HEADER RNA 26-JUN-20 6XKO TITLE CLASS III PREQ1 RIBOSWITCH MUTANT A84G COMPND MOL_ID: 1; COMPND 2 MOLECULE: CLASS III PREQ1 RIBOSWITCH; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: FAECALIBACTERIUM PRAUSNITZII; SOURCE 4 ORGANISM_TAXID: 853 KEYWDS PREQ1, QUEUOSINE, THREE-WAY HELICAL JUNCTION, APTAMER, METABOLITE, KEYWDS 2 TRANSLATIONAL REGULATION, HL(OUT)-TYPE PSEUDOKNOT, RIBOSWITCH, RNA EXPDTA X-RAY DIFFRACTION AUTHOR K.Y.SRIVASTAVA,J.L.JENKINS,J.E.WEDEKIND REVDAT 2 18-OCT-23 6XKO 1 REMARK REVDAT 1 29-DEC-21 6XKO 0 JRNL AUTH K.Y.SRIVASTAVA,J.L.JENKINS,J.E.WEDEKIND JRNL TITL NEW INSIGHTS INTO CLASS III PREQ1 METABOLITE BINDING JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.05 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 15744 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.210 REMARK 3 R VALUE (WORKING SET) : 0.208 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.970 REMARK 3 FREE R VALUE TEST SET COUNT : 1569 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 44.0500 - 6.1100 0.98 1423 161 0.1968 0.2230 REMARK 3 2 6.1100 - 4.8500 1.00 1347 149 0.1816 0.1674 REMARK 3 3 4.8500 - 4.2400 1.00 1319 139 0.1753 0.2112 REMARK 3 4 4.2400 - 3.8500 1.00 1291 139 0.1701 0.1848 REMARK 3 5 3.8500 - 3.5700 0.99 1288 143 0.1816 0.1972 REMARK 3 6 3.5700 - 3.3600 0.99 1251 141 0.2153 0.2505 REMARK 3 7 3.3600 - 3.2000 0.99 1264 141 0.2164 0.2210 REMARK 3 8 3.2000 - 3.0600 0.99 1261 129 0.2284 0.2373 REMARK 3 9 3.0600 - 2.9400 0.99 1249 146 0.2825 0.3135 REMARK 3 10 2.9400 - 2.8400 0.99 1238 141 0.3685 0.3654 REMARK 3 11 2.8400 - 2.7500 0.99 1244 140 0.4061 0.4292 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.390 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.160 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 85.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 2284 REMARK 3 ANGLE : 0.840 3555 REMARK 3 CHIRALITY : 0.036 474 REMARK 3 PLANARITY : 0.007 96 REMARK 3 DIHEDRAL : 13.787 1137 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 20 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESID 67:70) REMARK 3 ORIGIN FOR THE GROUP (A): -4.3181 58.3368 100.7618 REMARK 3 T TENSOR REMARK 3 T11: 0.8818 T22: 0.9597 REMARK 3 T33: 1.3132 T12: 0.1914 REMARK 3 T13: -0.0755 T23: 0.1228 REMARK 3 L TENSOR REMARK 3 L11: 0.1332 L22: 0.1579 REMARK 3 L33: 0.0808 L12: -0.1031 REMARK 3 L13: -0.0917 L23: 0.1083 REMARK 3 S TENSOR REMARK 3 S11: 0.3629 S12: -0.7415 S13: -0.9172 REMARK 3 S21: 0.3673 S22: 0.1288 S23: 0.9174 REMARK 3 S31: 0.5646 S32: -1.2320 S33: -0.0003 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 71:74) REMARK 3 ORIGIN FOR THE GROUP (A): 9.8115 52.8007 98.3401 REMARK 3 T TENSOR REMARK 3 T11: 0.7271 T22: 0.7311 REMARK 3 T33: 0.6054 T12: 0.1564 REMARK 3 T13: -0.0384 T23: -0.0578 REMARK 3 L TENSOR REMARK 3 L11: 0.1714 L22: 0.4464 REMARK 3 L33: 0.1013 L12: -0.0835 REMARK 3 L13: -0.0910 L23: -0.0090 REMARK 3 S TENSOR REMARK 3 S11: -0.4776 S12: 0.6588 S13: 0.2054 REMARK 3 S21: -0.0327 S22: 0.0974 S23: 0.2927 REMARK 3 S31: 0.3508 S32: 0.3495 S33: -0.0006 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 75:78) REMARK 3 ORIGIN FOR THE GROUP (A): 14.7846 48.0768 111.9935 REMARK 3 T TENSOR REMARK 3 T11: 1.0127 T22: 0.6355 REMARK 3 T33: 0.8461 T12: 0.2270 REMARK 3 T13: -0.1316 T23: -0.0591 REMARK 3 L TENSOR REMARK 3 L11: 0.2850 L22: 0.1202 REMARK 3 L33: 0.1672 L12: -0.1799 REMARK 3 L13: -0.0224 L23: 0.0496 REMARK 3 S TENSOR REMARK 3 S11: 0.4763 S12: 0.7098 S13: -0.6611 REMARK 3 S21: -0.2298 S22: -0.1778 S23: 0.2403 REMARK 3 S31: 1.0620 S32: 0.7911 S33: 0.0085 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN A AND RESID 79:83) REMARK 3 ORIGIN FOR THE GROUP (A): 13.1005 33.5723 110.6092 REMARK 3 T TENSOR REMARK 3 T11: 1.1905 T22: 0.7530 REMARK 3 T33: 1.3676 T12: 0.2422 REMARK 3 T13: 0.0464 T23: -0.0093 REMARK 3 L TENSOR REMARK 3 L11: 2.2102 L22: 0.5037 REMARK 3 L33: 4.5543 L12: -0.7056 REMARK 3 L13: 2.1011 L23: 0.1738 REMARK 3 S TENSOR REMARK 3 S11: -0.4566 S12: -1.1942 S13: -0.8595 REMARK 3 S21: 1.8049 S22: 0.4986 S23: -0.5641 REMARK 3 S31: 0.2844 S32: -1.0839 S33: 0.1939 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN A AND RESID 84:87) REMARK 3 ORIGIN FOR THE GROUP (A): 28.5772 34.4368 103.7958 REMARK 3 T TENSOR REMARK 3 T11: 0.6447 T22: 0.5384 REMARK 3 T33: 0.7947 T12: 0.2702 REMARK 3 T13: 0.0133 T23: 0.0625 REMARK 3 L TENSOR REMARK 3 L11: 0.9317 L22: 0.7698 REMARK 3 L33: 0.8167 L12: -0.3042 REMARK 3 L13: -0.3428 L23: 0.6749 REMARK 3 S TENSOR REMARK 3 S11: -0.2097 S12: 0.1200 S13: -0.1400 REMARK 3 S21: -0.6035 S22: 0.2559 S23: 1.0848 REMARK 3 S31: 0.2028 S32: -0.3113 S33: -0.0028 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN A AND RESID 88:91) REMARK 3 ORIGIN FOR THE GROUP (A): 39.9712 44.4282 95.6157 REMARK 3 T TENSOR REMARK 3 T11: 0.9933 T22: 0.6983 REMARK 3 T33: 0.8149 T12: 0.0433 REMARK 3 T13: 0.1025 T23: 0.1093 REMARK 3 L TENSOR REMARK 3 L11: 0.1872 L22: 0.3190 REMARK 3 L33: 0.0532 L12: -0.2391 REMARK 3 L13: -0.0976 L23: 0.1153 REMARK 3 S TENSOR REMARK 3 S11: 0.8839 S12: 0.4300 S13: 1.4664 REMARK 3 S21: -0.7377 S22: 0.0074 S23: 0.5801 REMARK 3 S31: 0.0118 S32: 0.1224 S33: 0.0027 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: (CHAIN A AND RESID 92:95) REMARK 3 ORIGIN FOR THE GROUP (A): 50.9073 31.9928 92.1649 REMARK 3 T TENSOR REMARK 3 T11: 0.8098 T22: 1.0045 REMARK 3 T33: 0.8705 T12: 0.1316 REMARK 3 T13: -0.1564 T23: 0.1281 REMARK 3 L TENSOR REMARK 3 L11: 0.4646 L22: 0.1879 REMARK 3 L33: 0.4686 L12: 0.1299 REMARK 3 L13: -0.2935 L23: -0.0576 REMARK 3 S TENSOR REMARK 3 S11: -0.3705 S12: -0.8521 S13: -0.5045 REMARK 3 S21: 0.9109 S22: 0.1882 S23: 0.1048 REMARK 3 S31: -0.8593 S32: 1.3723 S33: -0.0009 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: (CHAIN A AND RESID 96:101) REMARK 3 ORIGIN FOR THE GROUP (A): 67.1628 25.9114 90.8870 REMARK 3 T TENSOR REMARK 3 T11: 1.0150 T22: 1.3748 REMARK 3 T33: 1.8216 T12: 0.1774 REMARK 3 T13: -0.2001 T23: 0.2712 REMARK 3 L TENSOR REMARK 3 L11: 0.2424 L22: 0.3323 REMARK 3 L33: 0.2127 L12: 0.2302 REMARK 3 L13: 0.0037 L23: 0.1597 REMARK 3 S TENSOR REMARK 3 S11: -0.5023 S12: -0.8682 S13: -0.7908 REMARK 3 S21: 0.1150 S22: 0.2554 S23: -0.8626 REMARK 3 S31: 0.3756 S32: 1.1785 S33: -0.0084 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: (CHAIN A AND RESID 1:4) REMARK 3 ORIGIN FOR THE GROUP (A): 36.6574 39.0231 122.5312 REMARK 3 T TENSOR REMARK 3 T11: 1.1508 T22: 0.8802 REMARK 3 T33: 0.7825 T12: -0.0138 REMARK 3 T13: 0.2108 T23: 0.0007 REMARK 3 L TENSOR REMARK 3 L11: 1.4338 L22: 1.2422 REMARK 3 L33: 0.6971 L12: 1.2561 REMARK 3 L13: 0.7046 L23: 0.3850 REMARK 3 S TENSOR REMARK 3 S11: 0.1719 S12: 0.1464 S13: 1.4717 REMARK 3 S21: 0.5869 S22: 0.2020 S23: 0.4100 REMARK 3 S31: -0.8541 S32: -1.5836 S33: 0.0106 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: (CHAIN A AND RESID 5:9) REMARK 3 ORIGIN FOR THE GROUP (A): 39.0612 28.6523 107.0918 REMARK 3 T TENSOR REMARK 3 T11: 0.7516 T22: 0.6827 REMARK 3 T33: 0.5352 T12: 0.1872 REMARK 3 T13: 0.0062 T23: 0.0367 REMARK 3 L TENSOR REMARK 3 L11: 0.5794 L22: 0.5651 REMARK 3 L33: 0.3878 L12: -0.4624 REMARK 3 L13: -0.3590 L23: 0.1044 REMARK 3 S TENSOR REMARK 3 S11: 0.3122 S12: -0.0685 S13: -0.1562 REMARK 3 S21: -0.4389 S22: 0.1141 S23: -0.0531 REMARK 3 S31: -0.4524 S32: 0.3890 S33: 0.0011 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: (CHAIN A AND RESID 10:14) REMARK 3 ORIGIN FOR THE GROUP (A): 41.2226 36.2468 99.3037 REMARK 3 T TENSOR REMARK 3 T11: 0.8637 T22: 0.8880 REMARK 3 T33: 0.6331 T12: 0.0650 REMARK 3 T13: -0.0313 T23: 0.0926 REMARK 3 L TENSOR REMARK 3 L11: 0.6076 L22: 0.1273 REMARK 3 L33: 0.1710 L12: -0.0058 REMARK 3 L13: -0.1190 L23: 0.1405 REMARK 3 S TENSOR REMARK 3 S11: 0.3197 S12: -0.0594 S13: 0.2459 REMARK 3 S21: 0.1285 S22: 0.0209 S23: -0.1738 REMARK 3 S31: 0.0849 S32: 0.6578 S33: 0.0002 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: (CHAIN A AND RESID 15:18) REMARK 3 ORIGIN FOR THE GROUP (A): 33.0549 36.5747 111.1560 REMARK 3 T TENSOR REMARK 3 T11: 0.7442 T22: 0.5543 REMARK 3 T33: 0.6834 T12: 0.1065 REMARK 3 T13: 0.0828 T23: -0.0084 REMARK 3 L TENSOR REMARK 3 L11: 0.1157 L22: 0.0680 REMARK 3 L33: 0.2945 L12: 0.0923 REMARK 3 L13: -0.0658 L23: -0.0575 REMARK 3 S TENSOR REMARK 3 S11: -0.5670 S12: -0.4033 S13: 0.6967 REMARK 3 S21: -0.4894 S22: 0.5597 S23: 0.4424 REMARK 3 S31: -0.0641 S32: 0.4864 S33: 0.0034 REMARK 3 TLS GROUP : 13 REMARK 3 SELECTION: (CHAIN A AND RESID 19:26) REMARK 3 ORIGIN FOR THE GROUP (A): 34.9390 31.7207 126.2997 REMARK 3 T TENSOR REMARK 3 T11: 0.9408 T22: 0.6466 REMARK 3 T33: 0.7394 T12: 0.1202 REMARK 3 T13: 0.1662 T23: -0.0954 REMARK 3 L TENSOR REMARK 3 L11: 0.6017 L22: 0.5505 REMARK 3 L33: 0.0234 L12: -0.3560 REMARK 3 L13: -0.0796 L23: 0.1158 REMARK 3 S TENSOR REMARK 3 S11: 0.1934 S12: -0.2777 S13: 0.6521 REMARK 3 S21: 0.3360 S22: 0.4153 S23: 0.2521 REMARK 3 S31: -0.4811 S32: 0.1380 S33: -0.0019 REMARK 3 TLS GROUP : 14 REMARK 3 SELECTION: (CHAIN A AND RESID 27:30) REMARK 3 ORIGIN FOR THE GROUP (A): 23.7309 31.0576 142.0900 REMARK 3 T TENSOR REMARK 3 T11: 1.4376 T22: 1.4806 REMARK 3 T33: 1.0744 T12: 0.1317 REMARK 3 T13: 0.1850 T23: 0.3628 REMARK 3 L TENSOR REMARK 3 L11: 0.6267 L22: 0.8069 REMARK 3 L33: 0.3940 L12: -0.7112 REMARK 3 L13: 0.4974 L23: -0.5635 REMARK 3 S TENSOR REMARK 3 S11: 0.7519 S12: -1.6300 S13: -0.7041 REMARK 3 S21: 0.2223 S22: 0.8001 S23: 1.3120 REMARK 3 S31: 0.2675 S32: -0.0064 S33: 0.0268 REMARK 3 TLS GROUP : 15 REMARK 3 SELECTION: (CHAIN A AND RESID 31:40) REMARK 3 ORIGIN FOR THE GROUP (A): 30.5809 29.9275 151.2861 REMARK 3 T TENSOR REMARK 3 T11: 1.6548 T22: 2.2068 REMARK 3 T33: 1.3683 T12: 0.1593 REMARK 3 T13: 0.2181 T23: 0.1315 REMARK 3 L TENSOR REMARK 3 L11: 0.4205 L22: 0.1661 REMARK 3 L33: 0.2241 L12: 0.1660 REMARK 3 L13: -0.0748 L23: 0.1169 REMARK 3 S TENSOR REMARK 3 S11: 0.3028 S12: -1.2413 S13: 0.7133 REMARK 3 S21: -0.3479 S22: 1.0863 S23: 1.3168 REMARK 3 S31: -1.0351 S32: -1.2609 S33: 0.0021 REMARK 3 TLS GROUP : 16 REMARK 3 SELECTION: (CHAIN A AND RESID 41:44) REMARK 3 ORIGIN FOR THE GROUP (A): 35.2556 29.0617 144.0676 REMARK 3 T TENSOR REMARK 3 T11: 1.3663 T22: 1.4983 REMARK 3 T33: 0.8833 T12: 0.1259 REMARK 3 T13: 0.0164 T23: -0.0131 REMARK 3 L TENSOR REMARK 3 L11: 0.2272 L22: 0.1631 REMARK 3 L33: 0.4784 L12: 0.1225 REMARK 3 L13: -0.2198 L23: -0.2804 REMARK 3 S TENSOR REMARK 3 S11: -0.2396 S12: -0.4447 S13: 0.6519 REMARK 3 S21: -0.6379 S22: -0.1847 S23: -0.0692 REMARK 3 S31: -1.4885 S32: -2.2031 S33: 0.0027 REMARK 3 TLS GROUP : 17 REMARK 3 SELECTION: (CHAIN A AND RESID 45:49) REMARK 3 ORIGIN FOR THE GROUP (A): 24.8785 31.1470 131.7613 REMARK 3 T TENSOR REMARK 3 T11: 1.1999 T22: 0.9829 REMARK 3 T33: 1.0662 T12: -0.0105 REMARK 3 T13: 0.0450 T23: 0.0608 REMARK 3 L TENSOR REMARK 3 L11: 0.1621 L22: 0.0133 REMARK 3 L33: 0.0028 L12: 0.0281 REMARK 3 L13: 0.0188 L23: -0.0006 REMARK 3 S TENSOR REMARK 3 S11: 1.1947 S12: 0.9568 S13: -1.3166 REMARK 3 S21: 0.3238 S22: -0.4811 S23: 0.9691 REMARK 3 S31: -0.0104 S32: 1.0318 S33: 0.0042 REMARK 3 TLS GROUP : 18 REMARK 3 SELECTION: (CHAIN A AND RESID 50:54) REMARK 3 ORIGIN FOR THE GROUP (A): 24.1698 38.8308 111.6481 REMARK 3 T TENSOR REMARK 3 T11: 0.8980 T22: 0.7774 REMARK 3 T33: 0.9102 T12: 0.2245 REMARK 3 T13: 0.0415 T23: 0.1028 REMARK 3 L TENSOR REMARK 3 L11: 0.3142 L22: 0.2403 REMARK 3 L33: 0.0702 L12: 0.2757 REMARK 3 L13: 0.0873 L23: 0.0800 REMARK 3 S TENSOR REMARK 3 S11: 0.3306 S12: -0.0315 S13: 0.1187 REMARK 3 S21: 0.3195 S22: -0.4839 S23: 0.8807 REMARK 3 S31: -0.2288 S32: 0.6112 S33: 0.0017 REMARK 3 TLS GROUP : 19 REMARK 3 SELECTION: (CHAIN A AND RESID 55:58) REMARK 3 ORIGIN FOR THE GROUP (A): 9.9148 41.0844 103.9107 REMARK 3 T TENSOR REMARK 3 T11: 0.9122 T22: 0.8356 REMARK 3 T33: 0.9907 T12: 0.3016 REMARK 3 T13: -0.1493 T23: -0.1736 REMARK 3 L TENSOR REMARK 3 L11: 0.8266 L22: 1.1786 REMARK 3 L33: 0.8126 L12: -0.8761 REMARK 3 L13: -0.7753 L23: 0.9691 REMARK 3 S TENSOR REMARK 3 S11: -0.2667 S12: 1.3218 S13: -0.9274 REMARK 3 S21: 0.8563 S22: -0.3527 S23: 0.2689 REMARK 3 S31: 0.6274 S32: 0.0723 S33: -0.0121 REMARK 3 TLS GROUP : 20 REMARK 3 SELECTION: (CHAIN A AND RESID 59:66) REMARK 3 ORIGIN FOR THE GROUP (A): 6.3355 59.6637 105.8743 REMARK 3 T TENSOR REMARK 3 T11: 1.0098 T22: 0.5831 REMARK 3 T33: 0.8077 T12: 0.2378 REMARK 3 T13: -0.0590 T23: 0.0120 REMARK 3 L TENSOR REMARK 3 L11: 0.7860 L22: 0.5634 REMARK 3 L33: 0.2718 L12: -0.0315 REMARK 3 L13: -0.3862 L23: 0.2339 REMARK 3 S TENSOR REMARK 3 S11: 0.1653 S12: 0.1884 S13: 0.1887 REMARK 3 S21: -0.2800 S22: -0.2631 S23: 0.9302 REMARK 3 S31: 0.0343 S32: -0.3418 S33: -0.0002 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6XKO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-JUL-20. REMARK 100 THE DEPOSITION ID IS D_1000250311. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-OCT-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CHESS REMARK 200 BEAMLINE : A1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.62790 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 V708C REMARK 200 DATA SCALING SOFTWARE : HKL-2000 V708C REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15744 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.750 REMARK 200 RESOLUTION RANGE LOW (A) : 44.050 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 8.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : 9.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: PHENIX 1.17.1_3660 REMARK 200 STARTING MODEL: 4RZD REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 71.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 80% TACSIMATE PH 7.0, 10 MM MAGNESIUM REMARK 280 ACETATE, 6 MM COBALT HAXAMMINE, 1 MM SPERMINE, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 184.73600 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 92.36800 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 138.55200 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 46.18400 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 230.92000 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 184.73600 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 92.36800 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 46.18400 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 138.55200 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 230.92000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 U A 33 REMARK 465 C A 34 REMARK 465 U A 35 REMARK 465 C A 36 REMARK 465 G A 37 REMARK 465 A A 38 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 GTP A 1 C3' - O3' - P ANGL. DEV. = -22.7 DEGREES REMARK 500 A A 2 O3' - P - OP2 ANGL. DEV. = 28.0 DEGREES REMARK 500 A A 2 O3' - P - OP1 ANGL. DEV. = -20.1 DEGREES REMARK 500 A A 18 C2 - N3 - C4 ANGL. DEV. = -3.0 DEGREES REMARK 500 A A 18 C4 - C5 - N7 ANGL. DEV. = 3.6 DEGREES REMARK 500 A A 18 C5 - N7 - C8 ANGL. DEV. = -4.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PRF A 201 REMARK 999 REMARK 999 SEQUENCE REMARK 999 ADENINE 84 MUTATED TO GUANINE DBREF 6XKO A 1 101 PDB 6XKO 6XKO 1 101 SEQRES 1 A 101 GTP A G C A A C U U A G G A SEQRES 2 A 101 U U U U A G G C U C C C C SEQRES 3 A 101 G G C G U G U C U C G A A SEQRES 4 A 101 C C A U G C C G G G C C A SEQRES 5 A 101 A A C C C A U A G G G C U SEQRES 6 A 101 G G C G G U C C C U G U G SEQRES 7 A 101 C G G U C G A A A U U C A SEQRES 8 A 101 U C C G C C G G A G HET GTP A 1 41 HET PRF A 201 22 HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE HETNAM PRF 7-DEAZA-7-AMINOMETHYL-GUANINE FORMUL 1 GTP C10 H16 N5 O14 P3 FORMUL 2 PRF C7 H9 N5 O FORMUL 3 HOH *9(H2 O) LINK O3' GTP A 1 P A A 2 1555 1555 1.57 SITE 1 AC1 7 C A 7 U A 8 U A 17 A A 18 SITE 2 AC1 7 G A 84 A A 85 HOH A 302 CRYST1 83.798 83.798 277.104 90.00 90.00 120.00 P 65 2 2 12 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 0.011933 0.006890 0.000000 0.00000 SCALE2 0.000000 0.013780 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003609 0.00000 HETATM 1 PG GTP A 1 29.431 45.822 127.016 1.00114.31 P ANISOU 1 PG GTP A 1 15505 13853 14076 2896 3899 -669 P HETATM 2 O1G GTP A 1 30.625 45.445 127.887 1.00111.29 O ANISOU 2 O1G GTP A 1 15583 13152 13550 2572 3841 -998 O HETATM 3 O2G GTP A 1 28.515 46.771 127.788 1.00119.28 O ANISOU 3 O2G GTP A 1 15980 14427 14914 3310 4171 -882 O HETATM 4 O3G GTP A 1 28.685 44.542 126.663 1.00112.59 O ANISOU 4 O3G GTP A 1 15024 14296 13460 2636 3841 -506 O HETATM 5 O3B GTP A 1 29.986 46.599 125.689 1.00114.21 O ANISOU 5 O3B GTP A 1 15465 13505 14426 3063 3728 -286 O HETATM 6 PB GTP A 1 29.349 46.414 124.203 1.00114.36 P ANISOU 6 PB GTP A 1 15100 13882 14470 3119 3593 222 P HETATM 7 O1B GTP A 1 28.982 47.793 123.669 1.00118.44 O ANISOU 7 O1B GTP A 1 15448 14102 15451 3585 3638 420 O HETATM 8 O2B GTP A 1 30.275 45.683 123.232 1.00110.01 O ANISOU 8 O2B GTP A 1 14670 13349 13781 2751 3336 462 O HETATM 9 O3A GTP A 1 27.970 45.605 124.488 1.00115.56 O ANISOU 9 O3A GTP A 1 14895 14702 14310 3100 3718 213 O HETATM 10 PA GTP A 1 27.686 44.136 123.860 1.00112.18 P ANISOU 10 PA GTP A 1 14299 14871 13454 2710 3570 430 P HETATM 11 O1A GTP A 1 26.331 43.706 124.407 1.00114.46 O ANISOU 11 O1A GTP A 1 14276 15687 13526 2791 3749 341 O HETATM 12 O2A GTP A 1 27.747 44.156 122.327 1.00111.33 O ANISOU 12 O2A GTP A 1 14003 14846 13450 2704 3374 907 O HETATM 13 O5' GTP A 1 28.846 43.180 124.471 1.00107.61 O ANISOU 13 O5' GTP A 1 14125 14180 12581 2239 3456 166 O HETATM 14 C5' GTP A 1 29.962 42.838 123.671 1.00103.95 C ANISOU 14 C5' GTP A 1 13852 13526 12120 1970 3223 329 C HETATM 15 C4' GTP A 1 31.190 42.829 124.565 1.00101.80 C ANISOU 15 C4' GTP A 1 14036 12797 11846 1771 3192 -25 C HETATM 16 O4' GTP A 1 30.948 42.003 125.722 1.00101.01 O ANISOU 16 O4' GTP A 1 14033 12934 11413 1549 3271 -348 O HETATM 17 C3' GTP A 1 32.538 42.372 123.965 1.00 97.63 C ANISOU 17 C3' GTP A 1 13768 12024 11302 1434 2952 45 C HETATM 18 O3' GTP A 1 33.287 43.381 123.352 1.00 98.17 O ANISOU 18 O3' GTP A 1 13958 11609 11732 1606 2893 175 O HETATM 19 C2' GTP A 1 33.248 41.797 125.211 1.00 95.50 C ANISOU 19 C2' GTP A 1 13858 11593 10836 1149 2949 -369 C HETATM 20 O2' GTP A 1 34.006 42.795 125.838 1.00 96.59 O ANISOU 20 O2' GTP A 1 14300 11146 11255 1313 3014 -597 O HETATM 21 C1' GTP A 1 32.121 41.309 126.146 1.00 97.22 C ANISOU 21 C1' GTP A 1 13919 12244 10776 1159 3119 -552 C HETATM 22 N9 GTP A 1 31.953 39.852 125.994 1.00 94.18 N ANISOU 22 N9 GTP A 1 13452 12342 9988 760 2983 -497 N HETATM 23 C8 GTP A 1 30.838 39.187 125.555 1.00 94.70 C ANISOU 23 C8 GTP A 1 13158 12999 9826 738 3003 -292 C HETATM 24 N7 GTP A 1 31.101 37.864 125.529 1.00 91.22 N ANISOU 24 N7 GTP A 1 12769 12844 9046 310 2836 -305 N HETATM 25 C5 GTP A 1 32.362 37.678 125.964 1.00 88.56 C ANISOU 25 C5 GTP A 1 12817 12102 8730 64 2707 -523 C HETATM 26 C6 GTP A 1 33.124 36.539 126.142 1.00 84.76 C ANISOU 26 C6 GTP A 1 12538 11656 8009 -382 2503 -634 C HETATM 27 O6 GTP A 1 32.640 35.437 125.880 1.00 83.23 O ANISOU 27 O6 GTP A 1 12171 11940 7512 -628 2412 -528 O HETATM 28 N1 GTP A 1 34.415 36.657 126.616 1.00 82.82 N ANISOU 28 N1 GTP A 1 12685 10903 7881 -543 2396 -864 N HETATM 29 C2 GTP A 1 34.936 37.897 126.911 1.00 84.61 C ANISOU 29 C2 GTP A 1 13104 10600 8443 -267 2500 -980 C HETATM 30 N2 GTP A 1 36.174 38.025 127.363 1.00 82.81 N ANISOU 30 N2 GTP A 1 13250 9882 8331 -420 2397 -1198 N HETATM 31 N3 GTP A 1 34.172 39.020 126.729 1.00 88.37 N ANISOU 31 N3 GTP A 1 13382 11044 9150 174 2702 -868 N HETATM 32 C4 GTP A 1 32.907 38.912 126.266 1.00 90.34 C ANISOU 32 C4 GTP A 1 13242 11782 9303 338 2801 -645 C HETATM 33 H4' GTP A 1 31.317 43.889 124.786 1.00122.16 H HETATM 34 H3' GTP A 1 32.407 41.674 123.138 1.00117.15 H HETATM 35 H2' GTP A 1 33.935 40.991 124.954 1.00114.60 H HETATM 36 HO2' GTP A 1 33.619 42.997 126.715 1.00115.91 H HETATM 37 H1' GTP A 1 32.347 41.508 127.194 1.00116.66 H HETATM 38 H8 GTP A 1 29.894 39.652 125.272 1.00113.64 H HETATM 39 HN1 GTP A 1 34.998 35.805 126.750 1.00 99.39 H HETATM 40 HN21 GTP A 1 36.546 38.947 127.570 1.00 99.37 H HETATM 41 HN22 GTP A 1 36.751 37.202 127.503 1.00 99.37 H