HEADER HYDROLASE 22-DEC-21 7TC3 TITLE HUMAN APE1 IN THE APO FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA-(APURINIC OR APYRIMIDINIC SITE) ENDONUCLEASE, COMPND 3 MITOCHONDRIAL; COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: APEX1, APE, APE1, APEX, APX, HAP1, REF1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS AP ENDONUCLEASE1, APE1, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR L.S.PIDUGU,E.POZHARSKI,A.C.DROHAT REVDAT 3 25-OCT-23 7TC3 1 REMARK REVDAT 2 01-FEB-23 7TC3 1 JRNL REVDAT 1 21-DEC-22 7TC3 0 JRNL AUTH L.S.PIDUGU,H.W.SERVIUS,S.E.SEVDALIS,M.E.COOK,K.M.VARNEY, JRNL AUTH 2 E.POZHARSKI,A.C.DROHAT JRNL TITL CHARACTERIZING INHIBITORS OF HUMAN AP ENDONUCLEASE 1. JRNL REF PLOS ONE V. 18 80526 2023 JRNL REFN ESSN 1932-6203 JRNL PMID 36652434 JRNL DOI 10.1371/JOURNAL.PONE.0280526 REMARK 2 REMARK 2 RESOLUTION. 1.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV_3409 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) : 1.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.94 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 82165 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.152 REMARK 3 R VALUE (WORKING SET) : 0.151 REMARK 3 FREE R VALUE : 0.178 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 4098 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 38.9420 - 3.8448 1.00 2986 148 0.1258 0.1655 REMARK 3 2 3.8448 - 3.0521 1.00 2818 162 0.1220 0.1681 REMARK 3 3 3.0521 - 2.6664 1.00 2754 188 0.1383 0.1642 REMARK 3 4 2.6664 - 2.4226 1.00 2801 130 0.1472 0.1666 REMARK 3 5 2.4226 - 2.2490 1.00 2761 147 0.1436 0.1859 REMARK 3 6 2.2490 - 2.1164 1.00 2758 148 0.1457 0.1483 REMARK 3 7 2.1164 - 2.0104 1.00 2760 145 0.1465 0.1723 REMARK 3 8 2.0104 - 1.9229 1.00 2726 141 0.1469 0.1488 REMARK 3 9 1.9229 - 1.8489 1.00 2723 154 0.1476 0.1695 REMARK 3 10 1.8489 - 1.7851 1.00 2763 133 0.1500 0.1541 REMARK 3 11 1.7851 - 1.7293 1.00 2680 145 0.1585 0.2094 REMARK 3 12 1.7293 - 1.6799 1.00 2742 166 0.1595 0.1913 REMARK 3 13 1.6799 - 1.6356 1.00 2714 155 0.1673 0.1648 REMARK 3 14 1.6356 - 1.5957 1.00 2706 136 0.1651 0.1676 REMARK 3 15 1.5957 - 1.5594 1.00 2703 138 0.1649 0.1659 REMARK 3 16 1.5594 - 1.5263 1.00 2751 142 0.1709 0.1786 REMARK 3 17 1.5263 - 1.4957 1.00 2696 138 0.1785 0.2097 REMARK 3 18 1.4957 - 1.4675 1.00 2713 130 0.1838 0.2079 REMARK 3 19 1.4675 - 1.4413 1.00 2744 116 0.1922 0.2187 REMARK 3 20 1.4413 - 1.4169 1.00 2655 151 0.2016 0.2280 REMARK 3 21 1.4169 - 1.3940 1.00 2782 131 0.2127 0.2267 REMARK 3 22 1.3940 - 1.3726 1.00 2651 141 0.2132 0.2274 REMARK 3 23 1.3726 - 1.3524 1.00 2724 142 0.2359 0.2403 REMARK 3 24 1.3524 - 1.3333 1.00 2658 132 0.2701 0.2897 REMARK 3 25 1.3333 - 1.3153 1.00 2734 160 0.2824 0.3237 REMARK 3 26 1.3153 - 1.2982 0.99 2605 133 0.3116 0.3418 REMARK 3 27 1.2982 - 1.2820 0.97 2664 128 0.3305 0.3464 REMARK 3 28 1.2820 - 1.2665 0.92 2491 136 0.3523 0.3457 REMARK 3 29 1.2665 - 1.2520 0.67 1804 82 0.3735 0.3909 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.780 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.26 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 18 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESID 36:45) REMARK 3 ORIGIN FOR THE GROUP (A): 15.0705 19.8756 -7.5825 REMARK 3 T TENSOR REMARK 3 T11: 0.1532 T22: 0.3996 REMARK 3 T33: 0.3242 T12: 0.0354 REMARK 3 T13: 0.0200 T23: 0.0496 REMARK 3 L TENSOR REMARK 3 L11: 4.3898 L22: 4.5340 REMARK 3 L33: 6.3494 L12: -2.1219 REMARK 3 L13: 5.2325 L23: -1.8128 REMARK 3 S TENSOR REMARK 3 S11: -0.5489 S12: -0.9879 S13: -0.1248 REMARK 3 S21: 0.5079 S22: 0.3605 S23: -0.1942 REMARK 3 S31: -0.3866 S32: -0.8137 S33: -0.0149 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 46:58) REMARK 3 ORIGIN FOR THE GROUP (A): -3.3508 22.0978 -29.6324 REMARK 3 T TENSOR REMARK 3 T11: 0.2463 T22: 0.3862 REMARK 3 T33: 0.1225 T12: -0.0751 REMARK 3 T13: 0.0588 T23: -0.0041 REMARK 3 L TENSOR REMARK 3 L11: 5.1085 L22: 4.9552 REMARK 3 L33: 7.4480 L12: -1.4128 REMARK 3 L13: 5.4437 L23: 0.6351 REMARK 3 S TENSOR REMARK 3 S11: -0.2738 S12: 0.8793 S13: 0.1626 REMARK 3 S21: -0.6832 S22: -0.0564 S23: -0.0846 REMARK 3 S31: 0.0424 S32: 0.1898 S33: 0.2831 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 59:72) REMARK 3 ORIGIN FOR THE GROUP (A): -10.3048 26.1070 -15.0118 REMARK 3 T TENSOR REMARK 3 T11: 0.1290 T22: 0.1199 REMARK 3 T33: 0.1654 T12: 0.0049 REMARK 3 T13: -0.0442 T23: -0.0008 REMARK 3 L TENSOR REMARK 3 L11: 2.9932 L22: 2.4739 REMARK 3 L33: 8.0647 L12: -0.5226 REMARK 3 L13: 0.1485 L23: 0.8830 REMARK 3 S TENSOR REMARK 3 S11: -0.1274 S12: 0.0941 S13: 0.2397 REMARK 3 S21: -0.1206 S22: 0.0618 S23: 0.0071 REMARK 3 S31: -0.1608 S32: -0.2519 S33: 0.1009 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN A AND RESID 73:77) REMARK 3 ORIGIN FOR THE GROUP (A): -10.0449 35.6735 -2.6012 REMARK 3 T TENSOR REMARK 3 T11: 0.3252 T22: 0.2217 REMARK 3 T33: 0.3337 T12: 0.0518 REMARK 3 T13: -0.0597 T23: -0.1383 REMARK 3 L TENSOR REMARK 3 L11: 1.4725 L22: 6.7312 REMARK 3 L33: 4.6339 L12: 1.2856 REMARK 3 L13: -1.1415 L23: -1.7931 REMARK 3 S TENSOR REMARK 3 S11: 0.1570 S12: -0.5928 S13: 0.9282 REMARK 3 S21: 0.7126 S22: -0.0428 S23: 0.1132 REMARK 3 S31: -1.1000 S32: 0.0961 S33: -0.4386 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN A AND RESID 78:100) REMARK 3 ORIGIN FOR THE GROUP (A): -10.7776 30.9760 -11.0391 REMARK 3 T TENSOR REMARK 3 T11: 0.1527 T22: 0.1127 REMARK 3 T33: 0.2325 T12: 0.0398 REMARK 3 T13: -0.0567 T23: -0.0184 REMARK 3 L TENSOR REMARK 3 L11: 3.2069 L22: 3.3672 REMARK 3 L33: 6.6793 L12: 0.1509 REMARK 3 L13: -0.3573 L23: -0.2265 REMARK 3 S TENSOR REMARK 3 S11: -0.0832 S12: -0.0085 S13: 0.4853 REMARK 3 S21: 0.0236 S22: 0.0666 S23: 0.0006 REMARK 3 S31: -0.4733 S32: -0.0085 S33: -0.0180 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN A AND RESID 101:107) REMARK 3 ORIGIN FOR THE GROUP (A): -19.9851 34.1283 -0.9178 REMARK 3 T TENSOR REMARK 3 T11: 0.3645 T22: 0.2718 REMARK 3 T33: 0.4068 T12: 0.0892 REMARK 3 T13: 0.0484 T23: -0.0957 REMARK 3 L TENSOR REMARK 3 L11: 9.2845 L22: 4.9739 REMARK 3 L33: 8.8431 L12: 5.1402 REMARK 3 L13: -2.3682 L23: -5.4115 REMARK 3 S TENSOR REMARK 3 S11: 0.5124 S12: -0.4185 S13: 0.5052 REMARK 3 S21: 0.5364 S22: -0.2425 S23: 1.1205 REMARK 3 S31: -0.6957 S32: -0.2981 S33: -0.3294 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: (CHAIN A AND RESID 108:122) REMARK 3 ORIGIN FOR THE GROUP (A): -20.5427 31.9729 -10.8639 REMARK 3 T TENSOR REMARK 3 T11: 0.2908 T22: 0.1786 REMARK 3 T33: 0.2502 T12: 0.0809 REMARK 3 T13: -0.0450 T23: 0.0004 REMARK 3 L TENSOR REMARK 3 L11: 3.9097 L22: 3.1232 REMARK 3 L33: 4.1211 L12: -0.3867 REMARK 3 L13: -0.2178 L23: 0.1980 REMARK 3 S TENSOR REMARK 3 S11: -0.0123 S12: 0.1113 S13: 0.4931 REMARK 3 S21: 0.0627 S22: 0.0712 S23: 0.0588 REMARK 3 S31: -1.0577 S32: -0.4328 S33: -0.1165 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: (CHAIN A AND RESID 123:128) REMARK 3 ORIGIN FOR THE GROUP (A): -16.8285 22.9390 6.4455 REMARK 3 T TENSOR REMARK 3 T11: 0.6254 T22: 0.6107 REMARK 3 T33: 0.2271 T12: 0.0030 REMARK 3 T13: 0.0138 T23: -0.0360 REMARK 3 L TENSOR REMARK 3 L11: 9.8556 L22: 8.5921 REMARK 3 L33: 5.7357 L12: 6.3345 REMARK 3 L13: -0.4235 L23: -4.2185 REMARK 3 S TENSOR REMARK 3 S11: 1.0538 S12: -2.1750 S13: 0.2834 REMARK 3 S21: 1.8781 S22: -0.8410 S23: 0.6730 REMARK 3 S31: -1.5058 S32: -1.4246 S33: -0.0901 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: (CHAIN A AND RESID 129:160) REMARK 3 ORIGIN FOR THE GROUP (A): -21.5661 18.7077 -7.1934 REMARK 3 T TENSOR REMARK 3 T11: 0.1001 T22: 0.1638 REMARK 3 T33: 0.1777 T12: 0.0399 REMARK 3 T13: 0.0066 T23: -0.0233 REMARK 3 L TENSOR REMARK 3 L11: 4.8946 L22: 4.0039 REMARK 3 L33: 3.9316 L12: -0.2382 REMARK 3 L13: 0.7374 L23: -0.9827 REMARK 3 S TENSOR REMARK 3 S11: -0.0862 S12: -0.1560 S13: -0.2405 REMARK 3 S21: 0.0350 S22: 0.1223 S23: 0.4002 REMARK 3 S31: 0.0993 S32: -0.3533 S33: -0.0504 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: (CHAIN A AND RESID 161:165) REMARK 3 ORIGIN FOR THE GROUP (A): -23.8438 18.1304 -21.4511 REMARK 3 T TENSOR REMARK 3 T11: 0.2895 T22: 0.4084 REMARK 3 T33: 0.2663 T12: -0.0088 REMARK 3 T13: -0.0652 T23: -0.0440 REMARK 3 L TENSOR REMARK 3 L11: 3.6242 L22: 5.8104 REMARK 3 L33: 4.2708 L12: 3.3204 REMARK 3 L13: 2.9555 L23: 4.9765 REMARK 3 S TENSOR REMARK 3 S11: -0.0760 S12: 1.2144 S13: -0.1889 REMARK 3 S21: -1.1698 S22: 0.0397 S23: 0.5794 REMARK 3 S31: -0.0957 S32: -0.6492 S33: 0.0526 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: (CHAIN A AND RESID 166:185) REMARK 3 ORIGIN FOR THE GROUP (A): -9.6731 12.2809 -0.6897 REMARK 3 T TENSOR REMARK 3 T11: 0.1987 T22: 0.2021 REMARK 3 T33: 0.1877 T12: 0.0725 REMARK 3 T13: -0.0058 T23: 0.0033 REMARK 3 L TENSOR REMARK 3 L11: 5.0558 L22: 4.3101 REMARK 3 L33: 5.7742 L12: -2.6130 REMARK 3 L13: 2.7779 L23: -3.3958 REMARK 3 S TENSOR REMARK 3 S11: -0.4364 S12: -0.5205 S13: -0.0787 REMARK 3 S21: 0.5046 S22: 0.1840 S23: -0.2145 REMARK 3 S31: -0.0807 S32: 0.0173 S33: 0.2436 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: (CHAIN A AND RESID 186:189) REMARK 3 ORIGIN FOR THE GROUP (A): -12.4561 5.8982 -0.7622 REMARK 3 T TENSOR REMARK 3 T11: 0.2843 T22: 0.2200 REMARK 3 T33: 0.3490 T12: 0.0402 REMARK 3 T13: 0.0860 T23: 0.0846 REMARK 3 L TENSOR REMARK 3 L11: 4.7907 L22: 3.2551 REMARK 3 L33: 5.6345 L12: -0.0653 REMARK 3 L13: 4.3395 L23: -2.4008 REMARK 3 S TENSOR REMARK 3 S11: -0.2535 S12: -0.4141 S13: -0.6849 REMARK 3 S21: 0.5968 S22: 0.2327 S23: 0.4309 REMARK 3 S31: 0.4227 S32: 0.1059 S33: -0.0626 REMARK 3 TLS GROUP : 13 REMARK 3 SELECTION: (CHAIN A AND RESID 190:201) REMARK 3 ORIGIN FOR THE GROUP (A): -18.2162 5.3395 -10.4147 REMARK 3 T TENSOR REMARK 3 T11: 0.2047 T22: 0.1711 REMARK 3 T33: 0.3550 T12: -0.0444 REMARK 3 T13: 0.0276 T23: -0.0332 REMARK 3 L TENSOR REMARK 3 L11: 8.2716 L22: 6.7793 REMARK 3 L33: 3.0811 L12: -2.0618 REMARK 3 L13: 4.2519 L23: -1.7848 REMARK 3 S TENSOR REMARK 3 S11: -0.0059 S12: 0.2097 S13: -0.7566 REMARK 3 S21: -0.1294 S22: 0.1620 S23: 0.5905 REMARK 3 S31: 0.3423 S32: -0.3580 S33: -0.1388 REMARK 3 TLS GROUP : 14 REMARK 3 SELECTION: (CHAIN A AND RESID 202:206) REMARK 3 ORIGIN FOR THE GROUP (A): -22.2353 10.7575 -19.1610 REMARK 3 T TENSOR REMARK 3 T11: 0.2091 T22: 0.3785 REMARK 3 T33: 0.3211 T12: -0.1023 REMARK 3 T13: 0.0071 T23: -0.0817 REMARK 3 L TENSOR REMARK 3 L11: 2.2588 L22: 5.9764 REMARK 3 L33: 5.7305 L12: -0.3125 REMARK 3 L13: 3.5963 L23: -0.4288 REMARK 3 S TENSOR REMARK 3 S11: 0.0435 S12: 0.0371 S13: -0.4184 REMARK 3 S21: 0.1018 S22: 0.0357 S23: 0.8533 REMARK 3 S31: 0.3911 S32: -1.0311 S33: -0.1488 REMARK 3 TLS GROUP : 15 REMARK 3 SELECTION: (CHAIN A AND RESID 207:267) REMARK 3 ORIGIN FOR THE GROUP (A): -0.2590 10.6158 -10.9559 REMARK 3 T TENSOR REMARK 3 T11: 0.1328 T22: 0.1244 REMARK 3 T33: 0.2599 T12: 0.0304 REMARK 3 T13: -0.0021 T23: -0.0142 REMARK 3 L TENSOR REMARK 3 L11: 2.5049 L22: 1.7921 REMARK 3 L33: 1.5861 L12: 0.0541 REMARK 3 L13: -0.2986 L23: -0.2872 REMARK 3 S TENSOR REMARK 3 S11: -0.1478 S12: -0.0503 S13: -0.4973 REMARK 3 S21: 0.0199 S22: 0.0608 S23: -0.1837 REMARK 3 S31: 0.1878 S32: 0.1091 S33: 0.0632 REMARK 3 TLS GROUP : 16 REMARK 3 SELECTION: (CHAIN A AND RESID 268:272) REMARK 3 ORIGIN FOR THE GROUP (A): 6.6731 25.6037 -0.1754 REMARK 3 T TENSOR REMARK 3 T11: 0.2527 T22: 0.3296 REMARK 3 T33: 0.2895 T12: 0.0208 REMARK 3 T13: -0.1121 T23: -0.0906 REMARK 3 L TENSOR REMARK 3 L11: 3.2504 L22: 4.1323 REMARK 3 L33: 5.6779 L12: -3.4394 REMARK 3 L13: 0.0436 L23: 1.6281 REMARK 3 S TENSOR REMARK 3 S11: -0.3613 S12: -0.4754 S13: 0.6309 REMARK 3 S21: 0.2525 S22: 0.2365 S23: -0.6493 REMARK 3 S31: -0.4654 S32: 0.6526 S33: -0.0025 REMARK 3 TLS GROUP : 17 REMARK 3 SELECTION: (CHAIN A AND RESID 273:313) REMARK 3 ORIGIN FOR THE GROUP (A): -2.7607 20.1256 -15.2617 REMARK 3 T TENSOR REMARK 3 T11: 0.1225 T22: 0.1241 REMARK 3 T33: 0.1677 T12: 0.0003 REMARK 3 T13: -0.0108 T23: -0.0179 REMARK 3 L TENSOR REMARK 3 L11: 3.0451 L22: 1.5998 REMARK 3 L33: 2.6349 L12: 0.4119 REMARK 3 L13: 0.4758 L23: 0.4812 REMARK 3 S TENSOR REMARK 3 S11: -0.1142 S12: 0.1096 S13: -0.0265 REMARK 3 S21: -0.0734 S22: 0.0540 S23: -0.1211 REMARK 3 S31: -0.0275 S32: 0.0762 S33: 0.0498 REMARK 3 TLS GROUP : 18 REMARK 3 SELECTION: (CHAIN A AND RESID 314:318) REMARK 3 ORIGIN FOR THE GROUP (A): -12.1484 20.8747 -26.0331 REMARK 3 T TENSOR REMARK 3 T11: 0.1883 T22: 0.3184 REMARK 3 T33: 0.1355 T12: -0.0458 REMARK 3 T13: -0.0303 T23: -0.0146 REMARK 3 L TENSOR REMARK 3 L11: 8.4372 L22: 6.9267 REMARK 3 L33: 5.2425 L12: -0.3544 REMARK 3 L13: 6.3032 L23: 1.6450 REMARK 3 S TENSOR REMARK 3 S11: 0.0236 S12: 0.5475 S13: -0.3846 REMARK 3 S21: -0.3451 S22: 0.1759 S23: 0.2241 REMARK 3 S31: -0.1310 S32: -0.7842 S33: -0.1080 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 7TC3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-DEC-21. REMARK 100 THE DEPOSITION ID IS D_1000261506. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-MAY-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9774 REMARK 200 MONOCHROMATOR : SINGLE CRYSTAL, CYLINDRICALLY REMARK 200 BENT SI(220) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 82613 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.250 REMARK 200 RESOLUTION RANGE LOW (A) : 38.942 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 10.80 REMARK 200 R MERGE (I) : 0.04400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.27 REMARK 200 COMPLETENESS FOR SHELL (%) : 78.9 REMARK 200 DATA REDUNDANCY IN SHELL : 1.70 REMARK 200 R MERGE FOR SHELL (I) : 1.48400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 4LND REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.78 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG3350, SODIUM FORMATE, PH 7.5, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 23.32550 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 70.72100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.32550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 70.72100 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 615 LIES ON A SPECIAL POSITION. 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 GLY A 33 REMARK 465 SER A 34 REMARK 465 HIS A 35 REMARK 465 ASP A 124 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 46 OE1 OE2 REMARK 470 LYS A 58 CG CD CE NZ REMARK 470 LYS A 85 CE NZ REMARK 470 GLU A 110 CG CD OE1 OE2 REMARK 470 LYS A 125 CG CD CE NZ REMARK 470 GLU A 126 CG CD OE1 OE2 REMARK 470 ARG A 177 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 183 CG CD OE1 OE2 REMARK 470 LYS A 194 NZ REMARK 470 LYS A 224 CD CE NZ REMARK 470 LYS A 228 CE NZ REMARK 470 GLN A 245 CG CD OE1 NE2 REMARK 470 MET A 271 SD CE REMARK 470 LYS A 303 CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 650 O HOH A 802 2.15 REMARK 500 O HOH A 804 O HOH A 856 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 GLU A 110 33.97 -96.28 REMARK 500 LEU A 111 69.45 -119.99 REMARK 500 LEU A 114 53.86 -142.71 REMARK 500 SER A 129 -143.58 52.97 REMARK 500 REMARK 500 REMARK: NULL DBREF 7TC3 A 39 318 UNP P27695 APEX1_HUMAN 39 318 SEQADV 7TC3 GLY A 33 UNP P27695 EXPRESSION TAG SEQADV 7TC3 SER A 34 UNP P27695 EXPRESSION TAG SEQADV 7TC3 HIS A 35 UNP P27695 EXPRESSION TAG SEQADV 7TC3 MET A 36 UNP P27695 EXPRESSION TAG SEQADV 7TC3 ALA A 37 UNP P27695 EXPRESSION TAG SEQADV 7TC3 SER A 38 UNP P27695 EXPRESSION TAG SEQRES 1 A 286 GLY SER HIS MET ALA SER GLY GLU GLY PRO ALA LEU TYR SEQRES 2 A 286 GLU ASP PRO PRO ASP GLN LYS THR SER PRO SER GLY LYS SEQRES 3 A 286 PRO ALA THR LEU LYS ILE CYS SER TRP ASN VAL ASP GLY SEQRES 4 A 286 LEU ARG ALA TRP ILE LYS LYS LYS GLY LEU ASP TRP VAL SEQRES 5 A 286 LYS GLU GLU ALA PRO ASP ILE LEU CYS LEU GLN GLU THR SEQRES 6 A 286 LYS CYS SER GLU ASN LYS LEU PRO ALA GLU LEU GLN GLU SEQRES 7 A 286 LEU PRO GLY LEU SER HIS GLN TYR TRP SER ALA PRO SER SEQRES 8 A 286 ASP LYS GLU GLY TYR SER GLY VAL GLY LEU LEU SER ARG SEQRES 9 A 286 GLN CYS PRO LEU LYS VAL SER TYR GLY ILE GLY ASP GLU SEQRES 10 A 286 GLU HIS ASP GLN GLU GLY ARG VAL ILE VAL ALA GLU PHE SEQRES 11 A 286 ASP SER PHE VAL LEU VAL THR ALA TYR VAL PRO ASN ALA SEQRES 12 A 286 GLY ARG GLY LEU VAL ARG LEU GLU TYR ARG GLN ARG TRP SEQRES 13 A 286 ASP GLU ALA PHE ARG LYS PHE LEU LYS GLY LEU ALA SER SEQRES 14 A 286 ARG LYS PRO LEU VAL LEU CYS GLY ASP LEU ASN VAL ALA SEQRES 15 A 286 HIS GLU GLU ILE ASP LEU ARG ASN PRO LYS GLY ASN LYS SEQRES 16 A 286 LYS ASN ALA GLY PHE THR PRO GLN GLU ARG GLN GLY PHE SEQRES 17 A 286 GLY GLU LEU LEU GLN ALA VAL PRO LEU ALA ASP SER PHE SEQRES 18 A 286 ARG HIS LEU TYR PRO ASN THR PRO TYR ALA TYR THR PHE SEQRES 19 A 286 TRP THR TYR MET MET ASN ALA ARG SER LYS ASN VAL GLY SEQRES 20 A 286 TRP ARG LEU ASP TYR PHE LEU LEU SER HIS SER LEU LEU SEQRES 21 A 286 PRO ALA LEU CYS ASP SER LYS ILE ARG SER LYS ALA LEU SEQRES 22 A 286 GLY SER ASP HIS CYS PRO ILE THR LEU TYR LEU ALA LEU HET EDO A 401 4 HET EDO A 402 4 HET EDO A 403 8 HET EDO A 404 4 HET EDO A 405 4 HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 EDO 5(C2 H6 O2) FORMUL 7 HOH *376(H2 O) HELIX 1 AA1 GLY A 71 LYS A 78 1 8 HELIX 2 AA2 LYS A 79 ALA A 88 1 10 HELIX 3 AA3 PRO A 105 LEU A 111 5 7 HELIX 4 AA4 ASP A 148 ASP A 152 5 5 HELIX 5 AA5 GLY A 176 VAL A 180 5 5 HELIX 6 AA6 ARG A 181 SER A 201 1 21 HELIX 7 AA7 GLU A 216 LEU A 220 5 5 HELIX 8 AA8 THR A 233 VAL A 247 1 15 HELIX 9 AA9 SER A 252 TYR A 257 1 6 HELIX 10 AB1 ASN A 272 ASN A 277 1 6 HELIX 11 AB2 HIS A 289 PRO A 293 5 5 SHEET 1 AA1 6 HIS A 116 SER A 120 0 SHEET 2 AA1 6 VAL A 131 SER A 135 -1 O SER A 135 N HIS A 116 SHEET 3 AA1 6 ILE A 91 GLN A 95 -1 N LEU A 92 O LEU A 134 SHEET 4 AA1 6 LEU A 62 ASN A 68 1 N CYS A 65 O CYS A 93 SHEET 5 AA1 6 ILE A 312 LEU A 316 -1 O LEU A 314 N ILE A 64 SHEET 6 AA1 6 LEU A 295 ILE A 300 -1 N LYS A 299 O THR A 313 SHEET 1 AA2 6 LYS A 141 TYR A 144 0 SHEET 2 AA2 6 VAL A 157 GLU A 161 -1 O GLU A 161 N LYS A 141 SHEET 3 AA2 6 VAL A 166 TYR A 171 -1 O LEU A 167 N ALA A 160 SHEET 4 AA2 6 LEU A 205 ASP A 210 1 O CYS A 208 N VAL A 168 SHEET 5 AA2 6 ASP A 283 LEU A 287 -1 O LEU A 286 N LEU A 207 SHEET 6 AA2 6 ALA A 250 ASP A 251 -1 N ALA A 250 O LEU A 287 CISPEP 1 VAL A 247 PRO A 248 0 -6.93 CRYST1 46.651 141.442 45.264 90.00 90.00 90.00 P 21 21 2 4 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 0.021436 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007070 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022093 0.00000