HEADER HYDROLASE/DNA 05-OCT-19 6L2N TITLE CRYSTAL STRUCTURE OF THE R.PABI(Y68F-K154A)-DSDNA(GTAC-3BP-GTAC) TITLE 2 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: RE_R_PAB1 DOMAIN-CONTAINING PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (5'- COMPND 8 D(*TP*CP*AP*GP*CP*AP*GP*TP*AP*CP*TP*AP*AP*GP*TP*AP*CP*TP*GP*CP*TP*GP* COMPND 9 A)-3'); COMPND 10 CHAIN: C; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS ABYSSI (STRAIN GE5 / ORSAY); SOURCE 3 ORGANISM_TAXID: 272844; SOURCE 4 STRAIN: GE5 / ORSAY; SOURCE 5 GENE: PAB0105; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630 KEYWDS GLYCOSYLASE, COMPLEX, HYDROLASE, HYDROLASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR K.MIYAZONO,D.WANG,T.ITO,M.TANOKURA REVDAT 5 22-NOV-23 6L2N 1 REMARK REVDAT 4 27-MAY-20 6L2N 1 JRNL REVDAT 3 15-APR-20 6L2N 1 JRNL REVDAT 2 25-MAR-20 6L2N 1 REMARK REVDAT 1 18-MAR-20 6L2N 0 JRNL AUTH K.I.MIYAZONO,D.WANG,T.ITO,M.TANOKURA JRNL TITL DISTORTION OF DOUBLE-STRANDED DNA STRUCTURE BY THE BINDING JRNL TITL 2 OF THE RESTRICTION DNA GLYCOSYLASE R.PABI. JRNL REF NUCLEIC ACIDS RES. V. 48 5106 2020 JRNL REFN ESSN 1362-4962 JRNL PMID 32232412 JRNL DOI 10.1093/NAR/GKAA184 REMARK 2 REMARK 2 RESOLUTION. 2.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.12 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.84 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.510 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 3 NUMBER OF REFLECTIONS : 20891 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.230 REMARK 3 R VALUE (WORKING SET) : 0.229 REMARK 3 FREE R VALUE : 0.256 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 1980 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 41.8400 - 5.9008 0.97 2656 172 0.1781 0.2074 REMARK 3 2 5.9008 - 4.6856 0.98 2647 161 0.1832 0.2232 REMARK 3 3 4.6856 - 4.0939 0.98 2686 178 0.1808 0.2165 REMARK 3 4 4.0939 - 3.7199 0.98 2692 135 0.2223 0.3083 REMARK 3 5 3.7199 - 3.4534 0.98 2705 122 0.2273 0.2923 REMARK 3 6 3.4534 - 3.2499 0.99 2749 126 0.2564 0.2335 REMARK 3 7 3.2499 - 3.0872 0.99 2694 125 0.2883 0.3052 REMARK 3 8 3.0872 - 2.9528 0.97 2693 138 0.3065 0.2950 REMARK 3 9 2.9528 - 2.8392 0.98 2715 126 0.3309 0.3122 REMARK 3 10 2.8392 - 2.7412 0.99 2723 150 0.3194 0.3788 REMARK 3 11 2.7412 - 2.6555 1.00 2758 123 0.3404 0.3197 REMARK 3 12 2.6555 - 2.5796 0.99 2709 144 0.3726 0.3982 REMARK 3 13 2.5796 - 2.5117 0.95 2534 182 0.3618 0.3014 REMARK 3 14 2.5117 - 2.4504 0.79 2167 98 0.3837 0.4683 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.330 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 34.050 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 62.44 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 84.82 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 : 0.003 4077 REMARK 3 ANGLE : 0.602 5602 REMARK 3 CHIRALITY : 0.043 626 REMARK 3 PLANARITY : 0.003 631 REMARK 3 DIHEDRAL : 10.900 2403 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 21 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'C' AND (RESID -11 THROUGH -7 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.9513 -17.8885 -13.6084 REMARK 3 T TENSOR REMARK 3 T11: 1.3855 T22: 0.9671 REMARK 3 T33: 1.1660 T12: -0.1532 REMARK 3 T13: 0.5052 T23: -0.0232 REMARK 3 L TENSOR REMARK 3 L11: 2.0114 L22: 7.1255 REMARK 3 L33: 5.1659 L12: 0.1498 REMARK 3 L13: 6.9581 L23: 1.9450 REMARK 3 S TENSOR REMARK 3 S11: -2.6130 S12: -1.3273 S13: -0.6522 REMARK 3 S21: -1.7819 S22: 2.3368 S23: -0.1437 REMARK 3 S31: 0.5017 S32: 0.9926 S33: 0.6481 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'C' AND (RESID -6 THROUGH -2 ) REMARK 3 ORIGIN FOR THE GROUP (A): -1.6476 -29.5465 -3.7022 REMARK 3 T TENSOR REMARK 3 T11: 0.7235 T22: 0.9250 REMARK 3 T33: 0.8509 T12: 0.0259 REMARK 3 T13: 0.1466 T23: 0.0191 REMARK 3 L TENSOR REMARK 3 L11: 8.6664 L22: 7.9228 REMARK 3 L33: 3.3877 L12: 4.7625 REMARK 3 L13: -2.0212 L23: -5.0309 REMARK 3 S TENSOR REMARK 3 S11: -0.8196 S12: -0.2002 S13: 0.3270 REMARK 3 S21: -0.9331 S22: 0.2915 S23: 0.0628 REMARK 3 S31: 1.0562 S32: 0.4708 S33: 0.3868 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'C' AND (RESID -1 THROUGH 3 ) REMARK 3 ORIGIN FOR THE GROUP (A): -12.9515 -16.7554 2.3992 REMARK 3 T TENSOR REMARK 3 T11: 0.8109 T22: 1.0388 REMARK 3 T33: 0.9826 T12: 0.2213 REMARK 3 T13: 0.0562 T23: 0.1725 REMARK 3 L TENSOR REMARK 3 L11: 7.9480 L22: 5.7025 REMARK 3 L33: 5.5827 L12: -5.4147 REMARK 3 L13: 5.4425 L23: -1.5083 REMARK 3 S TENSOR REMARK 3 S11: -0.6173 S12: 0.1023 S13: -2.2031 REMARK 3 S21: 2.1993 S22: 0.4989 S23: 0.9526 REMARK 3 S31: -1.3343 S32: -0.3038 S33: 0.1536 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 4 THROUGH 11 ) REMARK 3 ORIGIN FOR THE GROUP (A): -25.9813 -4.7294 9.5473 REMARK 3 T TENSOR REMARK 3 T11: 1.0345 T22: 0.8994 REMARK 3 T33: 0.8214 T12: -0.0622 REMARK 3 T13: 0.0132 T23: -0.2446 REMARK 3 L TENSOR REMARK 3 L11: 5.7957 L22: 9.2596 REMARK 3 L33: 6.3961 L12: -2.1686 REMARK 3 L13: -4.7985 L23: 3.3576 REMARK 3 S TENSOR REMARK 3 S11: 0.9706 S12: -0.7803 S13: 0.9851 REMARK 3 S21: 0.3201 S22: 0.1040 S23: -0.9820 REMARK 3 S31: -1.5550 S32: 0.9107 S33: -0.8143 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 7 THROUGH 30 ) REMARK 3 ORIGIN FOR THE GROUP (A): 1.0248 -43.9954 -14.9867 REMARK 3 T TENSOR REMARK 3 T11: 0.5459 T22: 0.5698 REMARK 3 T33: 0.4025 T12: 0.0281 REMARK 3 T13: -0.0004 T23: 0.0470 REMARK 3 L TENSOR REMARK 3 L11: 8.3604 L22: 4.5103 REMARK 3 L33: 5.4289 L12: 5.8236 REMARK 3 L13: 1.7540 L23: 0.5075 REMARK 3 S TENSOR REMARK 3 S11: 0.0020 S12: 0.0487 S13: 0.3548 REMARK 3 S21: -0.0720 S22: 0.1939 S23: 0.0754 REMARK 3 S31: 0.0723 S32: -0.6379 S33: -0.1372 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 31 THROUGH 92 ) REMARK 3 ORIGIN FOR THE GROUP (A): 4.5636 -45.7985 -8.1329 REMARK 3 T TENSOR REMARK 3 T11: 0.5550 T22: 0.4582 REMARK 3 T33: 0.3454 T12: 0.0295 REMARK 3 T13: -0.0016 T23: 0.0136 REMARK 3 L TENSOR REMARK 3 L11: 4.3874 L22: 4.3646 REMARK 3 L33: 5.1873 L12: 2.5596 REMARK 3 L13: 0.1232 L23: 1.2937 REMARK 3 S TENSOR REMARK 3 S11: 0.2092 S12: -0.1484 S13: 0.2192 REMARK 3 S21: 0.2282 S22: 0.0150 S23: -0.1844 REMARK 3 S31: 0.2371 S32: 0.3935 S33: -0.2728 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 93 THROUGH 145 ) REMARK 3 ORIGIN FOR THE GROUP (A): 1.1857 -51.1956 11.4464 REMARK 3 T TENSOR REMARK 3 T11: 0.7616 T22: 0.5173 REMARK 3 T33: 0.3816 T12: -0.0040 REMARK 3 T13: -0.0266 T23: 0.0779 REMARK 3 L TENSOR REMARK 3 L11: 0.2315 L22: 2.2357 REMARK 3 L33: 7.4754 L12: 0.0477 REMARK 3 L13: 1.1297 L23: 2.8946 REMARK 3 S TENSOR REMARK 3 S11: 0.1484 S12: -0.2616 S13: -0.1462 REMARK 3 S21: 0.3632 S22: -0.0382 S23: -0.0124 REMARK 3 S31: 0.7506 S32: -0.2005 S33: -0.0983 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 146 THROUGH 223 ) REMARK 3 ORIGIN FOR THE GROUP (A): -0.8001 -48.6989 -4.1574 REMARK 3 T TENSOR REMARK 3 T11: 0.5691 T22: 0.4219 REMARK 3 T33: 0.3355 T12: -0.0105 REMARK 3 T13: -0.0336 T23: -0.0029 REMARK 3 L TENSOR REMARK 3 L11: 3.8098 L22: 2.2420 REMARK 3 L33: 4.3986 L12: 0.3486 REMARK 3 L13: -0.5448 L23: -0.7259 REMARK 3 S TENSOR REMARK 3 S11: 0.0919 S12: -0.0299 S13: 0.1025 REMARK 3 S21: 0.0327 S22: 0.1558 S23: -0.0527 REMARK 3 S31: 0.1821 S32: -0.1555 S33: -0.2393 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 8 THROUGH 30 ) REMARK 3 ORIGIN FOR THE GROUP (A): 1.1748 -14.0527 14.0723 REMARK 3 T TENSOR REMARK 3 T11: 1.8020 T22: 0.6665 REMARK 3 T33: 0.5443 T12: 0.1776 REMARK 3 T13: -0.0057 T23: 0.1651 REMARK 3 L TENSOR REMARK 3 L11: 4.7624 L22: 3.0445 REMARK 3 L33: 1.3897 L12: 0.3399 REMARK 3 L13: -0.7293 L23: 1.7862 REMARK 3 S TENSOR REMARK 3 S11: 0.2763 S12: 1.2920 S13: 0.6719 REMARK 3 S21: 0.2569 S22: -0.1064 S23: 0.5020 REMARK 3 S31: -2.1597 S32: -0.1546 S33: -0.1393 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 31 THROUGH 43 ) REMARK 3 ORIGIN FOR THE GROUP (A): -5.9395 -29.3104 18.0514 REMARK 3 T TENSOR REMARK 3 T11: 0.8153 T22: 0.8190 REMARK 3 T33: 0.5785 T12: 0.1505 REMARK 3 T13: -0.0645 T23: 0.0017 REMARK 3 L TENSOR REMARK 3 L11: 0.8169 L22: 3.3907 REMARK 3 L33: 6.7790 L12: -1.6337 REMARK 3 L13: 1.0711 L23: -2.4088 REMARK 3 S TENSOR REMARK 3 S11: 0.4635 S12: 0.4436 S13: -0.2953 REMARK 3 S21: -0.0004 S22: -0.0624 S23: 0.5461 REMARK 3 S31: -0.7027 S32: -1.2398 S33: -0.4331 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 44 THROUGH 55 ) REMARK 3 ORIGIN FOR THE GROUP (A): -14.6179 -21.7473 19.1760 REMARK 3 T TENSOR REMARK 3 T11: 1.3271 T22: 1.2205 REMARK 3 T33: 0.8399 T12: 0.6797 REMARK 3 T13: 0.1199 T23: 0.1205 REMARK 3 L TENSOR REMARK 3 L11: 2.6036 L22: 2.3201 REMARK 3 L33: 0.2160 L12: -0.3356 REMARK 3 L13: 0.1848 L23: 0.6448 REMARK 3 S TENSOR REMARK 3 S11: 0.4019 S12: -0.1089 S13: -0.4449 REMARK 3 S21: 0.2100 S22: 0.7608 S23: 0.3490 REMARK 3 S31: -0.7678 S32: -1.9785 S33: -0.9851 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 56 THROUGH 77 ) REMARK 3 ORIGIN FOR THE GROUP (A): 6.1841 -19.4190 16.6410 REMARK 3 T TENSOR REMARK 3 T11: 1.1516 T22: 0.5905 REMARK 3 T33: 0.5199 T12: 0.1779 REMARK 3 T13: 0.1268 T23: 0.0430 REMARK 3 L TENSOR REMARK 3 L11: 6.4843 L22: 2.4473 REMARK 3 L33: 4.9695 L12: 0.0862 REMARK 3 L13: 1.7226 L23: 0.3270 REMARK 3 S TENSOR REMARK 3 S11: -0.5425 S12: 0.4008 S13: 0.3789 REMARK 3 S21: -0.5197 S22: 0.5242 S23: -0.0970 REMARK 3 S31: -0.8808 S32: 0.0668 S33: -0.2135 REMARK 3 TLS GROUP : 13 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 78 THROUGH 92 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.6304 -8.7740 23.1702 REMARK 3 T TENSOR REMARK 3 T11: 2.7244 T22: 0.7126 REMARK 3 T33: 0.8321 T12: -0.5535 REMARK 3 T13: 0.3207 T23: -0.2187 REMARK 3 L TENSOR REMARK 3 L11: 4.2672 L22: 1.4631 REMARK 3 L33: 2.6541 L12: -2.4260 REMARK 3 L13: -2.3376 L23: 1.7010 REMARK 3 S TENSOR REMARK 3 S11: 0.6252 S12: -0.5080 S13: 2.3066 REMARK 3 S21: -0.7269 S22: 0.8019 S23: -0.3224 REMARK 3 S31: -3.5847 S32: 1.1846 S33: -0.7647 REMARK 3 TLS GROUP : 14 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 93 THROUGH 105 ) REMARK 3 ORIGIN FOR THE GROUP (A): 25.8402 -19.0956 29.4015 REMARK 3 T TENSOR REMARK 3 T11: 1.3884 T22: 1.5784 REMARK 3 T33: 0.6197 T12: -0.3716 REMARK 3 T13: 0.1690 T23: -0.0771 REMARK 3 L TENSOR REMARK 3 L11: 8.5247 L22: 7.0969 REMARK 3 L33: 2.4396 L12: 0.5221 REMARK 3 L13: 4.1128 L23: -1.3383 REMARK 3 S TENSOR REMARK 3 S11: 0.0403 S12: -1.8050 S13: -0.2434 REMARK 3 S21: 1.4348 S22: 1.1703 S23: 0.1715 REMARK 3 S31: -0.8708 S32: 1.1245 S33: -1.3242 REMARK 3 TLS GROUP : 15 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 106 THROUGH 129 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.0013 -47.9719 14.5657 REMARK 3 T TENSOR REMARK 3 T11: 0.5569 T22: 0.6014 REMARK 3 T33: 0.5163 T12: 0.1887 REMARK 3 T13: 0.0721 T23: 0.0089 REMARK 3 L TENSOR REMARK 3 L11: 4.7260 L22: 8.0882 REMARK 3 L33: 7.4833 L12: 4.4289 REMARK 3 L13: 2.8598 L23: 3.5874 REMARK 3 S TENSOR REMARK 3 S11: 0.1153 S12: -0.4156 S13: -0.8751 REMARK 3 S21: -0.6550 S22: 0.1458 S23: -1.2153 REMARK 3 S31: 0.4925 S32: 0.6226 S33: -0.2571 REMARK 3 TLS GROUP : 16 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 130 THROUGH 145 ) REMARK 3 ORIGIN FOR THE GROUP (A): 7.5504 -34.8544 22.6128 REMARK 3 T TENSOR REMARK 3 T11: 0.4764 T22: 0.5293 REMARK 3 T33: 0.3859 T12: -0.0362 REMARK 3 T13: -0.0208 T23: 0.0853 REMARK 3 L TENSOR REMARK 3 L11: 1.2094 L22: 9.8219 REMARK 3 L33: 9.9236 L12: 0.0581 REMARK 3 L13: 0.3225 L23: 3.3076 REMARK 3 S TENSOR REMARK 3 S11: 0.2701 S12: -0.0379 S13: 0.0446 REMARK 3 S21: 0.5295 S22: -0.5340 S23: -0.2696 REMARK 3 S31: -0.2862 S32: -0.1130 S33: 0.1862 REMARK 3 TLS GROUP : 17 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 146 THROUGH 159 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.9364 -32.5241 11.8244 REMARK 3 T TENSOR REMARK 3 T11: 1.0365 T22: 0.8587 REMARK 3 T33: 0.5647 T12: 0.0238 REMARK 3 T13: 0.1588 T23: -0.0253 REMARK 3 L TENSOR REMARK 3 L11: 5.1953 L22: 2.5738 REMARK 3 L33: 2.5289 L12: 0.0982 REMARK 3 L13: 0.4403 L23: 2.5114 REMARK 3 S TENSOR REMARK 3 S11: -0.3242 S12: 1.0786 S13: -0.0702 REMARK 3 S21: -0.9304 S22: 0.4930 S23: -0.6501 REMARK 3 S31: -0.1909 S32: 1.4557 S33: 0.1178 REMARK 3 TLS GROUP : 18 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 160 THROUGH 172 ) REMARK 3 ORIGIN FOR THE GROUP (A): 5.7830 -25.3834 18.9861 REMARK 3 T TENSOR REMARK 3 T11: 0.7916 T22: 0.4686 REMARK 3 T33: 0.4738 T12: 0.0469 REMARK 3 T13: 0.0545 T23: -0.0580 REMARK 3 L TENSOR REMARK 3 L11: 2.7048 L22: 7.4533 REMARK 3 L33: 7.6743 L12: -4.0053 REMARK 3 L13: 0.1159 L23: 0.3362 REMARK 3 S TENSOR REMARK 3 S11: 0.5213 S12: 0.5664 S13: -0.1694 REMARK 3 S21: -1.1371 S22: -0.0712 S23: -0.0315 REMARK 3 S31: -1.9876 S32: -0.0327 S33: -0.4944 REMARK 3 TLS GROUP : 19 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 173 THROUGH 193 ) REMARK 3 ORIGIN FOR THE GROUP (A): -6.6558 -12.3253 20.0820 REMARK 3 T TENSOR REMARK 3 T11: 2.2012 T22: 0.7458 REMARK 3 T33: 0.6877 T12: 0.7897 REMARK 3 T13: 0.1832 T23: -0.0144 REMARK 3 L TENSOR REMARK 3 L11: 4.7173 L22: 0.9197 REMARK 3 L33: 2.0710 L12: 0.3807 REMARK 3 L13: -1.6503 L23: -1.1574 REMARK 3 S TENSOR REMARK 3 S11: -1.4642 S12: 0.1774 S13: 1.2381 REMARK 3 S21: 2.2723 S22: 1.6183 S23: 0.4565 REMARK 3 S31: -2.6911 S32: -1.6142 S33: -0.3216 REMARK 3 TLS GROUP : 20 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 194 THROUGH 208 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.5435 -21.9328 24.4226 REMARK 3 T TENSOR REMARK 3 T11: 0.9389 T22: 0.7641 REMARK 3 T33: 0.4721 T12: -0.2493 REMARK 3 T13: 0.0336 T23: 0.0401 REMARK 3 L TENSOR REMARK 3 L11: 5.9319 L22: 9.0194 REMARK 3 L33: 3.5869 L12: -3.5674 REMARK 3 L13: -0.2535 L23: 0.2338 REMARK 3 S TENSOR REMARK 3 S11: -0.2798 S12: -0.7872 S13: 0.2062 REMARK 3 S21: 0.4846 S22: 0.5600 S23: -0.1160 REMARK 3 S31: -1.3944 S32: 0.7944 S33: -0.4119 REMARK 3 TLS GROUP : 21 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 209 THROUGH 223 ) REMARK 3 ORIGIN FOR THE GROUP (A): 25.1938 -19.1216 18.3965 REMARK 3 T TENSOR REMARK 3 T11: 1.1347 T22: 1.2922 REMARK 3 T33: 0.5951 T12: -0.5008 REMARK 3 T13: 0.1416 T23: -0.0846 REMARK 3 L TENSOR REMARK 3 L11: 3.4210 L22: 5.2842 REMARK 3 L33: 8.3744 L12: 0.7305 REMARK 3 L13: 0.5921 L23: 2.6524 REMARK 3 S TENSOR REMARK 3 S11: 0.1063 S12: -0.5077 S13: 0.2402 REMARK 3 S21: -0.5320 S22: -0.1254 S23: -0.7930 REMARK 3 S31: -1.0542 S32: 1.0935 S33: -0.0176 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 6L2N COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-OCT-19. REMARK 100 THE DEPOSITION ID IS D_1300014058. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-MAR-17 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : 5.9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-17A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98000 REMARK 200 MONOCHROMATOR : NULL 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 0.5.32 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20923 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.450 REMARK 200 RESOLUTION RANGE LOW (A) : 41.840 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 200 DATA REDUNDANCY : 4.700 REMARK 200 R MERGE (I) : 0.04400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.8 REMARK 200 DATA REDUNDANCY IN SHELL : 4.50 REMARK 200 R MERGE FOR SHELL (I) : 0.69100 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: MOLREP REMARK 200 STARTING MODEL: 5IFF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.96 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.46 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS PH 5.9, 51% 2-METHYL REMARK 280 -2,4-PENTANEDIOL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 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 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 93.56400 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 46.78200 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 46.78200 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 93.56400 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 14380 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 45910 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -82.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 350 BIOMT1 2 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 GLY A 224 REMARK 465 THR A 225 REMARK 465 SER A 226 REMARK 465 MET B 7 REMARK 465 PHE B 13 REMARK 465 GLU B 14 REMARK 465 ASN B 15 REMARK 465 GLY B 16 REMARK 465 LYS B 17 REMARK 465 GLY B 224 REMARK 465 THR B 225 REMARK 465 SER B 226 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 LYS A 48 -33.24 -134.94 REMARK 500 ASN A 56 9.05 81.22 REMARK 500 TYR A 74 56.33 -117.17 REMARK 500 GLU A 77 -100.97 50.56 REMARK 500 ASP B 54 -145.67 -98.16 REMARK 500 GLN B 65 93.48 -67.75 REMARK 500 ASP B 75 60.88 -169.96 REMARK 500 GLU B 77 -108.20 52.42 REMARK 500 ALA B 157 -159.44 -166.69 REMARK 500 REMARK 500 REMARK: NULL DBREF 6L2N A 8 226 UNP Q9V2B6 Q9V2B6_PYRAB 8 226 DBREF 6L2N B 8 226 UNP Q9V2B6 Q9V2B6_PYRAB 8 226 DBREF 6L2N C -11 11 PDB 6L2N 6L2N -11 11 SEQADV 6L2N MET A 7 UNP Q9V2B6 INITIATING METHIONINE SEQADV 6L2N PHE A 68 UNP Q9V2B6 TYR 68 ENGINEERED MUTATION SEQADV 6L2N ALA A 154 UNP Q9V2B6 LYS 154 ENGINEERED MUTATION SEQADV 6L2N MET B 7 UNP Q9V2B6 INITIATING METHIONINE SEQADV 6L2N PHE B 68 UNP Q9V2B6 TYR 68 ENGINEERED MUTATION SEQADV 6L2N ALA B 154 UNP Q9V2B6 LYS 154 ENGINEERED MUTATION SEQRES 1 A 220 MET GLU ALA SER VAL SER PHE GLU ASN GLY LYS ILE VAL SEQRES 2 A 220 VAL ARG LEU PRO ILE THR ARG PRO THR SER LYS ILE ARG SEQRES 3 A 220 VAL LYS LYS ILE GLU ASN GLY VAL GLY ILE PRO VAL SER SEQRES 4 A 220 THR ARG LYS LYS SER PHE PRO SER ASP GLU ASN LEU ARG SEQRES 5 A 220 ASP TYR TYR ILE GLU TRP GLN ILE SER PHE ALA ARG ASP SEQRES 6 A 220 GLY LYS TYR ASP TYR GLU LEU SER ARG MET VAL ARG LEU SEQRES 7 A 220 ALA HIS GLU HIS GLY ILE LEU THR TYR ASN ASP ILE TYR SEQRES 8 A 220 GLU LEU LEU LYS PHE ALA ASP ASP VAL LYS SER TYR LEU SEQRES 9 A 220 GLU ASP LYS GLY ILE ARG ARG GLU SER THR ASN GLU GLU SEQRES 10 A 220 LEU TYR GLY PHE ASN ILE TYR GLU ASP VAL TYR PRO VAL SEQRES 11 A 220 ALA LYS LYS GLU LEU PRO SER GLY GLU PHE ILE GLY ILE SEQRES 12 A 220 VAL LEU LYS HIS ALA GLN ARG ALA VAL GLY TYR GLN SER SEQRES 13 A 220 MET VAL TYR VAL CYS ILE PRO LEU THR ASN VAL GLU PRO SEQRES 14 A 220 SER LEU ALA GLY ARG VAL ALA ARG ARG ASN GLU VAL VAL SEQRES 15 A 220 LYS TYR GLU VAL PRO VAL ASP LEU MET LYS GLU LEU LEU SEQRES 16 A 220 LYS ALA PHE ILE ILE ALA SER GLU THR HIS LYS ASN ASP SEQRES 17 A 220 ILE VAL LYS PHE LEU ARG SER ILE ILE GLY THR SER SEQRES 1 B 220 MET GLU ALA SER VAL SER PHE GLU ASN GLY LYS ILE VAL SEQRES 2 B 220 VAL ARG LEU PRO ILE THR ARG PRO THR SER LYS ILE ARG SEQRES 3 B 220 VAL LYS LYS ILE GLU ASN GLY VAL GLY ILE PRO VAL SER SEQRES 4 B 220 THR ARG LYS LYS SER PHE PRO SER ASP GLU ASN LEU ARG SEQRES 5 B 220 ASP TYR TYR ILE GLU TRP GLN ILE SER PHE ALA ARG ASP SEQRES 6 B 220 GLY LYS TYR ASP TYR GLU LEU SER ARG MET VAL ARG LEU SEQRES 7 B 220 ALA HIS GLU HIS GLY ILE LEU THR TYR ASN ASP ILE TYR SEQRES 8 B 220 GLU LEU LEU LYS PHE ALA ASP ASP VAL LYS SER TYR LEU SEQRES 9 B 220 GLU ASP LYS GLY ILE ARG ARG GLU SER THR ASN GLU GLU SEQRES 10 B 220 LEU TYR GLY PHE ASN ILE TYR GLU ASP VAL TYR PRO VAL SEQRES 11 B 220 ALA LYS LYS GLU LEU PRO SER GLY GLU PHE ILE GLY ILE SEQRES 12 B 220 VAL LEU LYS HIS ALA GLN ARG ALA VAL GLY TYR GLN SER SEQRES 13 B 220 MET VAL TYR VAL CYS ILE PRO LEU THR ASN VAL GLU PRO SEQRES 14 B 220 SER LEU ALA GLY ARG VAL ALA ARG ARG ASN GLU VAL VAL SEQRES 15 B 220 LYS TYR GLU VAL PRO VAL ASP LEU MET LYS GLU LEU LEU SEQRES 16 B 220 LYS ALA PHE ILE ILE ALA SER GLU THR HIS LYS ASN ASP SEQRES 17 B 220 ILE VAL LYS PHE LEU ARG SER ILE ILE GLY THR SER SEQRES 1 C 23 DT DC DA DG DC DA DG DT DA DC DT DA DA SEQRES 2 C 23 DG DT DA DC DT DG DC DT DG DA HELIX 1 AA1 GLU A 77 HIS A 88 1 12 HELIX 2 AA2 THR A 92 VAL A 106 1 15 HELIX 3 AA3 TYR A 109 GLY A 114 5 6 HELIX 4 AA4 THR A 171 VAL A 173 5 3 HELIX 5 AA5 PRO A 193 SER A 208 1 16 HELIX 6 AA6 SER A 208 ILE A 223 1 16 HELIX 7 AA7 ASP B 54 ARG B 58 5 5 HELIX 8 AA8 GLU B 77 HIS B 88 1 12 HELIX 9 AA9 THR B 92 VAL B 106 1 15 HELIX 10 AB1 TYR B 109 GLY B 114 1 6 HELIX 11 AB2 THR B 171 VAL B 173 5 3 HELIX 12 AB3 PRO B 193 ILE B 206 1 14 HELIX 13 AB4 SER B 208 ILE B 223 1 16 SHEET 1 AA1 3 SER A 10 GLU A 14 0 SHEET 2 AA1 3 LYS A 17 PRO A 23 -1 O VAL A 19 N SER A 12 SHEET 3 AA1 3 VAL A 187 VAL A 192 -1 O VAL A 192 N ILE A 18 SHEET 1 AA212 VAL A 40 PRO A 43 0 SHEET 2 AA212 ILE A 31 GLU A 37 -1 N LYS A 35 O ILE A 42 SHEET 3 AA212 TYR A 60 ILE A 66 -1 O TYR A 61 N LYS A 34 SHEET 4 AA212 TYR A 160 PRO A 169 -1 O ILE A 168 N ILE A 62 SHEET 5 AA212 PHE A 146 HIS A 153 -1 N GLY A 148 O TYR A 165 SHEET 6 AA212 PHE A 127 GLU A 140 -1 N ALA A 137 O ILE A 149 SHEET 7 AA212 PHE B 127 GLU B 140 -1 O TYR B 130 N VAL A 136 SHEET 8 AA212 PHE B 146 HIS B 153 -1 O ILE B 149 N ALA B 137 SHEET 9 AA212 TYR B 160 PRO B 169 -1 O TYR B 165 N GLY B 148 SHEET 10 AA212 TYR B 60 ILE B 66 -1 N ILE B 62 O ILE B 168 SHEET 11 AA212 ILE B 31 GLU B 37 -1 N ARG B 32 O GLU B 63 SHEET 12 AA212 VAL B 40 PRO B 43 -1 O VAL B 40 N GLU B 37 SHEET 1 AA3 4 ARG A 116 LEU A 124 0 SHEET 2 AA3 4 PHE A 127 GLU A 140 -1 O GLU A 131 N GLU A 118 SHEET 3 AA3 4 PHE B 127 GLU B 140 -1 O TYR B 130 N VAL A 136 SHEET 4 AA3 4 ARG B 116 LEU B 124 -1 N LEU B 124 O PHE B 127 SHEET 1 AA4 3 SER B 10 VAL B 11 0 SHEET 2 AA4 3 VAL B 19 PRO B 23 -1 O ARG B 21 N SER B 10 SHEET 3 AA4 3 VAL B 187 GLU B 191 -1 O VAL B 188 N LEU B 22 CISPEP 1 GLU A 174 PRO A 175 0 2.16 CISPEP 2 GLU B 174 PRO B 175 0 11.03 CRYST1 83.682 83.682 140.346 90.00 90.00 120.00 P 32 2 1 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 0.011950 0.006899 0.000000 0.00000 SCALE2 0.000000 0.013799 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007125 0.00000