HEADER HYDROLASE 14-MAY-19 6RP7 TITLE THE CRYSTAL STRUCTURE OF A COMPLEX BETWEEN THE LLFPG PROTEIN, A THF- TITLE 2 DNA AND AN INHIBITOR 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: 3.2.2.23,4.2.99.18; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA (5'-D(*CP*TP*CP*TP*TP*TP*(3DR)P*TP*TP*TP*CP*TP*CP*G)- COMPND 10 3'); COMPND 11 CHAIN: D; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: DNA (5'-D(*GP*CP*GP*AP*GP*AP*AP*AP*CP*AP*AP*AP*GP*A)-3'); COMPND 15 CHAIN: E; COMPND 16 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LACTOCOCCUS LACTIS SUBSP. CREMORIS; SOURCE 3 ORGANISM_TAXID: 1359; SOURCE 4 GENE: MUTM, FPG, NCDO763_0992; 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 COMPLEX, INHIBITOR, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR F.COSTE,S.GOFFINONT,B.CASTAING REVDAT 2 24-JAN-24 6RP7 1 REMARK REVDAT 1 15-APR-20 6RP7 0 JRNL AUTH C.RIEUX,S.GOFFINONT,F.COSTE,Z.TBER,J.CROS,V.ROY,M.GUERIN, JRNL AUTH 2 V.GAUDON,S.BOURG,A.BIELA,V.AUCAGNE,L.AGROFOGLIO,N.GARNIER, JRNL AUTH 3 B.CASTAING JRNL TITL THIOPURINE DERIVATIVE-INDUCED FPG/NEI DNA GLYCOSYLASE JRNL TITL 2 INHIBITION: STRUCTURAL, DYNAMIC AND FUNCTIONAL INSIGHTS. JRNL REF INT J MOL SCI V. 21 2020 JRNL REFN ESSN 1422-0067 JRNL PMID 32192183 JRNL DOI 10.3390/IJMS21062058 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.83 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.120 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 77466 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.167 REMARK 3 R VALUE (WORKING SET) : 0.166 REMARK 3 FREE R VALUE : 0.186 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.940 REMARK 3 FREE R VALUE TEST SET COUNT : 3827 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 45.8465 - 5.9957 0.99 2729 120 0.1551 0.1374 REMARK 3 2 5.9957 - 4.7606 0.99 2733 117 0.1308 0.1568 REMARK 3 3 4.7606 - 4.1593 1.00 2720 149 0.1165 0.1293 REMARK 3 4 4.1593 - 3.7792 0.99 2697 164 0.1359 0.1352 REMARK 3 5 3.7792 - 3.5084 1.00 2735 114 0.1434 0.1858 REMARK 3 6 3.5084 - 3.3016 1.00 2723 133 0.1494 0.2011 REMARK 3 7 3.3016 - 3.1363 1.00 2758 140 0.1740 0.1646 REMARK 3 8 3.1363 - 2.9998 1.00 2731 119 0.1886 0.2150 REMARK 3 9 2.9998 - 2.8843 1.00 2714 163 0.2023 0.2326 REMARK 3 10 2.8843 - 2.7848 1.00 2736 131 0.2017 0.2888 REMARK 3 11 2.7848 - 2.6978 1.00 2737 117 0.2039 0.2235 REMARK 3 12 2.6978 - 2.6207 1.00 2716 163 0.2129 0.2430 REMARK 3 13 2.6207 - 2.5517 1.00 2754 135 0.1982 0.2575 REMARK 3 14 2.5517 - 2.4894 1.00 2732 125 0.1813 0.2046 REMARK 3 15 2.4894 - 2.4328 1.00 2726 157 0.1766 0.1766 REMARK 3 16 2.4328 - 2.3811 1.00 2761 147 0.1653 0.2098 REMARK 3 17 2.3811 - 2.3334 1.00 2697 157 0.1781 0.1883 REMARK 3 18 2.3334 - 2.2894 1.00 2698 171 0.1956 0.2245 REMARK 3 19 2.2894 - 2.2485 1.00 2702 149 0.1949 0.2338 REMARK 3 20 2.2485 - 2.2104 1.00 2737 157 0.1988 0.2148 REMARK 3 21 2.2104 - 2.1747 1.00 2723 129 0.2155 0.2156 REMARK 3 22 2.1747 - 2.1413 1.00 2740 144 0.2314 0.2746 REMARK 3 23 2.1413 - 2.1098 1.00 2736 154 0.2403 0.2421 REMARK 3 24 2.1098 - 2.0801 1.00 2723 128 0.2632 0.2735 REMARK 3 25 2.0801 - 2.0520 1.00 2720 137 0.2748 0.2954 REMARK 3 26 2.0520 - 2.0253 1.00 2725 158 0.2883 0.3072 REMARK 3 27 2.0253 - 2.0000 1.00 2736 149 0.3007 0.2863 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) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.450 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 52.56 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 : 12 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 1 THROUGH 14 ) REMARK 3 ORIGIN FOR THE GROUP (A): -30.7904 3.3472 11.4790 REMARK 3 T TENSOR REMARK 3 T11: 0.4729 T22: 0.4970 REMARK 3 T33: 0.4752 T12: 0.0212 REMARK 3 T13: -0.0477 T23: -0.0241 REMARK 3 L TENSOR REMARK 3 L11: 4.0673 L22: 3.2710 REMARK 3 L33: 2.9279 L12: 0.2579 REMARK 3 L13: 1.4599 L23: -0.6869 REMARK 3 S TENSOR REMARK 3 S11: -0.1934 S12: -0.2365 S13: 0.2702 REMARK 3 S21: -0.3164 S22: 0.1584 S23: 0.6984 REMARK 3 S31: -0.2479 S32: -0.8954 S33: 0.0631 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'E' AND (RESID 15 THROUGH 22 ) REMARK 3 ORIGIN FOR THE GROUP (A): -33.6307 6.0206 19.3993 REMARK 3 T TENSOR REMARK 3 T11: 0.4816 T22: 0.8601 REMARK 3 T33: 0.5251 T12: 0.1416 REMARK 3 T13: -0.0130 T23: -0.0984 REMARK 3 L TENSOR REMARK 3 L11: 8.1515 L22: 8.1927 REMARK 3 L33: 4.4302 L12: 4.4227 REMARK 3 L13: -5.9019 L23: -2.5898 REMARK 3 S TENSOR REMARK 3 S11: -0.4342 S12: 0.2969 S13: 0.5194 REMARK 3 S21: -0.0929 S22: 0.2428 S23: 0.0642 REMARK 3 S31: 1.1135 S32: -0.9875 S33: 0.3189 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'E' AND (RESID 23 THROUGH 28 ) REMARK 3 ORIGIN FOR THE GROUP (A): -25.1976 -1.8942 -0.2161 REMARK 3 T TENSOR REMARK 3 T11: 0.7080 T22: 0.5553 REMARK 3 T33: 0.5972 T12: -0.0684 REMARK 3 T13: -0.1588 T23: -0.1015 REMARK 3 L TENSOR REMARK 3 L11: 3.6850 L22: 9.6982 REMARK 3 L33: 2.5227 L12: 5.4804 REMARK 3 L13: 0.9295 L23: 2.8883 REMARK 3 S TENSOR REMARK 3 S11: -0.0055 S12: 0.4896 S13: -1.0171 REMARK 3 S21: -1.1166 S22: 0.1282 S23: 0.0854 REMARK 3 S31: 0.7055 S32: -0.6145 S33: -0.1314 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 16 ) REMARK 3 ORIGIN FOR THE GROUP (A): -3.3309 0.5114 16.5139 REMARK 3 T TENSOR REMARK 3 T11: 0.3818 T22: 0.3222 REMARK 3 T33: 0.5199 T12: 0.0413 REMARK 3 T13: 0.0035 T23: 0.0776 REMARK 3 L TENSOR REMARK 3 L11: 8.6113 L22: 2.8065 REMARK 3 L33: 3.6979 L12: 1.3023 REMARK 3 L13: -2.0338 L23: 0.1456 REMARK 3 S TENSOR REMARK 3 S11: 0.1271 S12: -0.2090 S13: -0.6382 REMARK 3 S21: 0.0060 S22: -0.1400 S23: -0.3685 REMARK 3 S31: 0.2549 S32: 0.1432 S33: 0.0362 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 17 THROUGH 72 ) REMARK 3 ORIGIN FOR THE GROUP (A): -4.3984 15.8404 13.7876 REMARK 3 T TENSOR REMARK 3 T11: 0.4343 T22: 0.2741 REMARK 3 T33: 0.3651 T12: -0.0178 REMARK 3 T13: 0.0240 T23: -0.0217 REMARK 3 L TENSOR REMARK 3 L11: 3.2171 L22: 2.6615 REMARK 3 L33: 2.5124 L12: 0.4624 REMARK 3 L13: -0.7616 L23: -0.8462 REMARK 3 S TENSOR REMARK 3 S11: 0.2132 S12: -0.1365 S13: 0.2876 REMARK 3 S21: 0.0239 S22: -0.2010 S23: -0.2887 REMARK 3 S31: -0.3563 S32: 0.2243 S33: 0.0025 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 73 THROUGH 91 ) REMARK 3 ORIGIN FOR THE GROUP (A): -7.5428 5.5546 2.7691 REMARK 3 T TENSOR REMARK 3 T11: 0.4064 T22: 0.3244 REMARK 3 T33: 0.3693 T12: 0.0201 REMARK 3 T13: -0.0008 T23: -0.0533 REMARK 3 L TENSOR REMARK 3 L11: 5.5850 L22: 1.7943 REMARK 3 L33: 8.5458 L12: 0.2691 REMARK 3 L13: -4.7662 L23: -1.5034 REMARK 3 S TENSOR REMARK 3 S11: -0.0764 S12: 0.7357 S13: -0.1662 REMARK 3 S21: -0.2718 S22: 0.0845 S23: -0.0886 REMARK 3 S31: 0.3601 S32: -0.3568 S33: -0.0236 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 92 THROUGH 141 ) REMARK 3 ORIGIN FOR THE GROUP (A): -9.5144 9.9060 17.6741 REMARK 3 T TENSOR REMARK 3 T11: 0.3677 T22: 0.2992 REMARK 3 T33: 0.3702 T12: 0.0094 REMARK 3 T13: -0.0002 T23: -0.0216 REMARK 3 L TENSOR REMARK 3 L11: 1.3796 L22: 1.3709 REMARK 3 L33: 2.2160 L12: 0.4790 REMARK 3 L13: -0.4725 L23: -0.4291 REMARK 3 S TENSOR REMARK 3 S11: 0.1530 S12: -0.1326 S13: -0.0566 REMARK 3 S21: 0.1165 S22: -0.1273 S23: -0.1670 REMARK 3 S31: -0.2026 S32: 0.0932 S33: -0.0243 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 142 THROUGH 193 ) REMARK 3 ORIGIN FOR THE GROUP (A): -23.0465 -6.0943 30.5460 REMARK 3 T TENSOR REMARK 3 T11: 0.3336 T22: 0.3472 REMARK 3 T33: 0.3873 T12: -0.0914 REMARK 3 T13: -0.0251 T23: 0.0242 REMARK 3 L TENSOR REMARK 3 L11: 2.6252 L22: 3.5555 REMARK 3 L33: 8.0363 L12: 0.5138 REMARK 3 L13: -0.8092 L23: 1.1947 REMARK 3 S TENSOR REMARK 3 S11: 0.0942 S12: -0.2462 S13: -0.1567 REMARK 3 S21: 0.2318 S22: -0.2303 S23: 0.1204 REMARK 3 S31: 0.3890 S32: -0.5835 S33: 0.1489 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 194 THROUGH 213 ) REMARK 3 ORIGIN FOR THE GROUP (A): -12.4918 -10.3143 30.7261 REMARK 3 T TENSOR REMARK 3 T11: 0.4824 T22: 0.3594 REMARK 3 T33: 0.4999 T12: -0.0074 REMARK 3 T13: -0.0696 T23: 0.0957 REMARK 3 L TENSOR REMARK 3 L11: 5.3574 L22: 5.0297 REMARK 3 L33: 4.6087 L12: 4.0153 REMARK 3 L13: -4.8518 L23: -3.5824 REMARK 3 S TENSOR REMARK 3 S11: -0.1247 S12: -0.9566 S13: -0.5044 REMARK 3 S21: 0.2982 S22: -0.3436 S23: -0.5803 REMARK 3 S31: 0.4887 S32: 1.0939 S33: 0.4081 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 214 THROUGH 239 ) REMARK 3 ORIGIN FOR THE GROUP (A): -9.6279 -10.9425 13.2261 REMARK 3 T TENSOR REMARK 3 T11: 0.7344 T22: 0.4620 REMARK 3 T33: 0.7082 T12: 0.0207 REMARK 3 T13: 0.0924 T23: -0.0592 REMARK 3 L TENSOR REMARK 3 L11: 6.5099 L22: 8.5086 REMARK 3 L33: 0.2813 L12: 6.2237 REMARK 3 L13: 1.3174 L23: 1.5240 REMARK 3 S TENSOR REMARK 3 S11: -0.5195 S12: 0.4211 S13: -1.1430 REMARK 3 S21: -0.7471 S22: 0.3358 S23: -1.0916 REMARK 3 S31: 0.6501 S32: 0.1505 S33: 0.2210 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 240 THROUGH 257 ) REMARK 3 ORIGIN FOR THE GROUP (A): -25.4566 -19.9779 16.8680 REMARK 3 T TENSOR REMARK 3 T11: 0.6534 T22: 0.4698 REMARK 3 T33: 0.6801 T12: -0.1327 REMARK 3 T13: 0.0510 T23: -0.0038 REMARK 3 L TENSOR REMARK 3 L11: 6.9126 L22: 2.9161 REMARK 3 L33: 4.2725 L12: -4.3753 REMARK 3 L13: -5.3351 L23: 3.5336 REMARK 3 S TENSOR REMARK 3 S11: -0.5956 S12: -0.4916 S13: -1.6754 REMARK 3 S21: -0.5184 S22: 0.2011 S23: 0.9551 REMARK 3 S31: 0.9971 S32: -0.1527 S33: 0.3019 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 258 THROUGH 271 ) REMARK 3 ORIGIN FOR THE GROUP (A): -27.4726 -14.5690 22.5884 REMARK 3 T TENSOR REMARK 3 T11: 0.5824 T22: 0.4506 REMARK 3 T33: 0.5450 T12: -0.1529 REMARK 3 T13: 0.0124 T23: -0.0539 REMARK 3 L TENSOR REMARK 3 L11: 4.5938 L22: 5.2343 REMARK 3 L33: 4.0336 L12: 1.6435 REMARK 3 L13: -1.5100 L23: -4.4530 REMARK 3 S TENSOR REMARK 3 S11: 0.1415 S12: 0.0500 S13: -0.6290 REMARK 3 S21: 0.6440 S22: -0.4852 S23: 0.0070 REMARK 3 S31: 0.0796 S32: 0.0787 S33: 0.2709 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 6RP7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-MAY-19. REMARK 100 THE DEPOSITION ID IS D_1292102346. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-JUL-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97857 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 : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41266 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 47.720 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : 0.06400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 5.80 REMARK 200 R MERGE FOR SHELL (I) : NULL 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: 1PM5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 67.63 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HEPES, CITRATE, VAPOR DIFFUSION, REMARK 280 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 70.52150 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 45.83450 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 45.83450 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 35.26075 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 45.83450 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 45.83450 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 105.78225 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 45.83450 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 45.83450 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 35.26075 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 45.83450 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 45.83450 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 105.78225 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 70.52150 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: 4090 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15630 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, D, E 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 ILE A 219 REMARK 465 ARG A 220 REMARK 465 THR A 221 REMARK 465 TYR A 222 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 12 CG CD OE1 OE2 REMARK 470 LYS A 15 CD CE NZ REMARK 470 ARG A 31 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 38 CG CD OE1 OE2 REMARK 470 ARG A 88 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 130 CE NZ REMARK 470 GLU A 138 CG CD OE1 OE2 REMARK 470 LYS A 230 CD CE NZ REMARK 470 LYS A 240 CE NZ REMARK 470 LYS A 244 CG CD CE NZ REMARK 470 ARG A 247 CG CD NE CZ NH1 NH2 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 NZ LYS A 256 O HOH A 401 2.13 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 -122.14 48.13 REMARK 500 GLU A 76 11.10 -142.27 REMARK 500 ASP A 107 101.59 -164.39 REMARK 500 VAL A 237 -37.62 -133.31 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 GOL A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue KD8 D 101 DBREF1 6RP7 A 1 271 UNP A0A165FVI1_LACLC DBREF2 6RP7 A A0A165FVI1 2 272 DBREF 6RP7 D 1 14 PDB 6RP7 6RP7 1 14 DBREF 6RP7 E 15 28 PDB 6RP7 6RP7 15 28 SEQRES 1 A 271 PRO GLU LEU PRO GLU VAL GLU THR VAL ARG ARG GLU LEU SEQRES 2 A 271 GLU LYS ARG ILE VAL GLY GLN LYS ILE ILE SER ILE GLU SEQRES 3 A 271 ALA THR TYR PRO ARG MET VAL LEU THR GLY PHE GLU GLN SEQRES 4 A 271 LEU LYS LYS GLU LEU THR GLY LYS THR ILE GLN GLY ILE SEQRES 5 A 271 SER ARG ARG GLY LYS TYR LEU ILE PHE GLU ILE GLY ASP SEQRES 6 A 271 ASP PHE ARG LEU ILE SER HIS LEU ARG MET GLU GLY LYS SEQRES 7 A 271 TYR ARG LEU ALA THR LEU ASP ALA PRO ARG GLU LYS HIS SEQRES 8 A 271 ASP HIS LEU THR MET LYS PHE ALA ASP GLY GLN LEU ILE SEQRES 9 A 271 TYR ALA ASP VAL ARG LYS PHE GLY THR TRP GLU LEU ILE SEQRES 10 A 271 SER THR ASP GLN VAL LEU PRO TYR PHE LEU LYS LYS LYS SEQRES 11 A 271 ILE GLY PRO GLU PRO THR TYR GLU ASP PHE ASP GLU LYS SEQRES 12 A 271 LEU PHE ARG GLU LYS LEU ARG LYS SER THR LYS LYS ILE SEQRES 13 A 271 LYS PRO TYR LEU LEU GLU GLN THR LEU VAL ALA GLY LEU SEQRES 14 A 271 GLY ASN ILE TYR VAL ASP GLU VAL LEU TRP LEU ALA LYS SEQRES 15 A 271 ILE HIS PRO GLU LYS GLU THR ASN GLN LEU ILE GLU SER SEQRES 16 A 271 SER ILE HIS LEU LEU HIS ASP SER ILE ILE GLU ILE LEU SEQRES 17 A 271 GLN LYS ALA ILE LYS LEU GLY GLY SER SER ILE ARG THR SEQRES 18 A 271 TYR SER ALA LEU GLY SER THR GLY LYS MET GLN ASN GLU SEQRES 19 A 271 LEU GLN VAL TYR GLY LYS THR GLY GLU LYS CYS SER ARG SEQRES 20 A 271 CYS GLY ALA GLU ILE GLN LYS ILE LYS VAL ALA GLY ARG SEQRES 21 A 271 GLY THR HIS PHE CYS PRO VAL CYS GLN GLN LYS SEQRES 1 D 14 DC DT DC DT DT DT 3DR DT DT DT DC DT DC SEQRES 2 D 14 DG SEQRES 1 E 14 DG DC DG DA DG DA DA DA DC DA DA DA DG SEQRES 2 E 14 DA HET 3DR D 7 11 HET GOL A 301 6 HET KD8 D 101 14 HETNAM 3DR 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE HETNAM GOL GLYCEROL HETNAM KD8 6,7-DIMETHYL-2-SULFANYLIDENE-1~{H}-PTERIDIN-4-ONE HETSYN 3DR ABASIC DIDEOXYRIBOSE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 3DR C5 H11 O6 P FORMUL 4 GOL C3 H8 O3 FORMUL 5 KD8 C8 H8 N4 O S FORMUL 6 HOH *177(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 LYS A 151 1 11 HELIX 6 AA6 LYS A 155 GLU A 162 1 8 HELIX 7 AA7 GLY A 170 LYS A 182 1 13 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 ARG A 80 O ILE A 104 SHEET 1 AA2 4 ILE A 49 ARG A 55 0 SHEET 2 AA2 4 TYR A 58 ILE A 63 -1 O ILE A 60 N SER A 53 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 253 VAL A 257 0 SHEET 2 AA3 2 ARG A 260 PHE A 264 -1 O PHE A 264 N GLN A 253 SSBOND 1 CYS A 245 CYS A 265 1555 1555 2.05 LINK O3' DT D 6 P 3DR D 7 1555 1555 1.60 LINK O3' 3DR D 7 P DT D 8 1555 1555 1.60 SITE 1 AC1 9 TYR A 58 HIS A 72 ARG A 74 THR A 113 SITE 2 AC1 9 GLU A 115 TYR A 125 LYS A 129 DT D 9 SITE 3 AC1 9 DT D 10 SITE 1 AC2 9 LEU A 161 GLU A 162 ARG A 260 HOH A 502 SITE 2 AC2 9 DT D 8 DT D 9 DT D 10 HOH D 201 SITE 3 AC2 9 HOH D 207 CRYST1 91.669 91.669 141.043 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 0.010909 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010909 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007090 0.00000