HEADER HYDROLASE/DNA 17-APR-14 4PD2 TITLE CRYSTAL STRUCTURE OF A COMPLEX BETWEEN A C248GH LLFPG MUTANT AND A THF TITLE 2 CONTAINING DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: FORMAMIDOPYRIMIDINE-DNA GLYCOSYLASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: FAPY-DNA GLYCOSYLASE,DNA-(APURINIC OR APYRIMIDINIC SITE) COMPND 5 LYASE MUTM,AP LYASE MUTM; COMPND 6 EC: 3.2.2.23; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: DNA (5'-D(*CP*TP*CP*TP*TP*TP*(3DR)P*TP*TP*TP*CP*TP*CP*G)- COMPND 11 3'); COMPND 12 CHAIN: B; COMPND 13 ENGINEERED: YES; COMPND 14 MOL_ID: 3; COMPND 15 MOLECULE: DNA (5'-D(*GP*CP*GP*AP*GP*AP*AP*AP*CP*AP*AP*AP*GP*A)-3'); COMPND 16 CHAIN: C; COMPND 17 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LACTOCOCCUS LACTIS SUBSP. CREMORIS; SOURCE 3 ORGANISM_TAXID: 1359; SOURCE 4 GENE: MUTM, FPG; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 10 ORGANISM_TAXID: 32630; SOURCE 11 MOL_ID: 3; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630 KEYWDS DNA GLYCOSYLASE, HYDROLASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR F.COSTE,B.CASTAING REVDAT 2 27-SEP-23 4PD2 1 SOURCE JRNL REMARK REVDAT 1 01-APR-15 4PD2 0 JRNL AUTH A.BIELA,F.COSTE,F.CULARD,M.GUERIN,S.GOFFINONT,K.GASTEIGER, JRNL AUTH 2 J.CIESLA,A.WINCZURA,Z.KAZIMIERCZUK,D.GASPARUTTO,T.CARELL, JRNL AUTH 3 B.TUDEK,B.CASTAING JRNL TITL ZINC FINGER OXIDATION OF FPG/NEI DNA GLYCOSYLASES BY JRNL TITL 2 2-THIOXANTHINE: BIOCHEMICAL AND X-RAY STRUCTURAL JRNL TITL 3 CHARACTERIZATION. JRNL REF NUCLEIC ACIDS RES. V. 42 10748 2014 JRNL REFN ESSN 1362-4962 JRNL PMID 25143530 JRNL DOI 10.1093/NAR/GKU613 REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.4_1496) 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) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.73 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.080 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 134864 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.154 REMARK 3 R VALUE (WORKING SET) : 0.153 REMARK 3 FREE R VALUE : 0.179 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 6837 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 45.7455 - 5.1247 0.94 4134 182 0.1380 0.1398 REMARK 3 2 5.1247 - 4.0684 0.96 4133 224 0.1041 0.1238 REMARK 3 3 4.0684 - 3.5544 0.96 4187 221 0.1222 0.1374 REMARK 3 4 3.5544 - 3.2295 0.97 4162 258 0.1297 0.1733 REMARK 3 5 3.2295 - 2.9980 0.97 4200 245 0.1508 0.1846 REMARK 3 6 2.9980 - 2.8213 0.98 4263 192 0.1699 0.1882 REMARK 3 7 2.8213 - 2.6800 0.98 4221 226 0.1742 0.2229 REMARK 3 8 2.6800 - 2.5634 0.98 4247 247 0.1701 0.2027 REMARK 3 9 2.5634 - 2.4647 0.98 4252 227 0.1594 0.2026 REMARK 3 10 2.4647 - 2.3797 0.98 4284 199 0.1528 0.1963 REMARK 3 11 2.3797 - 2.3053 0.99 4303 208 0.1547 0.1709 REMARK 3 12 2.3053 - 2.2394 0.99 4250 224 0.1488 0.1988 REMARK 3 13 2.2394 - 2.1804 0.99 4281 227 0.1416 0.1622 REMARK 3 14 2.1804 - 2.1272 0.99 4268 224 0.1480 0.1971 REMARK 3 15 2.1272 - 2.0789 0.99 4284 247 0.1575 0.1781 REMARK 3 16 2.0789 - 2.0346 0.99 4256 238 0.1622 0.1860 REMARK 3 17 2.0346 - 1.9939 0.99 4297 250 0.1520 0.1703 REMARK 3 18 1.9939 - 1.9563 0.99 4318 208 0.1576 0.1857 REMARK 3 19 1.9563 - 1.9214 0.99 4314 236 0.1599 0.1896 REMARK 3 20 1.9214 - 1.8888 0.99 4285 231 0.1737 0.2206 REMARK 3 21 1.8888 - 1.8583 0.99 4268 230 0.1828 0.1909 REMARK 3 22 1.8583 - 1.8297 0.99 4303 227 0.2003 0.2169 REMARK 3 23 1.8297 - 1.8028 0.99 4317 243 0.2188 0.2288 REMARK 3 24 1.8028 - 1.7774 0.99 4322 242 0.2327 0.2382 REMARK 3 25 1.7774 - 1.7534 0.99 4275 246 0.2410 0.2570 REMARK 3 26 1.7534 - 1.7306 0.99 4340 210 0.2388 0.2608 REMARK 3 27 1.7306 - 1.7090 1.00 4292 221 0.2438 0.2795 REMARK 3 28 1.7090 - 1.6884 1.00 4307 243 0.2523 0.2998 REMARK 3 29 1.6884 - 1.6688 1.00 4309 246 0.2821 0.2704 REMARK 3 30 1.6688 - 1.6500 1.00 4355 215 0.3027 0.3530 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) : 18.010 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.017 2840 REMARK 3 ANGLE : 1.680 3949 REMARK 3 CHIRALITY : 0.093 445 REMARK 3 PLANARITY : 0.009 407 REMARK 3 DIHEDRAL : 19.180 1122 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 16 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESID 1:20) REMARK 3 ORIGIN FOR THE GROUP (A): -2.1554 1.3795 -15.4925 REMARK 3 T TENSOR REMARK 3 T11: 0.2158 T22: 0.2188 REMARK 3 T33: 0.3196 T12: 0.0162 REMARK 3 T13: 0.0302 T23: -0.0007 REMARK 3 L TENSOR REMARK 3 L11: 0.2683 L22: 0.0994 REMARK 3 L33: 0.2265 L12: -0.1606 REMARK 3 L13: -0.0272 L23: -0.0408 REMARK 3 S TENSOR REMARK 3 S11: -0.1295 S12: 0.0763 S13: -0.2656 REMARK 3 S21: -0.1482 S22: 0.0765 S23: -0.2665 REMARK 3 S31: 0.0451 S32: 0.2008 S33: -0.0002 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 21:38) REMARK 3 ORIGIN FOR THE GROUP (A): -18.5638 8.7216 -6.3029 REMARK 3 T TENSOR REMARK 3 T11: 0.1997 T22: 0.3032 REMARK 3 T33: 0.2701 T12: 0.0090 REMARK 3 T13: 0.0083 T23: 0.0143 REMARK 3 L TENSOR REMARK 3 L11: 0.1180 L22: 0.0999 REMARK 3 L33: 0.2821 L12: 0.0519 REMARK 3 L13: 0.0084 L23: 0.0094 REMARK 3 S TENSOR REMARK 3 S11: -0.0274 S12: -0.2307 S13: -0.1318 REMARK 3 S21: 0.2152 S22: -0.0209 S23: 0.2452 REMARK 3 S31: -0.0109 S32: -0.1907 S33: 0.0003 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 39:56) REMARK 3 ORIGIN FOR THE GROUP (A): -16.1445 1.8708 -15.6597 REMARK 3 T TENSOR REMARK 3 T11: 0.1853 T22: 0.2241 REMARK 3 T33: 0.3194 T12: -0.0402 REMARK 3 T13: -0.0145 T23: 0.0086 REMARK 3 L TENSOR REMARK 3 L11: 0.2012 L22: 0.1673 REMARK 3 L33: 0.1930 L12: -0.1203 REMARK 3 L13: 0.1622 L23: -0.1922 REMARK 3 S TENSOR REMARK 3 S11: -0.0651 S12: 0.1518 S13: -0.2324 REMARK 3 S21: -0.2136 S22: 0.0958 S23: 0.1791 REMARK 3 S31: 0.0869 S32: -0.1793 S33: 0.0035 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN A AND RESID 57:83) REMARK 3 ORIGIN FOR THE GROUP (A): -9.9056 6.5140 -14.3485 REMARK 3 T TENSOR REMARK 3 T11: 0.1704 T22: 0.2105 REMARK 3 T33: 0.1977 T12: -0.0316 REMARK 3 T13: -0.0172 T23: -0.0106 REMARK 3 L TENSOR REMARK 3 L11: 0.5261 L22: 0.3813 REMARK 3 L33: 0.6350 L12: -0.3636 REMARK 3 L13: -0.4434 L23: 0.0677 REMARK 3 S TENSOR REMARK 3 S11: -0.0382 S12: 0.0358 S13: -0.2310 REMARK 3 S21: -0.0533 S22: 0.0043 S23: -0.1839 REMARK 3 S31: 0.1185 S32: -0.0389 S33: -0.0000 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN A AND RESID 84:97) REMARK 3 ORIGIN FOR THE GROUP (A): -9.6991 5.7954 0.8444 REMARK 3 T TENSOR REMARK 3 T11: 0.2740 T22: 0.2487 REMARK 3 T33: 0.2613 T12: 0.0032 REMARK 3 T13: -0.0161 T23: 0.0401 REMARK 3 L TENSOR REMARK 3 L11: 0.0237 L22: 0.0178 REMARK 3 L33: 0.0572 L12: 0.0210 REMARK 3 L13: -0.0386 L23: -0.0355 REMARK 3 S TENSOR REMARK 3 S11: 0.0262 S12: -0.0399 S13: -0.1172 REMARK 3 S21: 0.3216 S22: 0.0091 S23: 0.2798 REMARK 3 S31: -0.0003 S32: 0.0426 S33: -0.0001 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN A AND RESID 98:137) REMARK 3 ORIGIN FOR THE GROUP (A): -10.5561 9.9377 -17.9621 REMARK 3 T TENSOR REMARK 3 T11: 0.1778 T22: 0.2460 REMARK 3 T33: 0.2038 T12: -0.0073 REMARK 3 T13: -0.0190 T23: -0.0144 REMARK 3 L TENSOR REMARK 3 L11: 0.8721 L22: 0.6932 REMARK 3 L33: 0.2745 L12: -0.0292 REMARK 3 L13: -0.3928 L23: 0.0698 REMARK 3 S TENSOR REMARK 3 S11: 0.0203 S12: 0.0747 S13: -0.1557 REMARK 3 S21: -0.0111 S22: -0.0078 S23: -0.0067 REMARK 3 S31: 0.0173 S32: -0.0901 S33: 0.0000 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: (CHAIN A AND RESID 138:152) REMARK 3 ORIGIN FOR THE GROUP (A): 2.2044 18.8452 -38.8139 REMARK 3 T TENSOR REMARK 3 T11: 0.2746 T22: 0.3147 REMARK 3 T33: 0.2312 T12: -0.0600 REMARK 3 T13: -0.0148 T23: -0.0237 REMARK 3 L TENSOR REMARK 3 L11: -0.0091 L22: 0.0908 REMARK 3 L33: 0.2164 L12: 0.0078 REMARK 3 L13: 0.0137 L23: 0.1429 REMARK 3 S TENSOR REMARK 3 S11: -0.1192 S12: 0.1595 S13: -0.0843 REMARK 3 S21: -0.2980 S22: 0.0279 S23: 0.0491 REMARK 3 S31: -0.0893 S32: -0.1937 S33: -0.0000 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: (CHAIN A AND RESID 153:205) REMARK 3 ORIGIN FOR THE GROUP (A): 8.3688 21.5146 -29.2645 REMARK 3 T TENSOR REMARK 3 T11: 0.1857 T22: 0.2438 REMARK 3 T33: 0.2111 T12: -0.0284 REMARK 3 T13: 0.0084 T23: -0.0299 REMARK 3 L TENSOR REMARK 3 L11: 0.5992 L22: 0.4784 REMARK 3 L33: 0.9297 L12: 0.4862 REMARK 3 L13: 0.2921 L23: 0.0268 REMARK 3 S TENSOR REMARK 3 S11: -0.0496 S12: -0.0051 S13: 0.0331 REMARK 3 S21: -0.0404 S22: 0.0654 S23: -0.0461 REMARK 3 S31: -0.1323 S32: 0.1321 S33: 0.0000 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: (CHAIN A AND RESID 206:217) REMARK 3 ORIGIN FOR THE GROUP (A): 9.5772 6.6561 -21.7156 REMARK 3 T TENSOR REMARK 3 T11: 0.2157 T22: 0.3006 REMARK 3 T33: 0.3447 T12: -0.0016 REMARK 3 T13: 0.0210 T23: 0.0052 REMARK 3 L TENSOR REMARK 3 L11: 0.1078 L22: 0.0497 REMARK 3 L33: 0.0451 L12: -0.0574 REMARK 3 L13: -0.0053 L23: -0.0329 REMARK 3 S TENSOR REMARK 3 S11: -0.1062 S12: 0.0358 S13: -0.4795 REMARK 3 S21: 0.0913 S22: -0.0151 S23: -0.1155 REMARK 3 S31: 0.1464 S32: 0.1630 S33: -0.0005 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: (CHAIN A AND RESID 218:229) REMARK 3 ORIGIN FOR THE GROUP (A): 5.5878 6.0860 -6.7878 REMARK 3 T TENSOR REMARK 3 T11: 0.5535 T22: 0.7574 REMARK 3 T33: 0.4963 T12: 0.0341 REMARK 3 T13: -0.0358 T23: 0.0393 REMARK 3 L TENSOR REMARK 3 L11: 0.0045 L22: 0.0029 REMARK 3 L33: 0.0057 L12: 0.0051 REMARK 3 L13: 0.0055 L23: 0.0053 REMARK 3 S TENSOR REMARK 3 S11: -0.2106 S12: -0.0542 S13: -0.1894 REMARK 3 S21: 0.1854 S22: -0.0907 S23: -0.0870 REMARK 3 S31: -0.4127 S32: 0.1282 S33: -0.0005 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: (CHAIN A AND RESID 230:247) REMARK 3 ORIGIN FOR THE GROUP (A): 18.5245 16.1052 -16.1441 REMARK 3 T TENSOR REMARK 3 T11: 0.1990 T22: 0.3620 REMARK 3 T33: 0.3114 T12: -0.0242 REMARK 3 T13: -0.0231 T23: 0.0162 REMARK 3 L TENSOR REMARK 3 L11: 0.1825 L22: 0.0278 REMARK 3 L33: 0.1142 L12: 0.0805 REMARK 3 L13: 0.1359 L23: 0.0587 REMARK 3 S TENSOR REMARK 3 S11: 0.0819 S12: -0.3332 S13: -0.2727 REMARK 3 S21: 0.2438 S22: -0.0669 S23: -0.1845 REMARK 3 S31: 0.0697 S32: 0.2327 S33: 0.0003 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: (CHAIN A AND RESID 248:272) REMARK 3 ORIGIN FOR THE GROUP (A): 17.2018 26.9417 -20.7348 REMARK 3 T TENSOR REMARK 3 T11: 0.1765 T22: 0.2916 REMARK 3 T33: 0.2242 T12: -0.0541 REMARK 3 T13: 0.0046 T23: -0.0284 REMARK 3 L TENSOR REMARK 3 L11: 0.3217 L22: 0.2366 REMARK 3 L33: 0.1401 L12: 0.2313 REMARK 3 L13: 0.1543 L23: 0.0235 REMARK 3 S TENSOR REMARK 3 S11: 0.0025 S12: -0.0174 S13: 0.0095 REMARK 3 S21: 0.0266 S22: 0.0079 S23: -0.0213 REMARK 3 S31: -0.1943 S32: 0.1972 S33: 0.0012 REMARK 3 TLS GROUP : 13 REMARK 3 SELECTION: (CHAIN B AND RESID 1:8) REMARK 3 ORIGIN FOR THE GROUP (A): 3.0160 29.7597 -4.9365 REMARK 3 T TENSOR REMARK 3 T11: 0.2724 T22: 0.4062 REMARK 3 T33: 0.2780 T12: -0.0467 REMARK 3 T13: -0.0368 T23: -0.1332 REMARK 3 L TENSOR REMARK 3 L11: 0.0058 L22: 0.9259 REMARK 3 L33: 0.0049 L12: -0.0033 REMARK 3 L13: 0.0074 L23: 0.0541 REMARK 3 S TENSOR REMARK 3 S11: 0.0325 S12: -0.3062 S13: 0.1543 REMARK 3 S21: -0.1921 S22: -0.0267 S23: -0.4161 REMARK 3 S31: -0.3689 S32: 0.0144 S33: -0.0917 REMARK 3 TLS GROUP : 14 REMARK 3 SELECTION: (CHAIN B AND RESID 9:14) REMARK 3 ORIGIN FOR THE GROUP (A): -9.9957 31.9860 -19.1125 REMARK 3 T TENSOR REMARK 3 T11: 0.3451 T22: 0.3087 REMARK 3 T33: 0.4849 T12: 0.0214 REMARK 3 T13: -0.0206 T23: 0.0141 REMARK 3 L TENSOR REMARK 3 L11: 0.0317 L22: 0.0569 REMARK 3 L33: 0.0863 L12: 0.0251 REMARK 3 L13: -0.0731 L23: -0.0647 REMARK 3 S TENSOR REMARK 3 S11: 0.3314 S12: 0.3007 S13: -0.0892 REMARK 3 S21: -0.4032 S22: -0.4272 S23: 1.4810 REMARK 3 S31: -0.2798 S32: 0.2393 S33: -0.0000 REMARK 3 TLS GROUP : 15 REMARK 3 SELECTION: (CHAIN C AND RESID 15:20) REMARK 3 ORIGIN FOR THE GROUP (A): -4.3432 35.1787 -22.7498 REMARK 3 T TENSOR REMARK 3 T11: 0.5848 T22: 0.3835 REMARK 3 T33: 0.3540 T12: -0.0484 REMARK 3 T13: -0.1518 T23: 0.0666 REMARK 3 L TENSOR REMARK 3 L11: 0.0112 L22: 0.1448 REMARK 3 L33: 0.0253 L12: 0.0313 REMARK 3 L13: -0.0137 L23: -0.0055 REMARK 3 S TENSOR REMARK 3 S11: 0.0957 S12: -0.1324 S13: -0.2096 REMARK 3 S21: -0.2215 S22: -0.0353 S23: 0.0077 REMARK 3 S31: -0.3352 S32: 0.4154 S33: -0.0004 REMARK 3 TLS GROUP : 16 REMARK 3 SELECTION: (CHAIN C AND RESID 21:28) REMARK 3 ORIGIN FOR THE GROUP (A): -0.4692 26.0870 -2.2030 REMARK 3 T TENSOR REMARK 3 T11: 0.3467 T22: 0.3102 REMARK 3 T33: 0.2404 T12: -0.0727 REMARK 3 T13: -0.0262 T23: -0.0970 REMARK 3 L TENSOR REMARK 3 L11: 0.4442 L22: 1.2090 REMARK 3 L33: 1.7081 L12: 0.0160 REMARK 3 L13: 0.6886 L23: -0.8142 REMARK 3 S TENSOR REMARK 3 S11: 0.2349 S12: -0.3939 S13: 0.0494 REMARK 3 S21: 0.5004 S22: 0.1697 S23: -0.1308 REMARK 3 S31: -0.7327 S32: 0.1252 S33: 0.6404 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 4PD2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-APR-14. REMARK 100 THE DEPOSITION ID IS D_1000201179. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-FEB-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98400 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 : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 70733 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 47.560 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.1 REMARK 200 DATA REDUNDANCY : 4.900 REMARK 200 R MERGE (I) : 0.05800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.4 REMARK 200 DATA REDUNDANCY IN SHELL : 4.80 REMARK 200 R MERGE FOR SHELL (I) : 0.70500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB ENTRY 1PM5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HEPES, SODIUM CITRATE, PH 7.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 70.19450 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 45.72800 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 45.72800 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 35.09725 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 45.72800 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 45.72800 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 105.29175 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 45.72800 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 45.72800 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 35.09725 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 45.72800 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 45.72800 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 105.29175 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 70.19450 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3590 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15860 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.0 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 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 684 LIES ON A SPECIAL POSITION. 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 LYS A 15 CE NZ REMARK 470 GLN A 39 CG CD OE1 NE2 REMARK 470 LYS A 42 CD CE NZ REMARK 470 ARG A 88 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 130 CD CE NZ REMARK 470 GLU A 138 CG CD OE1 OE2 REMARK 470 LYS A 213 CD CE NZ REMARK 470 ILE A 219 CG1 CG2 CD1 REMARK 470 ARG A 220 CG CD NE CZ NH1 NH2 REMARK 470 THR A 221 OG1 CG2 REMARK 470 SER A 223 OG REMARK 470 LYS A 230 CD CE NZ REMARK 470 LYS A 257 CD CE NZ REMARK 470 LYS A 272 CD 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 617 O HOH A 643 1.97 REMARK 500 O HOH A 507 O HOH A 681 2.09 REMARK 500 OE2 GLU A 26 O HOH A 709 2.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 461 O HOH A 685 7555 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 DC B 13 O3' DC B 13 C3' -0.041 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 ARG A 74 -125.42 48.15 REMARK 500 ASP A 107 104.08 -162.48 REMARK 500 VAL A 166 144.25 -171.27 REMARK 500 VAL A 237 -35.64 -138.00 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 631 DISTANCE = 6.28 ANGSTROMS REMARK 525 HOH A 677 DISTANCE = 6.49 ANGSTROMS REMARK 525 HOH A 684 DISTANCE = 6.58 ANGSTROMS REMARK 525 HOH A 701 DISTANCE = 6.36 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 300 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 245 SG REMARK 620 2 HIS A 249 NE2 106.0 REMARK 620 3 CYS A 266 SG 109.9 112.3 REMARK 620 4 CYS A 269 SG 109.7 103.9 114.6 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 300 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4PCZ RELATED DB: PDB REMARK 900 RELATED ID: 4PDG RELATED DB: PDB REMARK 900 RELATED ID: 4PDI RELATED DB: PDB DBREF 4PD2 A 1 272 UNP P42371 FPG_LACLC 2 273 DBREF 4PD2 B 1 14 PDB 4PD2 4PD2 1 14 DBREF 4PD2 C 15 28 PDB 4PD2 4PD2 15 28 SEQADV 4PD2 A UNP P42371 ASP 139 DELETION SEQADV 4PD2 GLY A 248 UNP P42371 INSERTION SEQADV 4PD2 HIS A 249 UNP P42371 CYS 250 ENGINEERED MUTATION SEQRES 1 A 272 PRO GLU LEU PRO GLU VAL GLU THR VAL ARG ARG GLU LEU SEQRES 2 A 272 GLU LYS ARG ILE VAL GLY GLN LYS ILE ILE SER ILE GLU SEQRES 3 A 272 ALA THR TYR PRO ARG MET VAL LEU THR GLY PHE GLU GLN SEQRES 4 A 272 LEU LYS LYS GLU LEU THR GLY LYS THR ILE GLN GLY ILE SEQRES 5 A 272 SER ARG ARG GLY LYS TYR LEU ILE PHE GLU ILE GLY ASP SEQRES 6 A 272 ASP PHE ARG LEU ILE SER HIS LEU ARG MET GLU GLY LYS SEQRES 7 A 272 TYR ARG LEU ALA THR LEU ASP ALA PRO ARG GLU LYS HIS SEQRES 8 A 272 ASP HIS LEU THR MET LYS PHE ALA ASP GLY GLN LEU ILE SEQRES 9 A 272 TYR ALA ASP VAL ARG LYS PHE GLY THR TRP GLU LEU ILE SEQRES 10 A 272 SER THR ASP GLN VAL LEU PRO TYR PHE LEU LYS LYS LYS SEQRES 11 A 272 ILE GLY PRO GLU PRO THR TYR GLU ASP PHE ASP GLU LYS SEQRES 12 A 272 LEU PHE ARG GLU LYS LEU ARG LYS SER THR LYS LYS ILE SEQRES 13 A 272 LYS PRO TYR LEU LEU GLU GLN THR LEU VAL ALA GLY LEU SEQRES 14 A 272 GLY ASN ILE TYR VAL ASP GLU VAL LEU TRP LEU ALA LYS SEQRES 15 A 272 ILE HIS PRO GLU LYS GLU THR ASN GLN LEU ILE GLU SER SEQRES 16 A 272 SER ILE HIS LEU LEU HIS ASP SER ILE ILE GLU ILE LEU SEQRES 17 A 272 GLN LYS ALA ILE LYS LEU GLY GLY SER SER ILE ARG THR SEQRES 18 A 272 TYR SER ALA LEU GLY SER THR GLY LYS MET GLN ASN GLU SEQRES 19 A 272 LEU GLN VAL TYR GLY LYS THR GLY GLU LYS CYS SER ARG SEQRES 20 A 272 GLY HIS GLY ALA GLU ILE GLN LYS ILE LYS VAL ALA GLY SEQRES 21 A 272 ARG GLY THR HIS PHE CYS PRO VAL CYS GLN GLN LYS SEQRES 1 B 14 DC DT DC DT DT DT 3DR DT DT DT DC DT DC SEQRES 2 B 14 DG SEQRES 1 C 14 DG DC DG DA DG DA DA DA DC DA DA DA DG SEQRES 2 C 14 DA HET 3DR B 7 11 HET ZN A 300 1 HETNAM 3DR 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE HETNAM ZN ZINC ION HETSYN 3DR ABASIC DIDEOXYRIBOSE FORMUL 2 3DR C5 H11 O6 P FORMUL 4 ZN ZN 2+ FORMUL 5 HOH *368(H2 O) HELIX 1 AA1 GLU A 2 VAL A 18 1 17 HELIX 2 AA2 TYR A 29 VAL A 33 5 5 HELIX 3 AA3 GLY A 36 THR A 45 1 10 HELIX 4 AA4 GLN A 121 LYS A 129 1 9 HELIX 5 AA5 ASP A 141 SER A 152 1 12 HELIX 6 AA6 LYS A 155 GLU A 162 1 8 HELIX 7 AA7 GLY A 170 ALA A 181 1 12 HELIX 8 AA8 GLU A 188 LEU A 192 5 5 HELIX 9 AA9 ILE A 193 LEU A 214 1 22 HELIX 10 AB1 LYS A 230 LEU A 235 5 6 SHEET 1 AA1 4 SER A 24 ALA A 27 0 SHEET 2 AA1 4 ASP A 92 LYS A 97 -1 O LYS A 97 N SER A 24 SHEET 3 AA1 4 GLN A 102 ALA A 106 -1 O TYR A 105 N HIS A 93 SHEET 4 AA1 4 LYS A 78 ALA A 82 -1 N LYS A 78 O ALA A 106 SHEET 1 AA2 4 ILE A 49 ARG A 55 0 SHEET 2 AA2 4 TYR A 58 ILE A 63 -1 O GLU A 62 N GLN A 50 SHEET 3 AA2 4 PHE A 67 HIS A 72 -1 O SER A 71 N LEU A 59 SHEET 4 AA2 4 THR A 113 SER A 118 -1 O GLU A 115 N ILE A 70 SHEET 1 AA3 2 GLN A 254 VAL A 258 0 SHEET 2 AA3 2 ARG A 261 PHE A 265 -1 O PHE A 265 N GLN A 254 LINK O3' DT B 6 P 3DR B 7 1555 1555 1.62 LINK O3' 3DR B 7 P DT B 8 1555 1555 1.59 LINK SG CYS A 245 ZN ZN A 300 1555 1555 2.31 LINK NE2 HIS A 249 ZN ZN A 300 1555 1555 2.06 LINK SG CYS A 266 ZN ZN A 300 1555 1555 2.29 LINK SG CYS A 269 ZN ZN A 300 1555 1555 2.32 SITE 1 AC1 4 CYS A 245 HIS A 249 CYS A 266 CYS A 269 CRYST1 91.456 91.456 140.389 90.00 90.00 90.00 P 41 21 2 8 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 0.010934 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010934 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007123 0.00000