HEADER DEOXYRIBONUCLEIC ACID 04-FEB-01 1I1V TITLE A THEORETICAL MODEL OF TRIPLE-STRANDED DNA BOUND TO RECA TITLE 2 PROTEIN (N-S INTERCONVERSION MODEL) COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(P*GP*GP*G)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(P*CP*CP*C)-3'; COMPND 7 CHAIN: B, C; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES KEYWDS DEOXYRIBOSE-BASE STACKING EXPDTA THEORETICAL MODEL AUTHOR T.NISHINAKA,A.SHINOHARA,Y.ITO,S.YOKOYAMA,T.SHIBATA REVDAT 1 21-FEB-01 1I1V 0 JRNL AUTH T.NISHINAKA,A.SHINOHARA,Y.ITO,S.YOKOYAMA,T.SHIBATA JRNL TITL BASE PAIR SWITCHING BY INTERCONVERSION OF SUGAR JRNL TITL 2 PUCKERS IN DNA EXTENDED BY PROTEINS OF JRNL TITL 3 RECA-FAMILY: A MODEL FOR HOMOLOGY SEARCH IN JRNL TITL 4 HOMOLOGOUS GENETIC RECOMBINATION JRNL REF PROC.NAT.ACAD.SCI.USA V. 95 11071 1998 JRNL REFN ASTM PNASA6 US ISSN 0027-8424 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STRUCTURAL CALCULATION WAS REMARK 3 CARRIED OUT WITH PARAMETERS REVISED BY PARKINSON ET AL. REMARK 3 (PARKINSON, G. ET AL. (1996) ACTA CRYSTALLOGR. D 52, 57- REMARK 3 64.) REMARK 4 REMARK 4 1I1V COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-FEB-2001. REMARK 100 THE RCSB ID CODE IS RCSB012799. REMARK 102 REMARK 102 BASES C B 4 AND C C 7 ARE MISPAIRED. REMARK 102 BASES C B 5 AND C C 8 ARE MISPAIRED. REMARK 103 REMARK 103 THERE ARE NON-WATSON-CRICK HYDROGEN BONDS BETWEEN THE REMARK 103 FOLLOWING ATOMS: REMARK 103 N4 C B 4 AND O2 C C 7 REMARK 103 N4 C B 5 AND N3 C C 8 REMARK 105 REMARK 105 THE PROTEIN DATA BANK HAS ADOPTED THE SACCHARIDE CHEMISTS REMARK 105 NOMENCLATURE FOR ATOMS OF THE DEOXYRIBOSE/RIBOSE MOIETY REMARK 105 RATHER THAN THAT OF THE NUCLEOSIDE CHEMISTS. THE RING REMARK 105 OXYGEN ATOM IS LABELLED O4* INSTEAD OF O1*. REMARK 220 REMARK 220 EXPERIMENTAL DETAILS REMARK 220 EXPERIMENT TYPE : THEORETICAL MODELLING REMARK 220 REMARK 220 REMARK: ENERGY MINIMIZATION. THIS STRUCTURE DOES NOT REMARK 220 INCLUDE THE COORDINATES OF RECA PROTEIN BECAUSE REMARK 220 STRUCTURAL CALCULATION WAS PERFORMED WITHOUT THE REMARK 220 PROTEIN COORDINATES. REMARK 225 REMARK 225 THEORETICAL MODEL REMARK 225 THE COORDINATES IN THIS ENTRY REPRESENT A MODEL STRUCTURE. REMARK 225 PROTEIN DATA BANK CONVENTIONS REQUIRE THAT CRYST1 AND REMARK 225 SCALE RECORDS BE INCLUDED, BUT THE VALUES ON THESE REMARK 225 RECORDS ARE MEANINGLESS. REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1I1T RELATED DB: PDB REMARK 900 THEORETICAL MODEL OF DOUBLE-STRANDED DNA BOUND TO RECA REMARK 900 PROTEIN (N-TYPE SUGAR CONFORMATION) REMARK 900 RELATED ID: 1I1U RELATED DB: PDB REMARK 900 THEORETICAL MODEL OF DOUBLE-STRANDED DNA BOUND TO RECA REMARK 900 PROTEIN (S-TYPE SUGAR CONFORMATION) SEQRES 1 A 3 G G G SEQRES 1 B 3 C C C SEQRES 1 C 3 C C C CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 ATOM 1 P G A 1 -4.194 -2.775 83.485 1.00 0.00 P ATOM 2 O1P G A 1 -4.150 -1.372 83.971 1.00 0.00 O ATOM 3 O2P G A 1 -5.496 -3.484 83.406 1.00 0.00 O ATOM 4 O5* G A 1 -3.206 -3.642 84.385 1.00 0.00 O ATOM 5 C5* G A 1 -1.886 -3.981 83.919 1.00 0.00 C ATOM 6 C4* G A 1 -1.006 -4.373 85.083 1.00 0.00 C ATOM 7 O4* G A 1 0.040 -3.385 85.240 1.00 0.00 O ATOM 8 C3* G A 1 -1.728 -4.432 86.429 1.00 0.00 C ATOM 9 O3* G A 1 -2.114 -5.778 86.724 1.00 0.00 O ATOM 10 C2* G A 1 -0.670 -3.957 87.408 1.00 0.00 C ATOM 11 C1* G A 1 0.096 -2.934 86.586 1.00 0.00 C ATOM 12 N9 G A 1 -0.473 -1.591 86.630 1.00 0.00 N ATOM 13 C8 G A 1 -1.805 -1.257 86.641 1.00 0.00 C ATOM 14 N7 G A 1 -2.010 0.032 86.683 1.00 0.00 N ATOM 15 C5 G A 1 -0.735 0.581 86.701 1.00 0.00 C ATOM 16 C6 G A 1 -0.320 1.938 86.745 1.00 0.00 C ATOM 17 O6 G A 1 -1.018 2.958 86.779 1.00 0.00 O ATOM 18 N1 G A 1 1.067 2.048 86.749 1.00 0.00 N ATOM 19 C2 G A 1 1.943 0.990 86.715 1.00 0.00 C ATOM 20 N2 G A 1 3.247 1.301 86.725 1.00 0.00 N ATOM 21 N3 G A 1 1.568 -0.278 86.673 1.00 0.00 N ATOM 22 C4 G A 1 0.225 -0.408 86.669 1.00 0.00 C ATOM 23 H1 G A 1 1.461 2.977 86.779 1.00 0.00 H ATOM 24 1H2 G A 1 3.941 0.568 86.703 1.00 0.00 H ATOM 25 2H2 G A 1 3.535 2.269 86.754 1.00 0.00 H ATOM 26 P G A 2 -3.324 -6.053 87.745 1.00 0.00 P ATOM 27 O1P G A 2 -3.145 -7.408 88.325 1.00 0.00 O ATOM 28 O2P G A 2 -4.587 -5.718 87.039 1.00 0.00 O ATOM 29 O5* G A 2 -3.103 -4.981 88.902 1.00 0.00 O ATOM 30 C5* G A 2 -3.119 -5.373 90.288 1.00 0.00 C ATOM 31 C4* G A 2 -1.930 -6.254 90.594 1.00 0.00 C ATOM 32 O4* G A 2 -0.714 -5.499 90.382 1.00 0.00 O ATOM 33 C3* G A 2 -1.867 -6.751 92.037 1.00 0.00 C ATOM 34 O3* G A 2 -1.285 -8.057 92.086 1.00 0.00 O ATOM 35 C2* G A 2 -0.957 -5.740 92.709 1.00 0.00 C ATOM 36 C1* G A 2 0.017 -5.390 91.596 1.00 0.00 C ATOM 37 N9 G A 2 0.546 -4.032 91.675 1.00 0.00 N ATOM 38 C8 G A 2 -0.166 -2.860 91.592 1.00 0.00 C ATOM 39 N7 G A 2 0.584 -1.797 91.697 1.00 0.00 N ATOM 40 C5 G A 2 1.869 -2.297 91.861 1.00 0.00 C ATOM 41 C6 G A 2 3.105 -1.620 92.027 1.00 0.00 C ATOM 42 O6 G A 2 3.318 -0.402 92.064 1.00 0.00 O ATOM 43 N1 G A 2 4.164 -2.513 92.157 1.00 0.00 N ATOM 44 C2 G A 2 4.049 -3.881 92.132 1.00 0.00 C ATOM 45 N2 G A 2 5.189 -4.572 92.274 1.00 0.00 N ATOM 46 N3 G A 2 2.904 -4.524 91.978 1.00 0.00 N ATOM 47 C4 G A 2 1.862 -3.676 91.849 1.00 0.00 C ATOM 48 H1 G A 2 5.088 -2.125 92.280 1.00 0.00 H ATOM 49 1H2 G A 2 5.172 -5.582 92.264 1.00 0.00 H ATOM 50 2H2 G A 2 6.065 -4.083 92.392 1.00 0.00 H ATOM 51 P G A 3 -2.109 -9.272 92.739 1.00 0.00 P ATOM 52 O1P G A 3 -1.368 -10.532 92.479 1.00 0.00 O ATOM 53 O2P G A 3 -3.519 -9.145 92.290 1.00 0.00 O ATOM 54 O5* G A 3 -2.059 -8.976 94.303 1.00 0.00 O ATOM 55 C5* G A 3 -1.790 -10.030 95.247 1.00 0.00 C ATOM 56 C4* G A 3 -0.323 -10.045 95.609 1.00 0.00 C ATOM 57 O4* G A 3 0.225 -8.719 95.420 1.00 0.00 O ATOM 58 C3* G A 3 -0.035 -10.411 97.064 1.00 0.00 C ATOM 59 O3* G A 3 1.201 -11.127 97.158 1.00 0.00 O ATOM 60 C2* G A 3 0.082 -9.059 97.743 1.00 0.00 C ATOM 61 C1* G A 3 0.705 -8.203 96.654 1.00 0.00 C ATOM 62 N9 G A 3 0.333 -6.793 96.721 1.00 0.00 N ATOM 63 C8 G A 3 -0.937 -6.271 96.710 1.00 0.00 C ATOM 64 N7 G A 3 -0.956 -4.968 96.783 1.00 0.00 N ATOM 65 C5 G A 3 0.383 -4.608 96.846 1.00 0.00 C ATOM 66 C6 G A 3 0.987 -3.327 96.937 1.00 0.00 C ATOM 67 O6 G A 3 0.440 -2.218 96.982 1.00 0.00 O ATOM 68 N1 G A 3 2.375 -3.417 96.976 1.00 0.00 N ATOM 69 C2 G A 3 3.090 -4.589 96.933 1.00 0.00 C ATOM 70 N2 G A 3 4.425 -4.468 96.982 1.00 0.00 N ATOM 71 N3 G A 3 2.539 -5.789 96.848 1.00 0.00 N ATOM 72 C4 G A 3 1.192 -5.723 96.809 1.00 0.00 C ATOM 73 H1 G A 3 2.896 -2.555 97.041 1.00 0.00 H ATOM 74 1H2 G A 3 5.008 -5.293 96.954 1.00 0.00 H ATOM 75 2H2 G A 3 4.847 -3.553 97.047 1.00 0.00 H TER 76 G A 3 ATOM 77 P C B 4 7.996 3.518 101.321 1.00 0.00 P ATOM 78 O1P C B 4 7.859 4.835 101.992 1.00 0.00 O ATOM 79 O2P C B 4 9.306 2.818 101.337 1.00 0.00 O ATOM 80 O5* C B 4 7.536 3.684 99.805 1.00 0.00 O ATOM 81 C5* C B 4 8.502 3.696 98.736 1.00 0.00 C ATOM 82 C4* C B 4 8.904 2.283 98.381 1.00 0.00 C ATOM 83 O4* C B 4 7.776 1.402 98.594 1.00 0.00 O ATOM 84 C3* C B 4 9.312 2.090 96.921 1.00 0.00 C ATOM 85 O3* C B 4 10.331 1.090 96.821 1.00 0.00 O ATOM 86 C2* C B 4 8.031 1.611 96.266 1.00 0.00 C ATOM 87 C1* C B 4 7.388 0.790 97.371 1.00 0.00 C ATOM 88 N1 C B 4 5.919 0.771 97.325 1.00 0.00 N ATOM 89 C2 C B 4 5.264 -0.460 97.236 1.00 0.00 C ATOM 90 O2 C B 4 5.942 -1.497 97.198 1.00 0.00 O ATOM 91 N3 C B 4 3.912 -0.488 97.193 1.00 0.00 N ATOM 92 C4 C B 4 3.220 0.653 97.236 1.00 0.00 C ATOM 93 N4 C B 4 1.888 0.578 97.191 1.00 0.00 N ATOM 94 C5 C B 4 3.863 1.921 97.327 1.00 0.00 C ATOM 95 C6 C B 4 5.202 1.934 97.369 1.00 0.00 C ATOM 96 1H4 C B 4 1.334 1.422 97.221 1.00 0.00 H ATOM 97 2H4 C B 4 1.434 -0.322 97.126 1.00 0.00 H ATOM 98 P C B 5 11.815 1.507 96.367 1.00 0.00 P ATOM 99 O1P C B 5 12.655 0.283 96.339 1.00 0.00 O ATOM 100 O2P C B 5 12.228 2.662 97.203 1.00 0.00 O ATOM 101 O5* C B 5 11.629 2.020 94.870 1.00 0.00 O ATOM 102 C5* C B 5 12.274 1.346 93.772 1.00 0.00 C ATOM 103 C4* C B 5 11.843 -0.101 93.723 1.00 0.00 C ATOM 104 O4* C B 5 10.426 -0.184 94.009 1.00 0.00 O ATOM 105 C3* C B 5 12.032 -0.771 92.362 1.00 0.00 C ATOM 106 O3* C B 5 12.352 -2.155 92.533 1.00 0.00 O ATOM 107 C2* C B 5 10.672 -0.617 91.710 1.00 0.00 C ATOM 108 C1* C B 5 9.729 -0.727 92.897 1.00 0.00 C ATOM 109 N1 C B 5 8.478 0.028 92.739 1.00 0.00 N ATOM 110 C2 C B 5 7.282 -0.675 92.577 1.00 0.00 C ATOM 111 O2 C B 5 7.312 -1.915 92.572 1.00 0.00 O ATOM 112 N3 C B 5 6.125 0.011 92.432 1.00 0.00 N ATOM 113 C4 C B 5 6.136 1.346 92.443 1.00 0.00 C ATOM 114 N4 C B 5 4.972 1.983 92.296 1.00 0.00 N ATOM 115 C5 C B 5 7.342 2.088 92.607 1.00 0.00 C ATOM 116 C6 C B 5 8.479 1.395 92.750 1.00 0.00 C ATOM 117 1H4 C B 5 4.944 2.993 92.300 1.00 0.00 H ATOM 118 2H4 C B 5 4.119 1.455 92.181 1.00 0.00 H ATOM 119 P C B 6 13.408 -2.857 91.546 1.00 0.00 P ATOM 120 O1P C B 6 13.229 -4.328 91.641 1.00 0.00 O ATOM 121 O2P C B 6 14.739 -2.260 91.822 1.00 0.00 O ATOM 122 O5* C B 6 12.947 -2.389 90.094 1.00 0.00 O ATOM 123 C5* C B 6 13.904 -2.230 89.030 1.00 0.00 C ATOM 124 C4* C B 6 13.590 -3.181 87.899 1.00 0.00 C ATOM 125 O4* C B 6 12.172 -3.468 87.901 1.00 0.00 O ATOM 126 C3* C B 6 13.902 -2.633 86.507 1.00 0.00 C ATOM 127 O3* C B 6 15.184 -3.095 86.070 1.00 0.00 O ATOM 128 C2* C B 6 12.803 -3.229 85.648 1.00 0.00 C ATOM 129 C1* C B 6 11.624 -3.261 86.606 1.00 0.00 C ATOM 130 N1 C B 6 10.847 -2.014 86.642 1.00 0.00 N ATOM 131 C2 C B 6 9.452 -2.088 86.636 1.00 0.00 C ATOM 132 O2 C B 6 8.913 -3.204 86.602 1.00 0.00 O ATOM 133 N3 C B 6 8.729 -0.945 86.668 1.00 0.00 N ATOM 134 C4 C B 6 9.350 0.236 86.705 1.00 0.00 C ATOM 135 N4 C B 6 8.597 1.338 86.736 1.00 0.00 N ATOM 136 C5 C B 6 10.771 0.340 86.711 1.00 0.00 C ATOM 137 C6 C B 6 11.474 -0.799 86.679 1.00 0.00 C ATOM 138 1H4 C B 6 9.034 2.248 86.764 1.00 0.00 H ATOM 139 2H4 C B 6 7.590 1.262 86.731 1.00 0.00 H TER 140 C B 6 ATOM 141 P C C 7 -2.185 7.304 101.133 1.00 0.00 P ATOM 142 O1P C C 7 -3.048 8.318 101.791 1.00 0.00 O ATOM 143 O2P C C 7 -0.710 7.480 101.142 1.00 0.00 O ATOM 144 O5* C C 7 -2.662 7.154 99.621 1.00 0.00 O ATOM 145 C5* C C 7 -2.118 7.994 98.586 1.00 0.00 C ATOM 146 C4* C C 7 -0.661 7.665 98.359 1.00 0.00 C ATOM 147 O4* C C 7 -0.451 6.253 98.601 1.00 0.00 O ATOM 148 C3* C C 7 -0.170 7.920 96.935 1.00 0.00 C ATOM 149 O3* C C 7 1.201 8.332 96.951 1.00 0.00 O ATOM 150 C2* C C 7 -0.308 6.562 96.274 1.00 0.00 C ATOM 151 C1* C C 7 0.003 5.611 97.417 1.00 0.00 C ATOM 152 N1 C C 7 -0.681 4.314 97.320 1.00 0.00 N ATOM 153 C2 C C 7 0.087 3.148 97.277 1.00 0.00 C ATOM 154 O2 C C 7 1.323 3.244 97.322 1.00 0.00 O ATOM 155 N3 C C 7 -0.533 1.950 97.187 1.00 0.00 N ATOM 156 C4 C C 7 -1.866 1.891 97.142 1.00 0.00 C ATOM 157 N4 C C 7 -2.437 0.687 97.053 1.00 0.00 N ATOM 158 C5 C C 7 -2.674 3.064 97.184 1.00 0.00 C ATOM 159 C6 C C 7 -2.046 4.243 97.273 1.00 0.00 C ATOM 160 1H4 C C 7 -3.443 0.607 97.017 1.00 0.00 H ATOM 161 2H4 C C 7 -1.863 -0.143 97.024 1.00 0.00 H ATOM 162 P C C 8 1.646 9.651 96.148 1.00 0.00 P ATOM 163 O1P C C 8 3.119 9.793 96.265 1.00 0.00 O ATOM 164 O2P C C 8 0.764 10.760 96.591 1.00 0.00 O ATOM 165 O5* C C 8 1.295 9.315 94.631 1.00 0.00 O ATOM 166 C5* C C 8 1.766 10.154 93.559 1.00 0.00 C ATOM 167 C4* C C 8 3.202 9.819 93.227 1.00 0.00 C ATOM 168 O4* C C 8 3.411 8.399 93.410 1.00 0.00 O ATOM 169 C3* C C 8 3.602 10.117 91.783 1.00 0.00 C ATOM 170 O3* C C 8 4.975 10.516 91.723 1.00 0.00 O ATOM 171 C2* C C 8 3.407 8.782 91.090 1.00 0.00 C ATOM 172 C1* C C 8 3.783 7.792 92.180 1.00 0.00 C ATOM 173 N1 C C 8 3.083 6.503 92.087 1.00 0.00 N ATOM 174 C2 C C 8 3.827 5.324 92.177 1.00 0.00 C ATOM 175 O2 C C 8 5.054 5.402 92.333 1.00 0.00 O ATOM 176 N3 C C 8 3.191 4.133 92.091 1.00 0.00 N ATOM 177 C4 C C 8 1.867 4.094 91.923 1.00 0.00 C ATOM 178 N4 C C 8 1.282 2.897 91.844 1.00 0.00 N ATOM 179 C5 C C 8 1.085 5.282 91.828 1.00 0.00 C ATOM 180 C6 C C 8 1.728 6.453 91.914 1.00 0.00 C ATOM 181 1H4 C C 8 0.282 2.832 91.716 1.00 0.00 H ATOM 182 2H4 C C 8 1.838 2.057 91.912 1.00 0.00 H ATOM 183 P C C 9 5.455 11.548 90.588 1.00 0.00 P ATOM 184 O1P C C 9 6.647 12.275 91.093 1.00 0.00 O ATOM 185 O2P C C 9 4.260 12.314 90.150 1.00 0.00 O ATOM 186 O5* C C 9 5.912 10.612 89.384 1.00 0.00 O ATOM 187 C5* C C 9 5.495 9.235 89.317 1.00 0.00 C ATOM 188 C4* C C 9 6.227 8.521 88.205 1.00 0.00 C ATOM 189 O4* C C 9 5.833 7.128 88.197 1.00 0.00 O ATOM 190 C3* C C 9 5.918 9.049 86.805 1.00 0.00 C ATOM 191 O3* C C 9 6.926 9.979 86.394 1.00 0.00 O ATOM 192 C2* C C 9 5.969 7.799 85.947 1.00 0.00 C ATOM 193 C1* C C 9 5.434 6.735 86.891 1.00 0.00 C ATOM 194 N1 C C 9 3.969 6.614 86.887 1.00 0.00 N ATOM 195 C2 C C 9 3.399 5.340 86.849 1.00 0.00 C ATOM 196 O2 C C 9 4.145 4.350 86.819 1.00 0.00 O ATOM 197 N3 C C 9 2.051 5.218 86.845 1.00 0.00 N ATOM 198 C4 C C 9 1.283 6.309 86.878 1.00 0.00 C ATOM 199 N4 C C 9 -0.041 6.143 86.873 1.00 0.00 N ATOM 200 C5 C C 9 1.839 7.621 86.917 1.00 0.00 C ATOM 201 C6 C C 9 3.174 7.726 86.920 1.00 0.00 C ATOM 202 1H4 C C 9 -0.652 6.947 86.897 1.00 0.00 H ATOM 203 2H4 C C 9 -0.433 5.212 86.845 1.00 0.00 H TER 204 C C 9 MASTER 51 0 0 0 0 0 0 6 201 3 0 3 END