION' 
_refine_ls_shell.pdbx_total_number_of_bins_used   1 
_refine_ls_shell.d_res_high                       4.018 
_refine_ls_shell.d_res_low                        ? 
_refine_ls_shell.number_reflns_R_work             1819 
_refine_ls_shell.R_factor_R_work                  0.240 
_refine_ls_shell.percent_reflns_obs               61.000 
_refine_ls_shell.R_factor_R_free                  0.309 
_refine_ls_shell.R_factor_R_free_error            ? 
_refine_ls_shell.percent_reflns_R_free            ? 
_refine_ls_shell.number_reflns_R_free             203 
_refine_ls_shell.number_reflns_all                2022 
_refine_ls_shell.R_factor_all                     ? 
_refine_ls_shell.redundancy_reflns_obs            ? 
_refine_ls_shell.number_reflns_obs                ? 
# 
_struct.entry_id                  3GBI 
_struct.title                     'The Rational Design and Structural Analysis of a Self-Assembled Three-Dimensional DNA Crystal' 
_struct.pdbx_model_details        ? 
_struct.pdbx_CASP_flag            N 
_struct.pdbx_model_type_details   ? 
# 
_struct_keywords.entry_id        3GBI 
_struct_keywords.pdbx_keywords   DNA 
_struct_keywords.text            'nanotechnology, DNA crystals, DNA crossover, designed crystal lattice, 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 4 ? 
# 
loop_
_struct_ref.entity_id 
_struct_ref.pdbx_db_accession 
_struct_ref.db_code 
_struct_ref.db_name 
_struct_ref.id 
_struct_ref.pdbx_align_begin 
_struct_ref.pdbx_seq_one_letter_code 
_struct_ref.pdbx_db_isoform 
1 3GBI 3GBI PDB 1 1 GAGCAGCCTGTACGGACATCA ? 
2 3GBI 3GBI PDB 2 1 CCGTACA               ? 
3 3GBI 3GBI PDB 3 1 GGCTGC                ? 
4 3GBI 3GBI PDB 4 1 TCTGATGT              ? 
# 
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 3GBI A 1 ? 21 ? 3GBI 101 ? 121 ? 101 121 
2 2 3GBI B 1 ? 7  ? 3GBI 119 ? 125 ? 119 125 
3 3 3GBI C 1 ? 6  ? 3GBI 209 ? 214 ? 209 214 
4 4 3GBI D 1 ? 8  ? 3GBI 101 ? 108 ? 101 108 
# 
_pdbx_struct_assembly.id                   1 
_pdbx_struct_assembly.details              author_defined_assembly 
_pdbx_struct_assembly.method_details       ? 
_pdbx_struct_assembly.oligomeric_details   heptameric 
_pdbx_struct_assembly.oligomeric_count     7 
# 
_pdbx_struct_assembly_gen.assembly_id       1 
_pdbx_struct_assembly_gen.oper_expression   1,2,3 
_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_555 -y,x-y,z  -0.5000000000 -0.8660254038 0.0000000000 0.0000000000 0.8660254038  -0.5000000000 
0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 
3 'crystal symmetry operation' 3_555 -x+y,-x,z -0.5000000000 0.8660254038  0.0000000000 0.0000000000 -0.8660254038 -0.5000000000 
0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 
# 
_struct_biol.id        1 
_struct_biol.details   
;Authors state that the crystal is an infinite network made from three DNA strands that self-associate. In the current entry the asymmetric unit is comprised of 4 chains, 3 of which are fragments of longer DNA strands. Applying the space group H3 symmetry operators (X, Y, Z,), (-Y, X-Y, Z), and (-X+Y,-X,Z) to the contents of the asymmetric unit generates one trimeric unit of the self-associated DNA network. Additional details about the chemical composition and association are included in remark 400.
;
# 
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 ? B DC 1  P  ? ? ? 1_555 B DA 7 "O3'" ? ? B DC 119 B DA 125 2_555 ? ? ? ? ? ? ?               1.612 ? ? 
covale2  covale both ? B DC 1  P  ? ? ? 3_555 B DA 7 "O3'" ? ? B DC 119 B DA 125 1_555 ? ? ? ? ? ? ?               1.612 ? ? 
covale3  covale both ? C DG 1  P  ? ? ? 1_555 D DT 8 "O3'" ? ? C DG 209 D DT 108 3_555 ? ? ? ? ? ? ?               1.614 ? ? 
covale4  covale both ? C DG 1  P  ? ? ? 2_555 D DT 8 "O3'" ? ? C DG 209 D DT 108 1_555 ? ? ? ? ? ? ?               1.614 ? ? 
hydrog1  hydrog ?    ? A DG 3  N1 ? ? ? 1_555 C DC 6 N3    ? ? A DG 103 C DC 214 1_555 ? ? ? ? ? ? WATSON-CRICK    ?     ? ? 
hydrog2  hydrog ?    ? A DG 3  N2 ? ? ? 1_555 C DC 6 O2    ? ? A DG 103 C DC 214 1_555 ? ? ? ? ? ? WATSON-CRICK    ?     ? ? 
hydrog3  hydrog ?    ? A DG 3  O6 ? ? ? 1_555 C DC 6 N4    ? ? A DG 103 C DC 214 1_555 ? ? ? ? ? ? WATSON-CRICK    ?     ? ? 
hydrog4  hydrog ?    ? A DC 4  N3 ? ? ? 1_555 C DG 5 N1    ? ? A DC 104 C DG 213 1_555 ? ? ? ? ? ? WATSON-CRICK    ?     ? ? 
hydrog5  hydrog ?    ? A DC 4  N4 ? ? ? 1_555 C DG 5 O6    ? ? A DC 104 C DG 213 1_555 ? ? ? ? ? ? WATSON-CRICK    ?     ? ? 
hydrog6  hydrog ?    ? A DC 4  O2 ? ? ? 1_555 C DG 5 N2    ? ? A DC 104 C DG 213 1_555 ? ? ? ? ? ? WATSON-CRICK    ?     ? ? 
hydrog7  hydrog ?    ? A DA 5  N1 ? ? ? 1_555 C DT 4 N3    ? ? A DA 105 C DT 212 1_555 ? ? ? ? ? ? WATSON-CRICK    ?     ? ? 
hydrog8  hydrog ?    ? A DA 5  N6 ? ? ? 1_555 C DT 4 O4    ? ? A DA 105 C DT 212 1_555 ? ? ? ? ? ? WATSON-CRICK    ?     ? ? 
hydrog9  hydrog ?    ? A DG 6  N2 ? ? ? 1_555 C DC 3 N3    ? ? A DG 106 C DC 211 1_555 ? ? ? ? ? ? 'DG-DC PAIR'    ?     ? ? 
hydrog10 hydrog ?    ? A DC 7  N3 ? ? ? 1_555 C DG 2 N1    ? ? A DC 107 C DG 210 1_555 ? ? ? ? ? ? WATSON-CRICK    ?     ? ? 
hydrog11 hydrog ?    ? A DC 7  N4 ? ? ? 1_555 C DG 2 O6    ? ? A DC 107 C DG 210 1_555 ? ? ? ? ? ? WATSON-CRICK    ?     ? ? 
hydrog12 hydrog ?    ? A DC 7  O2 ? ? ? 1_555 C DG 2 N2    ? ? A DC 107 C DG 210 1_555 ? ? ? ? ? ? WATSON-CRICK    ?     ? ? 
hydrog13 hydrog ?    ? A DC 8  N3 ? ? ? 1_555 C DG 1 N1    ? ? A DC 108 C DG 209 1_555 ? ? ? ? ? ? WATSON-CRICK    ?     ? ? 
hydrog14 hydrog ?    ? A DC 8  N4 ? ? ? 1_555 C DG 1 O6    ? ? A DC 108 C DG 209 1_555 ? ? ? ? ? ? WATSON-CRICK    ?     ? ? 
hydrog15 hydrog ?    ? A DC 8  O2 ? ? ? 1_555 C DG 1 N2    ? ? A DC 108 C DG 209 1_555 ? ? ? ? ? ? WATSON-CRICK    ?     ? ? 
hydrog16 hydrog ?    ? A DT 9  N3 ? ? ? 1_555 B DA 7 N1    ? ? A DT 109 B DA 125 1_555 ? ? ? ? ? ? WATSON-CRICK    ?     ? ? 
hydrog17 hydrog ?    ? A DT 9  O4 ? ? ? 1_555 B DA 7 N6    ? ? A DT 109 B DA 125 1_555 ? ? ? ? ? ? WATSON-CRICK    ?     ? ? 
hydrog18 hydrog ?    ? A DG 10 N1 ? ? ? 1_555 B DA 5 N1    ? ? A DG 110 B DA 123 1_555 ? ? ? ? ? ? TYPE_8_PAIR     ?     ? ? 
hydrog19 hydrog ?    ? A DG 10 O6 ? ? ? 1_555 B DA 5 N6    ? ? A DG 110 B DA 123 1_555 ? ? ? ? ? ? TYPE_8_PAIR     ?     ? ? 
hydrog20 hydrog ?    ? A DG 10 N1 ? ? ? 1_555 B DC 6 N3    ? ? A DG 110 B DC 124 1_555 ? ? ? ? ? ? WATSON-CRICK    ?     ? ? 
hydrog21 hydrog ?    ? A DG 10 N2 ? ? ? 1_555 B DC 6 O2    ? ? A DG 110 B DC 124 1_555 ? ? ? ? ? ? WATSON-CRICK    ?     ? ? 
hydrog22 hydrog ?    ? A DG 10 O6 ? ? ? 1_555 B DC 6 N4    ? ? A DG 110 B DC 124 1_555 ? ? ? ? ? ? WATSON-CRICK    ?     ? ? 
hydrog23 hydrog ?    ? A DT 11 N3 ? ? ? 1_555 B DA 5 N1    ? ? A DT 111 B DA 123 1_555 ? ? ? ? ? ? WATSON-CRICK    ?     ? ? 
hydrog24 hydrog ?    ? A DT 11 O4 ? ? ? 1_555 B DA 5 N6    ? ? A DT 111 B DA 123 1_555 ? ? ? ? ? ? WATSON-CRICK    ?     ? ? 
hydrog25 hydrog ?    ? A DA 12 N1 ? ? ? 1_555 B DT 4 N3    ? ? A DA 112 B DT 122 1_555 ? ? ? ? ? ? WATSON-CRICK    ?     ? ? 
hydrog26 hydrog ?    ? A DA 12 N6 ? ? ? 1_555 B DT 4 O4    ? ? A DA 112 B DT 122 1_555 ? ? ? ? ? ? WATSON-CRICK    ?     ? ? 
hydrog27 hydrog ?    ? A DC 13 N3 ? ? ? 1_555 B DC 2 N4    ? ? A DC 113 B DC 120 1_555 ? ? ? ? ? ? 'DC-DC MISPAIR' ?     ? ? 
hydrog28 hydrog ?    ? A DC 13 N3 ? ? ? 1_555 B DG 3 N1    ? ? A DC 113 B DG 121 1_555 ? ? ? ? ? ? WATSON-CRICK    ?     ? ? 
hydrog29 hydrog ?    ? A DC 13 N4 ? ? ? 1_555 B DG 3 O6    ? ? A DC 113 B DG 121 1_555 ? ? ? ? ? ? WATSON-CRICK    ?     ? ? 
hydrog30 hydrog ?    ? A DC 13 O2 ? ? ? 1_555 B DG 3 N2    ? ? A DC 113 B DG 121 1_555 ? ? ? ? ? ? WATSON-CRICK    ?     ? ? 
hydrog31 hydrog ?    ? A DG 14 N1 ? ? ? 1_555 B DC 2 N3    ? ? A DG 114 B DC 120 1_555 ? ? ? ? ? ? WATSON-CRICK    ?     ? ? 
hydrog32 hydrog ?    ? A DG 14 N2 ? ? ? 1_555 B DC 2 O2    ? ? A DG 114 B DC 120 1_555 ? ? ? ? ? ? WATSON-CRICK    ?     ? ? 
hydrog33 hydrog ?    ? A DG 14 O6 ? ? ? 1_555 B DC 2 N4    ? ? A DG 114 B DC 120 1_555 ? ? ? ? ? ? WATSON-CRICK    ?     ? ? 
hydrog34 hydrog ?    ? A DG 15 N1 ? ? ? 1_555 B DC 1 N3    ? ? A DG 115 B DC 119 1_555 ? ? ? ? ? ? WATSON-CRICK    ?     ? ? 
hydrog35 hydrog ?    ? A DG 15 N2 ? ? ? 1_555 B DC 1 O2    ? ? A DG 115 B DC 119 1_555 ? ? ? ? ? ? WATSON-CRICK    ?     ? ? 
hydrog36 hydrog ?    ? A DG 15 O6 ? ? ? 1_555 B DC 1 N4    ? ? A DG 115 B DC 119 1_555 ? ? ? ? ? ? WATSON-CRICK    ?     ? ? 
hydrog37 hydrog ?    ? A DA 16 N1 ? ? ? 1_555 D DT 8 N3    ? ? A DA 116 D DT 108 1_555 ? ? ? ? ? ? WATSON-CRICK    ?     ? ? 
hydrog38 hydrog ?    ? A DA 16 N6 ? ? ? 1_555 D DT 8 O4    ? ? A DA 116 D DT 108 1_555 ? ? ? ? ? ? WATSON-CRICK    ?     ? ? 
hydrog39 hydrog ?    ? A DC 17 N3 ? ? ? 1_555 D DG 7 N1    ? ? A DC 117 D DG 107 1_555 ? ? ? ? ? ? WATSON-CRICK    ?     ? ? 
hydrog40 hydrog ?    ? A DC 17 N4 ? ? ? 1_555 D DG 7 O6    ? ? A DC 117 D DG 107 1_555 ? ? ? ? ? ? WATSON-CRICK    ?     ? ? 
hydrog41 hydrog ?    ? A DC 17 O2 ? ? ? 1_555 D DG 7 N2    ? ? A DC 117 D DG 107 1_555 ? ? ? ? ? ? WATSON-CRICK    ?     ? ? 
hydrog42 hydrog ?    ? A DA 18 N1 ? ? ? 1_555 D DT 6 N3    ? ? A DA 118 D DT 106 1_555 ? ? ? ? ? ? WATSON-CRICK    ?     ? ? 
hydrog43 hydrog ?    ? A DA 18 N6 ? ? ? 1_555 D DT 6 O4    ? ? A DA 118 D DT 106 1_555 ? ? ? ? ? ? WATSON-CRICK    ?     ? ? 
hydrog44 hydrog ?    ? A DT 19 N3 ? ? ? 1_555 D DA 5 N1    ? ? A DT 119 D DA 105 1_555 ? ? ? ? ? ? WATSON-CRICK    ?     ? ? 
hydrog45 hydrog ?    ? A DT 19 O4 ? ? ? 1_555 D DA 5 N6    ? ? A DT 119 D DA 105 1_555 ? ? ? ? ? ? WATSON-CRICK    ?     ? ? 
hydrog46 hydrog ?    ? A DC 20 N3 ? ? ? 1_555 D DG 4 N1    ? ? A DC 120 D DG 104 1_555 ? ? ? ? ? ? WATSON-CRICK    ?     ? ? 
hydrog47 hydrog ?    ? A DC 20 N4 ? ? ? 1_555 D DG 4 O6    ? ? A DC 120 D DG 104 1_555 ? ? ? ? ? ? WATSON-CRICK    ?     ? ? 
hydrog48 hydrog ?    ? A DC 20 O2 ? ? ? 1_555 D DG 4 N2    ? ? A DC 120 D DG 104 1_555 ? ? ? ? ? ? WATSON-CRICK    ?     ? ? 
hydrog49 hydrog ?    ? A DA 21 N1 ? ? ? 1_555 D DT 3 N3    ? ? A DA 121 D DT 103 1_555 ? ? ? ? ? ? WATSON-CRICK    ?     ? ? 
hydrog50 hydrog ?    ? A DA 21 N6 ? ? ? 1_555 D DT 3 O4    ? ? A DA 121 D DT 103 1_555 ? ? ? ? ? ? WATSON-CRICK    ?     ? ? 
# 
loop_
_struct_conn_type.id 
_struct_conn_type.criteria 
_struct_conn_type.reference 
covale ? ? 
hydrog ? ? 
# 
_pdbx_validate_rmsd_bond.id                        1 
_pdbx_validate_rmsd_bond.PDB_model_num             1 
_pdbx_validate_rmsd_bond.auth_atom_id_1            C5 
_pdbx_validate_rmsd_bond.auth_asym_id_1            D 
_pdbx_validate_rmsd_bond.auth_comp_id_1            DT 
_pdbx_validate_rmsd_bond.auth_seq_id_1             106 
_pdbx_validate_rmsd_bond.PDB_ins_code_1            ? 
_pdbx_validate_rmsd_bond.label_alt_id_1            ? 
_pdbx_validate_rmsd_bond.auth_atom_id_2            C7 
_pdbx_validate_rmsd_bond.auth_asym_id_2            D 
_pdbx_validate_rmsd_bond.auth_comp_id_2            DT 
_pdbx_validate_rmsd_bond.auth_seq_id_2             106 
_pdbx_validate_rmsd_bond.PDB_ins_code_2            ? 
_pdbx_validate_rmsd_bond.label_alt_id_2            ? 
_pdbx_validate_rmsd_bond.bond_value                1.532 
_pdbx_validate_rmsd_bond.bond_target_value         1.496 
_pdbx_validate_rmsd_bond.bond_deviation            0.036 
_pdbx_validate_rmsd_bond.bond_standard_deviation   0.006 
_pdbx_validate_rmsd_bond.linker_flag               N 
# 
loop_
_pdbx_validate_rmsd_angle.id 
_pdbx_validate_rmsd_angle.PDB_model_num 
_pdbx_validate_rmsd_angle.auth_atom_id_1 
_pdbx_validate_rmsd_angle.auth_asym_id_1 
_pdbx_validate_rmsd_angle.auth_comp_id_1 
_pdbx_validate_rmsd_angle.auth_seq_id_1 
_pdbx_validate_rmsd_angle.PDB_ins_code_1 
_pdbx_validate_rmsd_angle.label_alt_id_1 
_pdbx_validate_rmsd_angle.auth_atom_id_2 
_pdbx_validate_rmsd_angle.auth_asym_id_2 
_pdbx_validate_rmsd_angle.auth_comp_id_2 
_pdbx_validate_rmsd_angle.auth_seq_id_2 
_pdbx_validate_rmsd_angle.PDB_ins_code_2 
_pdbx_validate_rmsd_angle.label_alt_id_2 
_pdbx_validate_rmsd_angle.auth_atom_id_3 
_pdbx_validate_rmsd_angle.auth_asym_id_3 
_pdbx_validate_rmsd_angle.auth_comp_id_3 
_pdbx_validate_rmsd_angle.auth_seq_id_3 
_pdbx_validate_rmsd_angle.PDB_ins_code_3 
_pdbx_validate_rmsd_angle.label_alt_id_3 
_pdbx_validate_rmsd_angle.angle_value 
_pdbx_validate_rmsd_angle.angle_target_value 
_pdbx_validate_rmsd_angle.angle_deviation 
_pdbx_validate_rmsd_angle.angle_standard_deviation 
_pdbx_validate_rmsd_angle.linker_flag 
1  1 "O4'" A DA 102 ? ? "C1'" A DA 102 ? ? N9    A DA 102 ? ? 112.60 108.30 4.30  0.30 N 
2  1 "O4'" A DG 103 ? ? "C1'" A DG 103 ? ? N9    A DG 103 ? ? 112.60 108.30 4.30  0.30 N 
3  1 "C3'" A DA 105 ? ? "C2'" A DA 105 ? ? "C1'" A DA 105 ? ? 97.19  102.40 -5.21 0.80 N 
4  1 "O4'" A DA 105 ? ? "C1'" A DA 105 ? ? N9    A DA 105 ? ? 110.89 108.30 2.59  0.30 N 
5  1 "C1'" A DC 107 ? ? "O4'" A DC 107 ? ? "C4'" A DC 107 ? ? 103.88 110.10 -6.22 1.00 N 
6  1 "C3'" A DC 107 ? ? "C2'" A DC 107 ? ? "C1'" A DC 107 ? ? 97.34  102.40 -5.06 0.80 N 
7  1 "O4'" A DC 107 ? ? "C1'" A DC 107 ? ? N1    A DC 107 ? ? 112.74 108.30 4.44  0.30 N 
8  1 "O4'" A DT 111 ? ? "C1'" A DT 111 ? ? N1    A DT 111 ? ? 110.17 108.30 1.87  0.30 N 
9  1 "O4'" A DA 116 ? ? "C1'" A DA 116 ? ? N9    A DA 116 ? ? 111.99 108.30 3.69  0.30 N 
10 1 "O4'" A DC 117 ? ? "C1'" A DC 117 ? ? N1    A DC 117 ? ? 111.08 108.30 2.78  0.30 N 
11 1 "O4'" A DA 118 ? ? "C4'" A DA 118 ? ? "C3'" A DA 118 ? ? 101.45 104.50 -3.05 0.40 N 
12 1 "O4'" A DT 119 ? ? "C1'" A DT 119 ? ? N1    A DT 119 ? ? 110.20 108.30 1.90  0.30 N 
13 1 "C3'" A DA 121 ? ? "C2'" A DA 121 ? ? "C1'" A DA 121 ? ? 95.56  102.40 -6.84 0.80 N 
14 1 "O4'" A DA 121 ? ? "C1'" A DA 121 ? ? N9    A DA 121 ? ? 110.21 108.30 1.91  0.30 N 
15 1 "C3'" B DA 123 ? ? "C2'" B DA 123 ? ? "C1'" B DA 123 ? ? 95.50  102.40 -6.90 0.80 N 
16 1 "O4'" B DA 123 ? ? "C1'" B DA 123 ? ? N9    B DA 123 ? ? 111.74 108.30 3.44  0.30 N 
17 1 "O4'" C DG 210 ? ? "C1'" C DG 210 ? ? N9    C DG 210 ? ? 111.49 108.30 3.19  0.30 N 
18 1 "O4'" C DC 211 ? ? "C1'" C DC 211 ? ? N1    C DC 211 ? ? 111.27 108.30 2.97  0.30 N 
19 1 "O4'" C DG 213 ? ? "C1'" C DG 213 ? ? N9    C DG 213 ? ? 111.54 108.30 3.24  0.30 N 
20 1 "O4'" D DC 102 ? ? "C1'" D DC 102 ? ? N1    D DC 102 ? ? 110.26 108.30 1.96  0.30 N 
21 1 "O4'" D DT 103 ? ? "C1'" D DT 103 ? ? N1    D DT 103 ? ? 111.78 108.30 3.48  0.30 N 
22 1 "C3'" D DG 104 ? ? "C2'" D DG 104 ? ? "C1'" D DG 104 ? ? 96.44  102.40 -5.96 0.80 N 
23 1 "C3'" D DA 105 ? ? "C2'" D DA 105 ? ? "C1'" D DA 105 ? ? 97.27  102.40 -5.13 0.80 N 
24 1 "C1'" D DT 106 ? ? "O4'" D DT 106 ? ? "C4'" D DT 106 ? ? 103.69 110.10 -6.41 1.00 N 
25 1 "C3'" D DT 106 ? ? "C2'" D DT 106 ? ? "C1'" D DT 106 ? ? 97.28  102.40 -5.12 0.80 N 
26 1 "O4'" D DT 106 ? ? "C1'" D DT 106 ? ? N1    D DT 106 ? ? 111.08 108.30 2.78  0.30 N 
27 1 "O4'" D DT 108 ? ? "C1'" D DT 108 ? ? N1    D DT 108 ? ? 110.21 108.30 1.91  0.30 N 
# 
_pdbx_entry_details.entry_id                 3GBI 
_pdbx_entry_details.compound_details         
;THE STRUCTURE UNIT IS GENERATED FROM 7 DNA STRANDS WHICH FORM 
A NETWORK UNIT WITH INTERNAL 3-FOLD SYMMETRY. EXTENDING OF THE 
STRUCTURE UNIT IN 3-D SPACE RESULTS THE CRYSTAL AT R3 SPACE 
GROUP (REPRESENTED AS H3). THE DNA SEQUENCES OF THE 7 STRANDS 
ARE:
(#1) 3 STRANDS
5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*AP*CP*GP*GP*AP*CP*AP*TP
*CP*A)-3'

(#2) 1 STRAND
5'-D(*TP*AP*CP*AP*CP*CP*GP*TP*AP*CP*AP*CP*CP*GP*TP*AP*CP*AP*CP*
CP*G)-3'

(#3) 3 STRANDS
5'-D(*TP*CP*TP*GP*AP*TP*GP*TP*GP*GP*CP*TP*GP*C)-3'

THE ASYMMETRIC UNIT IS COMPRISED OF ONE FULL #1 STRAND (CHAIN A), 
7-RESIDUE REPEATING UNIT OF #2 STRAND (CHAIN B) AND TWO FRAGMENTS 
OF #3 STRAND (CHAINS C AND D).

THE #2 STRAND SELF-ASSOICATES TO FORM A CIRCULAR DNA MOLECULE 
WITH INTERNAL 3-FOLD SYMMETRY. IT HAS 3 SYMMETRIC AND SEQUENTIAL
REPEATING UNITS. CHAIN B IN THE ASYMMETRIC UNIT REPRESENTS ONE 
OF THESE REPEATING UNITS.

CHAINS D (FIRST 8 RESIDUES OF STRAND #3) AND C (NEXT 6 RESIDUES 
OF STRAND #3) TOGETHER FORM THE THIRD DNA STRAND (#3) OF THE 
EXPERIMENT. THIS DNA STRAND SPANS TWO ASYMMETRIC UNITS - HENCE IT 
WAS DIVIDED INTO THE CURRENT CHAINS C AND D FOR CONVENIENT
REPRESENTATION. CHAIN C (1_555) IS COVALENTLY LINKED TO
CHAIN D OF ANOTHER ASYMMETRIC UNIT (3_555); AND CHAIN D (1_555)
IS COVALENTLY LINKED TO CHAIN C OF ANOTHER ASYMMETRIC UNIT
(2_555).

THE SELECTION OF RESIDUES FROM THE DNA #2 AND #3
ARE DICTATED BY THEIR PROXIMITY (BASE PAIRING) TO CHAIN A.
;
_pdbx_entry_details.source_details           ? 
_pdbx_entry_details.nonpolymer_details       ? 
_pdbx_entry_details.sequence_details         ? 
_pdbx_entry_details.has_ligand_of_interest   ? 
# 
loop_
_chem_comp_atom.comp_id 
_chem_comp_atom.atom_id 
_chem_comp_atom.type_symbol 
_chem_comp_atom.pdbx_aromatic_flag 
_chem_comp_atom.pdbx_stereo_config 
_chem_comp_atom.pdbx_ordinal 
DA OP3    O N N 1   
DA P      P N N 2   
DA OP1    O N N 3   
DA OP2    O N N 4   
DA "O5'"  O N N 5   
DA "C5'"  C N N 6   
DA "C4'"  C N R 7   
DA "O4'"  O N N 8   
DA "C3'"  C N S 9   
DA "O3'"  O N N 10  
DA "C2'"  C N N 11  
DA "C1'"  C N R 12  
DA N9     N Y N 13  
DA C8     C Y N 14  
DA N7     N Y N 15  
DA C5     C Y N 16  
DA C6     C Y N 17  
DA N6     N N N 18  
DA N1     N Y N 19  
DA C2     C Y N 20  
DA N3     N Y N 21  
DA C4     C Y N 22  
DA HOP3   H N N 23  
DA HOP2   H N N 24  
DA "H5'"  H N N 25  
DA "H5''" H N N 26  
DA "H4'"  H N N 27  
DA "H3'"  H N N 28  
DA "HO3'" H N N 29  
DA "H2'"  H N N 30  
DA "H2''" H N N 31  
DA "H1'"  H N N 32  
DA H8     H N N 33  
DA H61    H N N 34  
DA H62    H N N 35  
DA H2     H N N 36  
DC OP3    O N N 37  
DC P      P N N 38  
DC OP1    O N N 39  
DC OP2    O N N 40  
DC "O5'"  O N N 41  
DC "C5'"  C N N 42  
DC "C4'"  C N R 43  
DC "O4'"  O N N 44  
DC "C3'"  C N S 45  
DC "O3'"  O N N 46  
DC "C2'"  C N N 47  
DC "C1'"  C N R 48  
DC N1     N N N 49  
DC C2     C N N 50  
DC O2     O N N 51  
DC N3     N N N 52  
DC C4     C N N 53  
DC N4     N N N 54  
DC C5     C N N 55  
DC C6     C N N 56  
DC HOP3   H N N 57  
DC HOP2   H N N 58  
DC "H5'"  H N N 59  
DC "H5''" H N N 60  
DC "H4'"  H N N 61  
DC "H3'"  H N N 62  
DC "HO3'" H N N 63  
DC "H2'"  H N N 64  
DC "H2''" H N N 65  
DC "H1'"  H N N 66  
DC H41    H N N 67  
DC H42    H N N 68  
DC H5     H N N 69  
DC H6     H N N 70  
DG OP3    O N N 71  
DG P      P N N 72  
DG OP1    O N N 73  
DG OP2    O N N 74  
DG "O5'"  O N N 75  
DG "C5'"  C N N 76  
DG "C4'"  C N R 77  
DG "O4'"  O N N 78  
DG "C3'"  C N S 79  
DG "O3'"  O N N 80  
DG "C2'"  C N N 81  
DG "C1'"  C N R 82  
DG N9     N Y N 83  
DG C8     C Y N 84  
DG N7     N Y N 85  
DG C5     C Y N 86  
DG C6     C N N 87  
DG O6     O N N 88  
DG N1     N N N 89  
DG C2     C N N 90  
DG N2     N N N 91  
DG N3     N N N 92  
DG C4     C Y N 93  
DG HOP3   H N N 94  
DG HOP2   H N N 95  
DG "H5'"  H N N 96  
DG "H5''" H N N 97  
DG "H4'"  H N N 98  
DG "H3'"  H N N 99  
DG "HO3'" H N N 100 
DG "H2'"  H N N 101 
DG "H2''" H N N 102 
DG "H1'"  H N N 103 
DG H8     H N N 104 
DG H1     H N N 105 
DG H21    H N N 106 
DG H22    H N N 107 
DT OP3    O N N 108 
DT P      P N N 109 
DT OP1    O N N 110 
DT OP2    O N N 111 
DT "O5'"  O N N 112 
DT "C5'"  C N N 113 
DT "C4'"  C N R 114 
DT "O4'"  O N N 115 
DT "C3'"  C N S 116 
DT "O3'"  O N N 117 
DT "C2'"  C N N 118 
DT "C1'"  C N R 119 
DT N1     N N N 120 
DT C2     C N N 121 
DT O2     O N N 122 
DT N3     N N N 123 
DT C4     C N N 124 
DT O4     O N N 125 
DT C5     C N N 126 
DT C7     C N N 127 
DT C6     C N N 128 
DT HOP3   H N N 129 
DT HOP2   H N N 130 
DT "H5'"  H N N 131 
DT "H5''" H N N 132 
DT "H4'"  H N N 133 
DT "H3'"  H N N 134 
DT "HO3'" H N N 135 
DT "H2'"  H N N 136 
DT "H2''" H N N 137 
DT "H1'"  H N N 138 
DT H3     H N N 139 
DT H71    H N N 140 
DT H72    H N N 141 
DT H73    H N N 142 
DT H6     H N N 143 
# 
loop_
_chem_comp_bond.comp_id 
_chem_comp_bond.atom_id_1 
_chem_comp_bond.atom_id_2 
_chem_comp_bond.value_order 
_chem_comp_bond.pdbx_aromatic_flag 
_chem_comp_bond.pdbx_stereo_config 
_chem_comp_bond.pdbx_ordinal 
DA OP3   P      sing N N 1   
DA OP3   HOP3   sing N N 2   
DA P     OP1    doub N N 3   
DA P     OP2    sing N N 4   
DA P     "O5'"  sing N N 5   
DA OP2   HOP2   sing N N 6   
DA "O5'" "C5'"  sing N N 7   
DA "C5'" "C4'"  sing N N 8   
DA "C5'" "H5'"  sing N N 9   
DA "C5'" "H5''" sing N N 10  
DA "C4'" "O4'"  sing N N 11  
DA "C4'" "C3'"  sing N N 12  
DA "C4'" "H4'"  sing N N 13  
DA "O4'" "C1'"  sing N N 14  
DA "C3'" "O3'"  sing N N 15  
DA "C3'" "C2'"  sing N N 16  
DA "C3'" "H3'"  sing N N 17  
DA "O3'" "HO3'" sing N N 18  
DA "C2'" "C1'"  sing N N 19  
DA "C2'" "H2'"  sing N N 20  
DA "C2'" "H2''" sing N N 21  
DA "C1'" N9     sing N N 22  
DA "C1'" "H1'"  sing N N 23  
DA N9    C8     sing Y N 24  
DA N9    C4     sing Y N 25  
DA C8    N7     doub Y N 26  
DA C8    H8     sing N N 27  
DA N7    C5     sing Y N 28  
DA C5    C6     sing Y N 29  
DA C5    C4     doub Y N 30  
DA C6    N6     sing N N 31  
DA C6    N1     doub Y N 32  
DA N6    H61    sing N N 33  
DA N6    H62    sing N N 34  
DA N1    C2     sing Y N 35  
DA C2    N3     doub Y N 36  
DA C2    H2     sing N N 37  
DA N3    C4     sing Y N 38  
DC OP3   P      sing N N 39  
DC OP3   HOP3   sing N N 40  
DC P     OP1    doub N N 41  
DC P     OP2    sing N N 42  
DC P     "O5'"  sing N N 43  
DC OP2   HOP2   sing N N 44  
DC "O5'" "C5'"  sing N N 45  
DC "C5'" "C4'"  sing N N 46  
DC "C5'" "H5'"  sing N N 47  
DC "C5'" "H5''" sing N N 48  
DC "C4'" "O4'"  sing N N 49  
DC "C4'" "C3'"  sing N N 50  
DC "C4'" "H4'"  sing N N 51  
DC "O4'" "C1'"  sing N N 52  
DC "C3'" "O3'"  sing N N 53  
DC "C3'" "C2'"  sing N N 54  
DC "C3'" "H3'"  sing N N 55  
DC "O3'" "HO3'" sing N N 56  
DC "C2'" "C1'"  sing N N 57  
DC "C2'" "H2'"  sing N N 58  
DC "C2'" "H2''" sing N N 59  
DC "C1'" N1     sing N N 60  
DC "C1'" "H1'"  sing N N 61  
DC N1    C2     sing N N 62  
DC N1    C6     sing N N 63  
DC C2    O2     doub N N 64  
DC C2    N3     sing N N 65  
DC N3    C4     doub N N 66  
DC C4    N4     sing N N 67  
DC C4    C5     sing N N 68  
DC N4    H41    sing N N 69  
DC N4    H42    sing N N 70  
DC C5    C6     doub N N 71  
DC C5    H5     sing N N 72  
DC C6    H6     sing N N 73  
DG OP3   P      sing N N 74  
DG OP3   HOP3   sing N N 75  
DG P     OP1    doub N N 76  
DG P     OP2    sing N N 77  
DG P     "O5'"  sing N N 78  
DG OP2   HOP2   sing N N 79  
DG "O5'" "C5'"  sing N N 80  
DG "C5'" "C4'"  sing N N 81  
DG "C5'" "H5'"  sing N N 82  
DG "C5'" "H5''" sing N N 83  
DG "C4'" "O4'"  sing N N 84  
DG "C4'" "C3'"  sing N N 85  
DG "C4'" "H4'"  sing N N 86  
DG "O4'" "C1'"  sing N N 87  
DG "C3'" "O3'"  sing N N 88  
DG "C3'" "C2'"  sing N N 89  
DG "C3'" "H3'"  sing N N 90  
DG "O3'" "HO3'" sing N N 91  
DG "C2'" "C1'"  sing N N 92  
DG "C2'" "H2'"  sing N N 93  
DG "C2'" "H2''" sing N N 94  
DG "C1'" N9     sing N N 95  
DG "C1'" "H1'"  sing N N 96  
DG N9    C8     sing Y N 97  
DG N9    C4     sing Y N 98  
DG C8    N7     doub Y N 99  
DG C8    H8     sing N N 100 
DG N7    C5     sing Y N 101 
DG C5    C6     sing N N 102 
DG C5    C4     doub Y N 103 
DG C6    O6     doub N N 104 
DG C6    N1     sing N N 105 
DG N1    C2     sing N N 106 
DG N1    H1     sing N N 107 
DG C2    N2     sing N N 108 
DG C2    N3     doub N N 109 
DG N2    H21    sing N N 110 
DG N2    H22    sing N N 111 
DG N3    C4     sing N N 112 
DT OP3   P      sing N N 113 
DT OP3   HOP3   sing N N 114 
DT P     OP1    doub N N 115 
DT P     OP2    sing N N 116 
DT P     "O5'"  sing N N 117 
DT OP2   HOP2   sing N N 118 
DT "O5'" "C5'"  sing N N 119 
DT "C5'" "C4'"  sing N N 120 
DT "C5'" "H5'"  sing N N 121 
DT "C5'" "H5''" sing N N 122 
DT "C4'" "O4'"  sing N N 123 
DT "C4'" "C3'"  sing N N 124 
DT "C4'" "H4'"  sing N N 125 
DT "O4'" "C1'"  sing N N 126 
DT "C3'" "O3'"  sing N N 127 
DT "C3'" "C2'"  sing N N 128 
DT "C3'" "H3'"  sing N N 129 
DT "O3'" "HO3'" sing N N 130 
DT "C2'" "C1'"  sing N N 131 
DT "C2'" "H2'"  sing N N 132 
DT "C2'" "H2''" sing N N 133 
DT "C1'" N1     sing N N 134 
DT "C1'" "H1'"  sing N N 135 
DT N1    C2     sing N N 136 
DT N1    C6     sing N N 137 
DT C2    O2     doub N N 138 
DT C2    N3     sing N N 139 
DT N3    C4     sing N N 140 
DT N3    H3     sing N N 141 
DT C4    O4     doub N N 142 
DT C4    C5     sing N N 143 
DT C5    C7     sing N N 144 
DT C5    C6     doub N N 145 
DT C7    H71    sing N N 146 
DT C7    H72    sing N N 147 
DT C7    H73    sing N N 148 
DT C6    H6     sing N N 149 
# 
loop_
_ndb_struct_conf_na.entry_id 
_ndb_struct_conf_na.feature 
3GBI 'double helix'         
3GBI 'b-form double helix'  
3GBI 'mismatched base pair' 
# 
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 DG 3  1_555 C DC 6 1_555 -0.339 -0.255 1.131  10.421  7.577   -3.950  1  A_DG103:DC214_C A 103 ? C 214 ? 19 1 
1 A DC 4  1_555 C DG 5 1_555 0.198  -0.137 0.693  -8.699  -7.249  -8.925  2  A_DC104:DG213_C A 104 ? C 213 ? 19 1 
1 A DA 5  1_555 C DT 4 1_555 -0.061 -0.184 0.385  -14.211 -18.029 -9.386  3  A_DA105:DT212_C A 105 ? C 212 ? 20 1 
1 A DG 6  1_555 C DC 3 1_555 2.220  0.281  -0.081 0.211   -1.754  3.601   4  A_DG106:DC211_C A 106 ? C 211 ? ?  ? 
1 A DC 7  1_555 C DG 2 1_555 0.208  -0.306 -1.012 12.676  13.331  -12.689 5  A_DC107:DG210_C A 107 ? C 210 ? 19 1 
1 A DC 8  1_555 C DG 1 1_555 0.291  -0.116 -0.324 -3.890  -8.958  -7.533  6  A_DC108:DG209_C A 108 ? C 209 ? 19 1 
1 A DT 9  1_555 B DA 7 1_555 0.099  -0.155 0.880  -16.146 18.527  -0.152  7  A_DT109:DA125_B A 109 ? B 125 ? 20 1 
1 A DG 10 1_555 B DC 6 1_555 -0.321 -0.259 0.575  -22.498 -9.596  -8.824  8  A_DG110:DC124_B A 110 ? B 124 ? 19 1 
1 A DT 11 1_555 B DA 5 1_555 -0.012 -0.092 -0.087 -8.424  10.601  -12.047 9  A_DT111:DA123_B A 111 ? B 123 ? 20 1 
1 A DA 12 1_555 B DT 4 1_555 -0.105 -0.020 -0.006 -27.279 -14.283 -10.041 10 A_DA112:DT122_B A 112 ? B 122 ? 20 1 
1 A DC 13 1_555 B DG 3 1_555 0.219  -0.474 1.961  -27.559 7.372   -4.888  11 A_DC113:DG121_B A 113 ? B 121 ? 19 1 
1 A DG 14 1_555 B DC 2 1_555 -0.284 -0.384 1.002  -24.398 -14.288 -11.026 12 A_DG114:DC120_B A 114 ? B 120 ? 19 1 
1 A DG 15 1_555 B DC 1 1_555 -0.249 -0.088 0.173  -17.964 -3.624  -8.962  13 A_DG115:DC119_B A 115 ? B 119 ? 19 1 
1 A DA 16 1_555 D DT 8 1_555 0.008  -0.216 0.832  3.294   3.092   -4.762  14 A_DA116:DT108_D A 116 ? D 108 ? 20 1 
1 A DC 17 1_555 D DG 7 1_555 0.332  -0.154 0.441  7.501   -2.508  -7.189  15 A_DC117:DG107_D A 117 ? D 107 ? 19 1 
1 A DA 18 1_555 D DT 6 1_555 -0.126 -0.103 -0.055 -18.801 -16.679 -5.067  16 A_DA118:DT106_D A 118 ? D 106 ? 20 1 
1 A DT 19 1_555 D DA 5 1_555 -0.105 -0.008 0.301  -32.859 -10.734 -3.989  17 A_DT119:DA105_D A 119 ? D 105 ? 20 1 
1 A DC 20 1_555 D DG 4 1_555 0.145  0.182  0.319  -23.669 -5.736  8.064   18 A_DC120:DG104_D A 120 ? D 104 ? 19 1 
1 A DA 21 1_555 D DT 3 1_555 0.058  -0.141 0.244  1.063   9.309   -2.855  19 A_DA121:DT103_D A 121 ? D 103 ? 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 DG 3  1_555 C DC 6 1_555 A DC 4  1_555 C DG 5 1_555 -0.382 -0.876 3.788 2.297   12.267  45.968 -2.198 0.682  3.438 15.377  
-2.880  47.543 1  AA_DG103DC104:DG213DC214_CC A 103 ? C 214 ? A 104 ? C 213 ? 
1 A DC 4  1_555 C DG 5 1_555 A DA 5  1_555 C DT 4 1_555 -0.759 -0.015 3.678 -2.626  9.423   32.721 -1.722 0.821  3.585 16.278  
4.536   34.114 2  AA_DC104DA105:DT212DG213_CC A 104 ? C 213 ? A 105 ? C 212 ? 
1 A DA 5  1_555 C DT 4 1_555 A DG 6  1_555 C DC 3 1_555 -0.535 -0.840 2.912 1.562   -2.171  42.240 -0.965 0.884  2.929 -3.008  
-2.165  42.321 3  AA_DA105DG106:DC211DT212_CC A 105 ? C 212 ? A 106 ? C 211 ? 
1 A DG 6  1_555 C DC 3 1_555 A DC 7  1_555 C DG 2 1_555 0.277  -1.613 3.053 3.114   -7.578  22.499 -1.378 0.363  3.413 -18.647 
-7.663  23.926 4  AA_DG106DC107:DG210DC211_CC A 106 ? C 211 ? A 107 ? C 210 ? 
1 A DC 7  1_555 C DG 2 1_555 A DC 8  1_555 C DG 1 1_555 0.982  -0.174 3.681 -0.310  12.201  42.136 -1.536 -1.349 3.496 16.558  
0.420   43.791 5  AA_DC107DC108:DG209DG210_CC A 107 ? C 210 ? A 108 ? C 209 ? 
1 A DC 8  1_555 C DG 1 1_555 A DT 9  1_555 B DA 7 1_555 -0.698 -2.092 4.099 -12.822 -17.856 18.922 2.001  -3.048 4.283 -40.418 
29.023  28.929 6  AA_DC108DT109:DA125DG209_BC A 108 ? C 209 ? A 109 ? B 125 ? 
1 A DT 9  1_555 B DA 7 1_555 A DG 10 1_555 B DC 6 1_555 0.827  -1.579 3.185 7.574   19.013  28.849 -5.070 -0.385 1.960 33.379  
-13.297 35.245 7  AA_DT109DG110:DC124DA125_BB A 109 ? B 125 ? A 110 ? B 124 ? 
1 A DG 10 1_555 B DC 6 1_555 A DT 11 1_555 B DA 5 1_555 -0.143 0.010  2.732 5.757   1.869   37.675 -0.181 0.824  2.680 2.871   
-8.844  38.140 8  AA_DG110DT111:DA123DC124_BB A 110 ? B 124 ? A 111 ? B 123 ? 
1 A DT 11 1_555 B DA 5 1_555 A DA 12 1_555 B DT 4 1_555 -1.304 -0.247 3.749 -4.283  9.463   37.038 -1.744 1.362  3.701 14.549  
6.584   38.418 9  AA_DT111DA112:DT122DA123_BB A 111 ? B 123 ? A 112 ? B 122 ? 
1 A DA 12 1_555 B DT 4 1_555 A DC 13 1_555 B DG 3 1_555 -0.826 -0.083 3.581 -16.294 -3.269  33.569 0.371  -1.204 3.587 -5.278  
26.304  37.351 10 AA_DA112DC113:DG121DT122_BB A 112 ? B 122 ? A 113 ? B 121 ? 
1 A DC 13 1_555 B DG 3 1_555 A DG 14 1_555 B DC 2 1_555 -1.058 2.307  3.564 -1.130  -32.803 39.936 4.641  1.155  1.420 -40.753 
1.403   51.264 11 AA_DC113DG114:DC120DG121_BB A 113 ? B 121 ? A 114 ? B 120 ? 
1 A DG 14 1_555 B DC 2 1_555 A DG 15 1_555 B DC 1 1_555 0.464  0.415  3.555 2.011   -10.497 37.731 1.972  -0.434 3.345 -15.847 
-3.036  39.163 12 AA_DG114DG115:DC119DC120_BB A 114 ? B 120 ? A 115 ? B 119 ? 
1 A DG 15 1_555 B DC 1 1_555 A DA 16 1_555 D DT 8 1_555 0.018  -0.279 2.591 -6.779  3.891   30.399 -1.093 -1.037 2.475 7.270   
12.667  31.365 13 AA_DG115DA116:DT108DC119_DB A 115 ? B 119 ? A 116 ? D 108 ? 
1 A DA 16 1_555 D DT 8 1_555 A DC 17 1_555 D DG 7 1_555 -0.702 -1.622 3.141 5.345   -5.230  31.350 -2.006 2.202  3.203 -9.510  
-9.718  32.208 14 AA_DA116DC117:DG107DT108_DD A 116 ? D 108 ? A 117 ? D 107 ? 
1 A DC 17 1_555 D DG 7 1_555 A DA 18 1_555 D DT 6 1_555 -0.450 -0.339 3.344 3.337   9.510   42.407 -1.382 0.932  3.157 12.929  
-4.537  43.535 15 AA_DC117DA118:DT106DG107_DD A 117 ? D 107 ? A 118 ? D 106 ? 
1 A DA 18 1_555 D DT 6 1_555 A DT 19 1_555 D DA 5 1_555 -0.670 0.117  3.561 -3.579  -12.060 31.624 2.317  0.519  3.350 -21.113 
6.267   33.975 16 AA_DA118DT119:DA105DT106_DD A 118 ? D 106 ? A 119 ? D 105 ? 
1 A DT 19 1_555 D DA 5 1_555 A DC 20 1_555 D DG 4 1_555 -0.244 -1.099 2.684 4.558   -6.116  29.518 -1.055 1.237  2.782 -11.758 
-8.763  30.466 17 AA_DT119DC120:DG104DA105_DD A 119 ? D 105 ? A 120 ? D 104 ? 
1 A DC 20 1_555 D DG 4 1_555 A DA 21 1_555 D DT 3 1_555 0.200  0.200  2.495 2.319   -0.618  38.725 0.359  -0.085 2.499 -0.931  
-3.493  38.797 18 AA_DC120DA121:DT103DG104_DD A 120 ? D 104 ? A 121 ? D 103 ? 
# 
_atom_sites.entry_id                    3GBI 
_atom_sites.fract_transf_matrix[1][1]   0.009332 
_atom_sites.fract_transf_matrix[1][2]   0.005388 
_atom_sites.fract_transf_matrix[1][3]   0.000000 
_atom_sites.fract_transf_matrix[2][1]   0.000000 
_atom_sites.fract_transf_matrix[2][2]   0.010775 
_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]   0.010736 
_atom_sites.fract_transf_vector[1]      0.00000 
_atom_sites.fract_transf_vector[2]      0.00000 
_atom_sites.fract_transf_vector[3]      0.00000 
# 
loop_
_atom_type.symbol 
C 
N 
O 
P 
# 
loop_