# -------------------------------------------------------------------------- # # Example CIF for an A type DNA structure with a single strand # in the asymmetric unit. This example is compliant with # the Macromolecular CIF Dictionary (cif_mm.dic) version 0.9.01. # # Prepared by: Anke Gelbin, John Westbrook, and Helen Berman # Nucleic Acid Database Project # Rutgers University # e-mail: ndbadmin@ndbserver.rutgers.edu # www: http://ndbserver.rutgers.edu # #--------------------------------------------------------------------------- data_ADH041 ############### ## ENTRY ## ############### _entry.id example_mcif chemdig rzepa ADH041 ############### ## ATOM_SITE ## ############### loop_ _atom_site.id _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_asym_id _atom_site.auth_seq_id _atom_site.cartn_x _atom_site.cartn_y _atom_site.cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.label_entity_id _atom_site.label_seq_id 1 O5* G A 1 7.231 -2.196 -5.399 1.00 22.25 1 1 2 C5* G A 1 6.950 -3.464 -4.723 1.00 15.86 1 1 3 C4* G A 1 8.299 -4.018 -4.302 1.00 15.20 1 1 4 O4* G A 1 9.257 -3.779 -5.318 1.00 10.85 1 1 5 C3* G A 1 8.912 -3.354 -3.074 1.00 15.62 1 1 6 O3* G A 1 8.397 -3.826 -1.833 1.00 20.67 1 1 7 C2* G A 1 10.385 -3.707 -3.244 1.00 12.71 1 1 8 C1* G A 1 10.538 -3.558 -4.728 1.00 7.78 1 1 9 N9 G A 1 11.032 -2.213 -5.038 1.00 5.96 1 1 10 C8 G A 1 10.432 -1.200 -5.709 1.00 5.64 1 1 11 N7 G A 1 11.206 -0.153 -5.904 1.00 6.81 1 1 12 C5 G A 1 12.419 -0.515 -5.331 1.00 8.61 1 1 13 C6 G A 1 13.658 0.170 -5.193 1.00 8.05 1 1 14 O6 G A 1 13.934 1.328 -5.562 1.00 11.41 1 1 15 N1 G A 1 14.628 -0.540 -4.543 1.00 7.19 1 1 16 C2 G A 1 14.419 -1.813 -4.100 1.00 5.46 1 1 17 N2 G A 1 15.466 -2.434 -3.532 1.00 10.14 1 1 18 N3 G A 1 13.296 -2.481 -4.196 1.00 5.15 1 1 19 C4 G A 1 12.330 -1.788 -4.809 1.00 8.28 1 1 20 P T A 2 7.699 -2.741 -0.810 1.00 19.59 1 2 21 O1P T A 2 7.159 -1.711 -1.757 1.00 18.85 1 2 22 O2P T A 2 6.588 -3.545 -0.207 1.00 20.41 1 2 23 O5* T A 2 8.933 -2.362 0.047 1.00 14.20 1 2 24 C5* T A 2 9.636 -3.349 0.820 1.00 18.12 1 2 25 C4* T A 2 11.049 -2.839 0.982 1.00 17.74 1 2 26 O4* T A 2 11.615 -2.545 -0.283 1.00 17.74 1 2 27 C3* T A 2 11.176 -1.528 1.745 1.00 19.12 1 2 28 O3* T A 2 11.070 -1.673 3.152 1.00 22.36 1 2 29 C2* T A 2 12.585 -1.081 1.307 1.00 17.85 1 2 30 C1* T A 2 12.606 -1.507 -0.128 1.00 12.64 1 2 31 N1 T A 2 12.308 -0.353 -1.012 1.00 9.55 1 2 32 C2 T A 2 13.411 0.413 -1.363 1.00 7.45 1 2 33 O2 T A 2 14.530 0.162 -0.925 1.00 8.22 1 2 34 N3 T A 2 13.206 1.451 -2.217 1.00 8.01 1 2 35 C4 T A 2 11.985 1.728 -2.744 1.00 7.67 1 2 36 O4 T A 2 11.930 2.715 -3.546 1.00 10.46 1 2 37 C5 T A 2 10.878 0.902 -2.409 1.00 3.98 1 2 38 C5M T A 2 9.516 1.217 -2.978 1.00 3.03 1 2 39 C6 T A 2 11.091 -0.102 -1.563 1.00 5.06 1 2 40 P C A 3 10.321 -0.536 3.970 1.00 28.15 1 3 41 O1P C A 3 9.682 0.255 2.867 1.00 27.97 1 3 42 O2P C A 3 9.389 -1.196 4.922 1.00 29.35 1 3 43 O5* C A 3 11.483 0.260 4.710 1.00 22.68 1 3 44 C5* C A 3 12.402 0.758 3.726 1.00 24.92 1 3 45 C4* C A 3 13.581 1.388 4.420 1.00 23.08 1 3 46 O4* C A 3 14.560 1.558 3.404 1.00 27.27 1 3 47 C3* C A 3 13.343 2.737 5.038 1.00 23.43 1 3 48 O3* C A 3 13.572 2.758 6.463 1.00 25.54 1 3 49 C2* C A 3 14.321 3.686 4.356 1.00 25.72 1 3 50 C1* C A 3 14.696 2.945 3.098 1.00 22.89 1 3 51 N1 C A 3 13.785 3.345 2.018 1.00 20.44 1 3 52 C2 C A 3 14.211 4.401 1.228 1.00 19.82 1 3 53 O2 C A 3 15.296 4.924 1.457 1.00 19.34 1 3 54 N3 C A 3 13.381 4.797 0.226 1.00 20.88 1 3 55 C4 C A 3 12.159 4.218 0.015 1.00 22.27 1 3 56 N4 C A 3 11.380 4.652 -0.987 1.00 21.02 1 3 57 C5 C A 3 11.738 3.145 0.847 1.00 22.07 1 3 58 C6 C A 3 12.581 2.749 1.819 1.00 20.93 1 3 59 P T A 4 13.249 4.145 7.228 1.00 26.13 1 4 60 O1P T A 4 11.785 4.341 6.832 1.00 25.37 1 4 61 O2P T A 4 13.504 3.907 8.673 1.00 32.53 1 4 62 O5* T A 4 14.194 5.248 6.662 1.00 17.95 1 4 63 C5* T A 4 15.607 5.380 6.834 1.00 15.14 1 4 64 C4* T A 4 15.973 6.673 6.116 1.00 15.44 1 4 65 O4* T A 4 15.700 6.524 4.745 1.00 16.75 1 4 66 C3* T A 4 15.173 7.899 6.524 1.00 14.00 1 4 67 O3* T A 4 15.645 8.491 7.720 1.00 18.73 1 4 68 C2* T A 4 15.360 8.814 5.326 1.00 15.19 1 4 69 C1* T A 4 15.428 7.848 4.189 1.00 15.15 1 4 70 N1 T A 4 14.160 7.776 3.450 1.00 13.97 1 4 71 C2 T A 4 13.990 8.644 2.390 1.00 13.15 1 4 72 O2 T A 4 14.858 9.470 2.156 1.00 13.53 1 4 73 N3 T A 4 12.832 8.538 1.666 1.00 11.60 1 4 74 C4 T A 4 11.870 7.622 1.959 1.00 11.54 1 4 75 O4 T A 4 10.840 7.610 1.211 1.00 13.43 1 4 76 C5 T A 4 12.061 6.725 3.049 1.00 12.09 1 4 77 C5M T A 4 11.053 5.677 3.416 1.00 7.58 1 4 78 C6 T A 4 13.211 6.827 3.743 1.00 14.34 1 4 79 P A A 5 14.790 9.516 8.579 1.00 27.61 1 5 80 O1P A A 5 13.338 9.227 8.330 1.00 14.47 1 5 81 O2P A A 5 15.309 9.627 9.977 1.00 22.02 1 5 82 O5* A A 5 15.181 10.942 7.875 1.00 19.11 1 5 83 C5* A A 5 13.921 11.619 7.555 1.00 12.04 1 5 84 C4* A A 5 14.364 12.649 6.531 1.00 11.89 1 5 85 O4* A A 5 14.560 12.019 5.296 1.00 12.02 1 5 86 C3* A A 5 13.325 13.734 6.322 1.00 11.99 1 5 87 O3* A A 5 13.606 14.841 7.166 1.00 18.44 1 5 88 C2* A A 5 13.474 14.066 4.853 1.00 12.81 1 5 89 C1* A A 5 13.879 12.725 4.267 1.00 8.63 1 5 90 N9 A A 5 12.670 12.040 3.802 1.00 6.64 1 5 91 C8 A A 5 12.040 10.955 4.317 1.00 4.88 1 5 92 N7 A A 5 10.964 10.606 3.647 1.00 7.15 1 5 93 C5 A A 5 10.912 11.517 2.589 1.00 5.96 1 5 94 C6 A A 5 10.002 11.653 1.511 1.00 6.23 1 5 95 N6 A A 5 8.980 10.832 1.294 1.00 5.89 1 5 96 N1 A A 5 10.274 12.674 0.657 1.00 3.00 1 5 97 C2 A A 5 11.359 13.474 0.844 1.00 7.72 1 5 98 N3 A A 5 12.262 13.402 1.824 1.00 4.19 1 5 99 C4 A A 5 11.968 12.394 2.660 1.00 5.64 1 5 100 P G A 6 12.487 15.964 7.442 1.00 12.38 1 6 101 O1P G A 6 11.321 15.168 7.816 1.00 19.23 1 6 102 O2P G A 6 13.121 16.811 8.453 1.00 19.19 1 6 103 O5* G A 6 12.381 16.573 5.970 1.00 17.14 1 6 104 C5* G A 6 12.708 17.952 5.680 1.00 15.41 1 6 105 C4* G A 6 12.142 18.250 4.314 1.00 13.87 1 6 106 O4* G A 6 11.998 17.028 3.598 1.00 13.41 1 6 107 C3* G A 6 10.746 18.846 4.258 1.00 14.92 1 6 108 O3* G A 6 10.683 20.233 4.560 1.00 13.67 1 6 109 C2* G A 6 10.355 18.586 2.793 1.00 10.87 1 6 110 C1* G A 6 10.981 17.250 2.577 1.00 10.44 1 6 111 N9 G A 6 10.040 16.152 2.781 1.00 8.54 1 6 112 C8 G A 6 10.155 15.245 3.797 1.00 9.12 1 6 113 N7 G A 6 9.240 14.296 3.731 1.00 13.90 1 6 114 C5 G A 6 8.495 14.619 2.601 1.00 8.41 1 6 115 C6 G A 6 7.363 13.994 2.030 1.00 9.70 1 6 116 O6 G A 6 6.780 12.981 2.451 1.00 10.74 1 6 117 N1 G A 6 6.903 14.632 0.896 1.00 9.85 1 6 118 C2 G A 6 7.482 15.752 0.396 1.00 3.88 1 6 119 N2 G A 6 6.899 16.258 -0.684 1.00 7.71 1 6 120 N3 G A 6 8.546 16.369 0.898 1.00 6.92 1 6 121 C4 G A 6 8.989 15.760 2.013 1.00 8.28 1 6 122 P A A 7 9.504 20.535 5.636 1.00 11.52 1 7 123 O1P A A 7 9.529 19.437 6.534 1.00 11.92 1 7 124 O2P A A 7 9.929 21.884 6.128 1.00 18.21 1 7 125 O5* A A 7 8.201 20.586 4.673 1.00 8.91 1 7 126 C5* A A 7 8.342 21.586 3.620 1.00 6.45 1 7 127 C4* A A 7 7.248 21.318 2.626 1.00 3.39 1 7 128 O4* A A 7 7.376 20.033 2.057 1.00 5.79 1 7 129 C3* A A 7 5.844 21.323 3.231 1.00 3.85 1 7 130 O3* A A 7 5.439 22.642 3.445 1.00 7.81 1 7 131 C2* A A 7 5.069 20.565 2.156 1.00 5.70 1 7 132 C1* A A 7 6.056 19.527 1.752 1.00 3.87 1 7 133 N9 A A 7 5.895 18.301 2.540 1.00 4.66 1 7 134 C8 A A 7 6.707 17.875 3.561 1.00 6.62 1 7 135 N7 A A 7 6.324 16.743 4.112 1.00 2.28 1 7 136 C5 A A 7 5.218 16.381 3.349 1.00 1.74 1 7 137 C6 A A 7 4.379 15.258 3.413 1.00 4.78 1 7 138 N6 A A 7 4.550 14.283 4.297 1.00 9.36 1 7 139 N1 A A 7 3.362 15.241 2.513 1.00 5.07 1 7 140 C2 A A 7 3.171 16.249 1.632 1.00 4.94 1 7 141 N3 A A 7 3.911 17.365 1.538 1.00 4.89 1 7 142 C4 A A 7 4.933 17.339 2.404 1.00 4.26 1 7 143 P C A 8 4.209 23.208 4.243 1.00 14.05 1 8 144 O1P C A 8 4.294 22.557 5.545 1.00 16.14 1 8 145 O2P C A 8 4.494 24.749 4.243 1.00 18.27 1 8 146 O5* C A 8 2.932 22.914 3.421 1.00 10.49 1 8 147 C5* C A 8 2.749 21.642 2.712 1.00 14.57 1 8 148 C4* C A 8 1.349 21.825 2.134 1.00 15.98 1 8 149 O4* C A 8 0.689 20.633 1.831 1.00 17.74 1 8 150 C3* C A 8 0.468 22.544 3.162 1.00 15.68 1 8 151 O3* C A 8 -0.208 23.621 2.486 1.00 23.46 1 8 152 C2* C A 8 -0.375 21.450 3.741 1.00 14.98 1 8 153 C1* C A 8 -0.021 20.191 3.007 1.00 13.74 1 8 154 N1 C A 8 0.834 19.292 3.819 1.00 14.40 1 8 155 C2 C A 8 0.464 17.960 3.871 1.00 13.07 1 8 156 O2 C A 8 -0.540 17.539 3.305 1.00 14.67 1 8 157 N3 C A 8 1.243 17.096 4.580 1.00 12.98 1 8 158 C4 C A 8 2.332 17.535 5.274 1.00 13.43 1 8 159 N4 C A 8 3.000 16.637 5.997 1.00 12.91 1 8 160 C5 C A 8 2.707 18.909 5.212 1.00 12.96 1 8 161 C6 C A 8 1.945 19.735 4.489 1.00 10.13 1 8 163 O1 HOH S 9 14.585 15.313 1.617 1.00 14.98 2 . 164 O2 HOH S 10 14.594 0.902 9.098 1.00 22.76 2 . 165 O3 HOH S 11 16.943 10.508 6.253 1.00 57.46 2 . ################ ## ATOM_SITES ## ################ _atom_sites.entry_id ADH041 _atom_sites.fract_transf_matrix[1][1] 0.023496 _atom_sites.fract_transf_matrix[1][2] 0.0 _atom_sites.fract_transf_matrix[1][3] 0.0 _atom_sites.fract_transf_matrix[2][1] 0.0 _atom_sites.fract_transf_matrix[2][2] 0.023496 _atom_sites.fract_transf_matrix[2][3] 0.0 _atom_sites.fract_transf_matrix[3][1] 0.0 _atom_sites.fract_transf_matrix[3][2] 0.0 _atom_sites.fract_transf_matrix[3][3] 0.040634 ########## ## CELL ## ########## _cell.entry_id ADH041 _cell.length_a 42.560 _cell.length_b 42.560 _cell.length_c 24.610 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 ############### ## CHEM_COMP ## ############### loop_ _chem_comp.id _chem_comp.name A ADENINE T THYMINE C CYTOSINE G GUANINE HOH WATER ############## ## CITATION ## ############## loop_ _citation.id chemdig rzepa _citation.title chemdig rzepa _citation.country _citation.journal_abbrev _citation.journal_volume _citation.page_first _citation.year _citation.page_last _citation.journal_id_ASTM _citation.journal_id_ISSN primary ; Crystal and Molecular Structure of d(GTCTAGAC) ; DK 'Acta Crystallogr.,Sect.B' 48 714 1992 719 ASBSDK 0108-7681 ##################### ## CITATION_AUTHOR ## ##################### loop_ _citation_author.citation_id _citation_author.name primary 'Cervi, A.' primary 'Langlois DEstaintot, B.' primary 'Hunter, W. N.' ############### ## COMPUTING ## ############### _computing.entry_id ADH041 _computing.structure_refinement 'NUCLSQ' ############ ## DIFFRN ## ############ _diffrn.id ds1 _diffrn.crystal_id 1 _diffrn.ambient_temp 295.00 ######################## ## DIFFRN_MEASUREMENT ## ######################## _diffrn_measurement.diffrn_id ds1 _diffrn_measurement.device DIFFRACTOMETER _diffrn_measurement.device_type 'RIGAKU AFC-5' ################### ## DIFFRN_SOURCE ## ################### _diffrn_source.diffrn_id ds1 _diffrn_source.type 'ROTATING ANODE' ###################### ## DIFFRN_RADIATION ## ###################### _diffrn_radiation.diffrn_id ds1 _diffrn_radiation.wavelength_id 1 ################################# ## DIFFRN_RADIATION_WAVELENGTH ## ################################# _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.54 _diffrn_radiation_wavelength.wt 1.0 ############ ## ENTITY ## ############ loop_ _entity.id _entity.type _entity.src_method 1 polymer 'man' 2 water . ##################### ## ENTITY_KEYWORDS ## ##################### loop_ _entity_keywords.entity_id _entity_keywords.text 1 'NUCLEIC ACID' ################# ## ENTITY_POLY ## ################# loop_ _entity_poly.entity_id _entity_poly.number_of_monomers _entity_poly.type 1 8 'polydeoxyribonucleotide' ##################### ## ENTITY_POLY_SEQ ## ##################### loop_ _entity_poly_seq.entity_id _entity_poly_seq.mon_id _entity_poly_seq.num 1 G 1 1 T 2 1 C 3 1 T 4 1 A 5 1 G 6 1 A 7 1 C 8 ######################## ## EXPTL_CRYSTAL_GROW ## ######################## _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'vapor diffusion' _exptl_crystal_grow.pH 6.8 _exptl_crystal_grow.temp 295.0 ############################# ## EXPTL_CRYSTAL_GROW_COMP ## ############################# loop_ _exptl_crystal_grow_comp.crystal_id _exptl_crystal_grow_comp.id _exptl_crystal_grow_comp.sol_id _exptl_crystal_grow_comp.name 1 1 1 'MPD' 1 2 1 'Na Cacodylate' 1 3 1 'MgCl2' 1 4 1 'Spermine HCL' 1 5 2 'MPD' ############ ## STRUCT ## ############ _struct.entry_id ADH041 _struct.title ; 5'-D(*GP*TP*CP*TP*AP*GP*AP*C)-3' ; ##################### ## STRUCT_KEYWORDS ## ##################### _struct_keywords.entry_id ADH041 _struct_keywords.text 'DEOXYRIBONUCLEIC ACID' ################# ## STRUCT_ASYM ## ################# loop_ _struct_asym.id _struct_asym.entity_id _struct_asym.details A 1 'NUCLEIC ACID' S 2 'H2O' ################# ## STRUCT_BIOL ## ################# _struct_biol.id 1 _struct_biol.details 'FULL DUPLEX A DNA' ##################### ## STRUCT_BIOL_GEN ## ##################### loop_ _struct_biol_gen.biol_id _struct_biol_gen.asym_id _struct_biol_gen.symmetry 1 A 1_555 1 A 7_555 1 S 1_555 1 S 7_555 ########################## ## STRUCT_BIOL_KEYWORDS ## ########################## loop_ _struct_biol_keywords.biol_id _struct_biol_keywords.text 1 'DNA' 1 'A DNA' 1 'DNA DUPLEX' ################# ## STRUCT_CONF ## ################# loop_ _struct_conf.id _struct_conf.conf_type_id _struct_conf.beg_label_comp_id _struct_conf.beg_label_asym_id _struct_conf.beg_label_seq_id _struct_conf.end_label_comp_id _struct_conf.end_label_asym_id _struct_conf.end_label_seq_id CHAIN-A HELX_RH_A_N G A 1 C A 8 ###################### ## STRUCT_CONN_TYPE ## ###################### loop_ _struct_conn_type.id _struct_conn_type.criteria hydrog ; N to O distance > 2.5 Angstroms and < 3.5 Angstroms, N - O - C angle < 120 degrees ; ###################### ## STRUCT_CONF_TYPE ## ###################### loop_ _struct_conf_type.id _struct_conf_type.criteria HELX_RH_A_N 'AUTHOR JUDGEMENT' ################# ## STRUCT_CONN ## ################# loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_symmetry _struct_conn.details 1 hydrog G A 1 N2 1_555 C A 8 O2 7_555 WATSON-CRICK 2 hydrog G A 1 N1 1_555 C A 8 N3 7_555 WATSON-CRICK 3 hydrog G A 1 O6 1_555 C A 8 N4 7_555 WATSON-CRICK 4 hydrog T A 2 N3 1_555 A A 7 N1 7_555 WATSON-CRICK 5 hydrog T A 2 O4 1_555 A A 7 N6 7_555 WATSON-CRICK 6 hydrog C A 3 O2 1_555 G A 6 N2 7_555 WATSON-CRICK 7 hydrog C A 3 N3 1_555 G A 6 N1 7_555 WATSON-CRICK 8 hydrog C A 3 N4 1_555 G A 6 O6 7_555 WATSON-CRICK 9 hydrog T A 4 N3 1_555 A A 5 N1 7_555 WATSON-CRICK 10 hydrog T A 4 O4 1_555 A A 5 N6 7_555 WATSON-CRICK 11 hydrog A A 5 N1 1_555 T A 4 N3 7_555 WATSON-CRICK 12 hydrog A A 5 N6 1_555 T A 4 O4 7_555 WATSON-CRICK 13 hydrog G A 6 N2 1_555 C A 3 O2 7_555 WATSON-CRICK 14 hydrog G A 6 N1 1_555 C A 3 N3 7_555 WATSON-CRICK 15 hydrog G A 6 O6 1_555 C A 3 N4 7_555 WATSON-CRICK 16 hydrog A A 7 N1 1_555 T A 2 N3 7_555 WATSON-CRICK 17 hydrog A A 7 N6 1_555 T A 2 O4 7_555 WATSON-CRICK 18 hydrog C A 8 O2 1_555 G A 1 N2 7_555 WATSON-CRICK 19 hydrog C A 8 N3 1_555 G A 1 N1 7_555 WATSON-CRICK 20 hydrog C A 8 N4 1_555 G A 1 O6 7_555 WATSON-CRICK ############## ## SYMMETRY ## ############## _symmetry.entry_id ADH041 _symmetry.space_group_name_H-M 'P 43 21 2'