HEADER DNA BINDING PROTEIN 28-FEB-23 8IKD TITLE STRUCTURE OF DNA BINDING DOMAIN OF MCRBC ENDONUCLEASE BOUND TO DNA: TITLE 2 Y41F-L68Y DOUBLE MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: TYPE IV METHYL-DIRECTED RESTRICTION ENZYME ECOKMCRB COMPND 3 SUBUNIT; COMPND 4 CHAIN: A, B; COMPND 5 SYNONYM: ECOKMCRBC,5-METHYLCYTOSINE-SPECIFIC RESTRICTION ENZYME B; COMPND 6 EC: 3.1.21.-; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: DNA (5'-D(*GP*AP*GP*AP*CP*CP*GP*GP*TP*AP*GP*C)-3'); COMPND 11 CHAIN: C; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: DNA (5'-D(*GP*CP*TP*AP*CP*CP*GP*GP*TP*CP*TP*C)-3'); COMPND 15 CHAIN: D; COMPND 16 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI K-12; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 GENE: MCRB, RGLB, B4346, JW5871; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 ORGANISM_SCIENTIFIC: DNA MOLECULE; SOURCE 10 ORGANISM_TAXID: 2853804; SOURCE 11 MOL_ID: 3; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: DNA MOLECULE; SOURCE 14 ORGANISM_TAXID: 2853804 KEYWDS MCRB-NTD, 5-METHYLCYTOSINE, RESTRICTION ENDONUCLEASE, DNA BINDING KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR V.A.ADHAV,K.SAIKRISHNAN REVDAT 1 28-FEB-24 8IKD 0 JRNL AUTH V.A.ADHAV,K.SAIKRISHNAN JRNL TITL STRUCTURAL BASIS OF TARGET RECOGNITION BY THE DNA BINDING JRNL TITL 2 DOMAIN OF MCRBC JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.45 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.5 REMARK 3 NUMBER OF REFLECTIONS : 20237 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.770 REMARK 3 FREE R VALUE TEST SET COUNT : 1978 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 39.4500 - 5.0600 0.97 1461 184 0.1783 0.1973 REMARK 3 2 5.0600 - 4.0200 0.99 1419 140 0.1389 0.1917 REMARK 3 3 4.0200 - 3.5100 0.98 1396 151 0.1630 0.2037 REMARK 3 4 3.5100 - 3.1900 0.96 1332 150 0.1842 0.2582 REMARK 3 5 3.1900 - 2.9600 0.91 1279 134 0.2071 0.2648 REMARK 3 6 2.9600 - 2.7900 0.92 1265 137 0.2099 0.2503 REMARK 3 7 2.7900 - 2.6500 0.91 1271 139 0.2317 0.2908 REMARK 3 8 2.6500 - 2.5300 0.93 1267 133 0.2353 0.2892 REMARK 3 9 2.5300 - 2.4300 0.93 1283 140 0.2395 0.2891 REMARK 3 10 2.4300 - 2.3500 0.92 1259 138 0.2425 0.2933 REMARK 3 11 2.3500 - 2.2800 0.94 1262 144 0.2582 0.2896 REMARK 3 12 2.2800 - 2.2100 0.90 1243 125 0.3218 0.3840 REMARK 3 13 2.2100 - 2.1500 0.93 1267 142 0.2854 0.3661 REMARK 3 14 2.1500 - 2.1000 0.91 1255 121 0.3169 0.3815 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) : 0.289 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.221 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 32.05 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.55 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 : 0.002 3727 REMARK 3 ANGLE : 0.476 5253 REMARK 3 CHIRALITY : 0.036 548 REMARK 3 PLANARITY : 0.002 506 REMARK 3 DIHEDRAL : 22.424 827 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 19 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 102 THROUGH 120 ) REMARK 3 ORIGIN FOR THE GROUP (A): 6.7050 6.9702 -17.6195 REMARK 3 T TENSOR REMARK 3 T11: 0.1995 T22: 0.2847 REMARK 3 T33: 0.2670 T12: 0.0149 REMARK 3 T13: -0.0250 T23: 0.0261 REMARK 3 L TENSOR REMARK 3 L11: 6.8537 L22: 6.1404 REMARK 3 L33: 6.7903 L12: 1.8949 REMARK 3 L13: -1.0452 L23: -0.0745 REMARK 3 S TENSOR REMARK 3 S11: 0.0413 S12: 0.1827 S13: 0.4942 REMARK 3 S21: -0.0165 S22: 0.1139 S23: -0.5691 REMARK 3 S31: -0.1219 S32: 0.7966 S33: -0.1522 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 121 THROUGH 133 ) REMARK 3 ORIGIN FOR THE GROUP (A): -3.2372 11.2412 -25.3219 REMARK 3 T TENSOR REMARK 3 T11: 0.2548 T22: 0.3287 REMARK 3 T33: 0.2542 T12: -0.0097 REMARK 3 T13: 0.0118 T23: -0.0339 REMARK 3 L TENSOR REMARK 3 L11: 5.5233 L22: 6.2160 REMARK 3 L33: 2.6928 L12: -4.2082 REMARK 3 L13: 0.1423 L23: 0.4640 REMARK 3 S TENSOR REMARK 3 S11: 0.0145 S12: 0.2125 S13: 0.0699 REMARK 3 S21: -0.0047 S22: -0.3296 S23: -0.1091 REMARK 3 S31: -0.3531 S32: 0.1264 S33: 0.2726 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 134 THROUGH 151 ) REMARK 3 ORIGIN FOR THE GROUP (A): -8.3114 -1.3631 -29.4362 REMARK 3 T TENSOR REMARK 3 T11: 0.3056 T22: 0.3918 REMARK 3 T33: 0.2686 T12: -0.0564 REMARK 3 T13: 0.0198 T23: -0.0928 REMARK 3 L TENSOR REMARK 3 L11: 3.7214 L22: 4.9507 REMARK 3 L33: 3.7666 L12: -0.7659 REMARK 3 L13: 0.3982 L23: -1.2117 REMARK 3 S TENSOR REMARK 3 S11: 0.1243 S12: 0.8122 S13: -0.3233 REMARK 3 S21: -0.6474 S22: -0.1963 S23: -0.0679 REMARK 3 S31: 0.4432 S32: 0.0772 S33: 0.0140 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 2 THROUGH 13 ) REMARK 3 ORIGIN FOR THE GROUP (A): -3.9944 -2.0229 3.1692 REMARK 3 T TENSOR REMARK 3 T11: 0.5290 T22: 0.5608 REMARK 3 T33: 0.6038 T12: -0.2530 REMARK 3 T13: 0.0184 T23: 0.2073 REMARK 3 L TENSOR REMARK 3 L11: 0.7397 L22: 1.9603 REMARK 3 L33: 1.8122 L12: 0.3636 REMARK 3 L13: -0.2848 L23: -0.0371 REMARK 3 S TENSOR REMARK 3 S11: -0.1829 S12: -0.0735 S13: -0.4193 REMARK 3 S21: -0.1258 S22: 0.2910 S23: 0.0428 REMARK 3 S31: 0.5147 S32: -0.1868 S33: 0.0709 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 2 THROUGH 13 ) REMARK 3 ORIGIN FOR THE GROUP (A): -3.9830 -1.9554 3.1833 REMARK 3 T TENSOR REMARK 3 T11: 0.3747 T22: 0.3718 REMARK 3 T33: 0.1091 T12: 0.2146 REMARK 3 T13: -0.0636 T23: -0.2348 REMARK 3 L TENSOR REMARK 3 L11: 0.2563 L22: 1.0275 REMARK 3 L33: 2.9691 L12: 0.2261 REMARK 3 L13: -0.4102 L23: 0.4943 REMARK 3 S TENSOR REMARK 3 S11: -0.2074 S12: 0.0385 S13: -0.1322 REMARK 3 S21: -0.0808 S22: 0.1273 S23: -0.0636 REMARK 3 S31: 0.5366 S32: -0.0377 S33: 0.1953 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 2 THROUGH 27 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.5332 3.8165 23.2855 REMARK 3 T TENSOR REMARK 3 T11: 0.1575 T22: 0.2491 REMARK 3 T33: 0.2170 T12: -0.0312 REMARK 3 T13: -0.0164 T23: -0.0002 REMARK 3 L TENSOR REMARK 3 L11: 2.0826 L22: 2.5117 REMARK 3 L33: 4.8386 L12: 0.5413 REMARK 3 L13: -0.1481 L23: -0.8217 REMARK 3 S TENSOR REMARK 3 S11: -0.0282 S12: 0.2011 S13: 0.0424 REMARK 3 S21: 0.0333 S22: -0.0083 S23: -0.1853 REMARK 3 S31: -0.1736 S32: 0.4707 S33: 0.0068 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 28 THROUGH 38 ) REMARK 3 ORIGIN FOR THE GROUP (A): 7.1992 -9.1190 24.5825 REMARK 3 T TENSOR REMARK 3 T11: 0.2755 T22: 0.3116 REMARK 3 T33: 0.3168 T12: 0.0348 REMARK 3 T13: -0.0119 T23: 0.0340 REMARK 3 L TENSOR REMARK 3 L11: 2.4687 L22: 2.1881 REMARK 3 L33: 1.7545 L12: 0.2219 REMARK 3 L13: -0.6462 L23: 1.7983 REMARK 3 S TENSOR REMARK 3 S11: -0.1518 S12: -0.2539 S13: -0.1530 REMARK 3 S21: 0.2081 S22: 0.1644 S23: -0.0193 REMARK 3 S31: 0.3858 S32: 0.1926 S33: 0.0290 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 39 THROUGH 82 ) REMARK 3 ORIGIN FOR THE GROUP (A): -2.7442 -2.1318 21.7567 REMARK 3 T TENSOR REMARK 3 T11: 0.2228 T22: 0.1841 REMARK 3 T33: 0.1817 T12: 0.0266 REMARK 3 T13: 0.0033 T23: 0.0116 REMARK 3 L TENSOR REMARK 3 L11: 1.5557 L22: 1.4142 REMARK 3 L33: 2.4428 L12: 0.6025 REMARK 3 L13: -0.3579 L23: -0.2719 REMARK 3 S TENSOR REMARK 3 S11: -0.0613 S12: -0.0138 S13: -0.0610 REMARK 3 S21: 0.0850 S22: 0.0634 S23: -0.1756 REMARK 3 S31: 0.0670 S32: 0.1157 S33: 0.0063 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 83 THROUGH 101 ) REMARK 3 ORIGIN FOR THE GROUP (A): -11.4044 -12.7507 26.1003 REMARK 3 T TENSOR REMARK 3 T11: 0.3770 T22: 0.2814 REMARK 3 T33: 0.4274 T12: -0.1489 REMARK 3 T13: -0.0588 T23: 0.0347 REMARK 3 L TENSOR REMARK 3 L11: 3.0233 L22: 3.8477 REMARK 3 L33: 5.7822 L12: -0.7967 REMARK 3 L13: -0.9211 L23: -0.4442 REMARK 3 S TENSOR REMARK 3 S11: -0.0604 S12: -0.0865 S13: -0.7308 REMARK 3 S21: 0.3100 S22: 0.1730 S23: 0.0562 REMARK 3 S31: 0.7339 S32: -0.3117 S33: -0.1413 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 102 THROUGH 120 ) REMARK 3 ORIGIN FOR THE GROUP (A): -14.8756 1.9229 25.3779 REMARK 3 T TENSOR REMARK 3 T11: 0.1788 T22: 0.1951 REMARK 3 T33: 0.1900 T12: -0.0195 REMARK 3 T13: -0.0214 T23: 0.0136 REMARK 3 L TENSOR REMARK 3 L11: 4.6856 L22: 2.5232 REMARK 3 L33: 5.4895 L12: -1.2844 REMARK 3 L13: -2.0790 L23: 0.6414 REMARK 3 S TENSOR REMARK 3 S11: 0.1893 S12: -0.2570 S13: 0.2053 REMARK 3 S21: -0.1191 S22: 0.1027 S23: 0.1124 REMARK 3 S31: -0.1886 S32: -0.2983 S33: -0.2647 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 121 THROUGH 133 ) REMARK 3 ORIGIN FOR THE GROUP (A): -4.9219 4.5383 33.5795 REMARK 3 T TENSOR REMARK 3 T11: 0.2303 T22: 0.2428 REMARK 3 T33: 0.3053 T12: 0.0236 REMARK 3 T13: -0.0317 T23: -0.0265 REMARK 3 L TENSOR REMARK 3 L11: 4.3096 L22: 5.0710 REMARK 3 L33: 1.0591 L12: 3.7750 REMARK 3 L13: 0.2958 L23: -0.4855 REMARK 3 S TENSOR REMARK 3 S11: 0.0809 S12: -0.2554 S13: 0.1385 REMARK 3 S21: 0.4660 S22: 0.0468 S23: -0.1581 REMARK 3 S31: -0.0011 S32: -0.0708 S33: -0.1080 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 134 THROUGH 160 ) REMARK 3 ORIGIN FOR THE GROUP (A): -0.6999 -11.9101 32.4494 REMARK 3 T TENSOR REMARK 3 T11: 0.2524 T22: 0.2826 REMARK 3 T33: 0.2928 T12: 0.0143 REMARK 3 T13: -0.0181 T23: 0.0110 REMARK 3 L TENSOR REMARK 3 L11: 2.2359 L22: 2.2656 REMARK 3 L33: 1.7263 L12: -0.1700 REMARK 3 L13: -0.4436 L23: -0.6093 REMARK 3 S TENSOR REMARK 3 S11: -0.0223 S12: -0.1512 S13: -0.2823 REMARK 3 S21: 0.3533 S22: -0.0483 S23: 0.0676 REMARK 3 S31: 0.4039 S32: -0.0792 S33: 0.1024 REMARK 3 TLS GROUP : 13 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 17 ) REMARK 3 ORIGIN FOR THE GROUP (A): -16.5142 8.7394 -19.3033 REMARK 3 T TENSOR REMARK 3 T11: 0.2673 T22: 0.4436 REMARK 3 T33: 0.4182 T12: 0.1024 REMARK 3 T13: -0.0050 T23: 0.0539 REMARK 3 L TENSOR REMARK 3 L11: 3.8686 L22: 1.5000 REMARK 3 L33: 2.2809 L12: 1.2251 REMARK 3 L13: 1.7181 L23: -0.2942 REMARK 3 S TENSOR REMARK 3 S11: -0.0369 S12: 0.4915 S13: 0.3268 REMARK 3 S21: -0.2319 S22: -0.0251 S23: 0.3878 REMARK 3 S31: -0.2447 S32: -0.4068 S33: 0.0717 REMARK 3 TLS GROUP : 14 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 18 THROUGH 27 ) REMARK 3 ORIGIN FOR THE GROUP (A): -17.4772 6.1183 -9.1692 REMARK 3 T TENSOR REMARK 3 T11: 0.2235 T22: 0.3626 REMARK 3 T33: 0.2657 T12: 0.0025 REMARK 3 T13: 0.0513 T23: 0.0233 REMARK 3 L TENSOR REMARK 3 L11: 4.8908 L22: 4.6106 REMARK 3 L33: 9.2006 L12: 0.2902 REMARK 3 L13: 3.3453 L23: 4.0296 REMARK 3 S TENSOR REMARK 3 S11: 0.1471 S12: -0.2698 S13: -0.0513 REMARK 3 S21: 0.1045 S22: 0.0927 S23: 0.0269 REMARK 3 S31: 0.1914 S32: -0.5931 S33: -0.2306 REMARK 3 TLS GROUP : 15 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 28 THROUGH 38 ) REMARK 3 ORIGIN FOR THE GROUP (A): -15.2137 -4.1483 -19.4678 REMARK 3 T TENSOR REMARK 3 T11: 0.3031 T22: 0.3303 REMARK 3 T33: 0.3203 T12: -0.0304 REMARK 3 T13: -0.0013 T23: -0.0247 REMARK 3 L TENSOR REMARK 3 L11: 1.5769 L22: 2.2627 REMARK 3 L33: 3.9728 L12: -0.1698 REMARK 3 L13: -0.2983 L23: 2.1584 REMARK 3 S TENSOR REMARK 3 S11: 0.1223 S12: 0.0051 S13: -0.0572 REMARK 3 S21: -0.2460 S22: -0.0213 S23: -0.0808 REMARK 3 S31: 0.0829 S32: -0.2855 S33: -0.0790 REMARK 3 TLS GROUP : 16 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 39 THROUGH 73 ) REMARK 3 ORIGIN FOR THE GROUP (A): -6.1492 1.4321 -13.6094 REMARK 3 T TENSOR REMARK 3 T11: 0.2148 T22: 0.1633 REMARK 3 T33: 0.1649 T12: 0.0043 REMARK 3 T13: -0.0110 T23: 0.0114 REMARK 3 L TENSOR REMARK 3 L11: 1.5102 L22: 0.7457 REMARK 3 L33: 2.4642 L12: -0.1802 REMARK 3 L13: -0.1481 L23: -0.1021 REMARK 3 S TENSOR REMARK 3 S11: 0.0154 S12: -0.0535 S13: -0.1442 REMARK 3 S21: -0.0435 S22: -0.0165 S23: -0.0061 REMARK 3 S31: -0.1665 S32: -0.0220 S33: 0.0327 REMARK 3 TLS GROUP : 17 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 74 THROUGH 82 ) REMARK 3 ORIGIN FOR THE GROUP (A): -1.9673 5.0105 -21.5163 REMARK 3 T TENSOR REMARK 3 T11: 0.1925 T22: 0.2835 REMARK 3 T33: 0.1772 T12: -0.0148 REMARK 3 T13: 0.0445 T23: -0.0371 REMARK 3 L TENSOR REMARK 3 L11: 2.6015 L22: 1.2699 REMARK 3 L33: 3.6743 L12: -1.7727 REMARK 3 L13: 0.8236 L23: -0.1645 REMARK 3 S TENSOR REMARK 3 S11: -0.0412 S12: 0.0112 S13: -0.0154 REMARK 3 S21: -0.1425 S22: -0.1508 S23: -0.3670 REMARK 3 S31: 0.0092 S32: -0.0160 S33: 0.1615 REMARK 3 TLS GROUP : 18 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 83 THROUGH 92 ) REMARK 3 ORIGIN FOR THE GROUP (A): 1.5564 -9.6247 -15.7189 REMARK 3 T TENSOR REMARK 3 T11: 0.4031 T22: 0.3451 REMARK 3 T33: 0.4225 T12: 0.0569 REMARK 3 T13: -0.0034 T23: 0.0767 REMARK 3 L TENSOR REMARK 3 L11: 1.6637 L22: 2.0424 REMARK 3 L33: 2.4350 L12: -1.0307 REMARK 3 L13: 1.9800 L23: -0.9458 REMARK 3 S TENSOR REMARK 3 S11: 0.3413 S12: 0.0198 S13: -0.4285 REMARK 3 S21: -0.0999 S22: 0.0405 S23: -0.4815 REMARK 3 S31: 0.9286 S32: 0.4971 S33: -0.2838 REMARK 3 TLS GROUP : 19 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 93 THROUGH 101 ) REMARK 3 ORIGIN FOR THE GROUP (A): 6.1078 -2.8630 -29.2662 REMARK 3 T TENSOR REMARK 3 T11: 0.3976 T22: 0.3695 REMARK 3 T33: 0.3760 T12: 0.1016 REMARK 3 T13: 0.0470 T23: -0.0910 REMARK 3 L TENSOR REMARK 3 L11: 3.0636 L22: 1.1606 REMARK 3 L33: 3.9571 L12: 1.8087 REMARK 3 L13: -0.5697 L23: -0.9339 REMARK 3 S TENSOR REMARK 3 S11: -0.0679 S12: 0.6037 S13: -0.3391 REMARK 3 S21: -0.7204 S22: 0.0117 S23: -0.0797 REMARK 3 S31: -0.0918 S32: -0.1737 S33: 0.0755 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 8IKD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-MAR-23. REMARK 100 THE DEPOSITION ID IS D_1300035893. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-JAN-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9762 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20321 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 61.860 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.4 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : 0.12000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.16 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.30 REMARK 200 R MERGE FOR SHELL (I) : 0.85300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.200 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: 3SSE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.88 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1-0.2 M BIS-TRIS PH 5.5 AND 12-24% REMARK 280 PEG 4000, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 17.95450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 72.42450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.20500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 72.42450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.95450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.20500 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5910 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17060 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 MET A 1 REMARK 465 PRO A 161 REMARK 465 LEU A 162 REMARK 465 GLU A 163 REMARK 465 GLY A 164 REMARK 465 HIS A 165 REMARK 465 HIS A 166 REMARK 465 HIS A 167 REMARK 465 HIS A 168 REMARK 465 HIS A 169 REMARK 465 HIS A 170 REMARK 465 SER B 95 REMARK 465 PHE B 152 REMARK 465 ASN B 153 REMARK 465 SER B 154 REMARK 465 GLY B 155 REMARK 465 LYS B 156 REMARK 465 SER B 157 REMARK 465 VAL B 158 REMARK 465 ILE B 159 REMARK 465 PRO B 160 REMARK 465 PRO B 161 REMARK 465 LEU B 162 REMARK 465 GLU B 163 REMARK 465 GLY B 164 REMARK 465 HIS B 165 REMARK 465 HIS B 166 REMARK 465 HIS B 167 REMARK 465 HIS B 168 REMARK 465 HIS B 169 REMARK 465 HIS B 170 REMARK 465 DT C 1 REMARK 465 DA D 1 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 ARG A 19 CD NE CZ NH1 NH2 REMARK 470 ASP A 97 CG OD1 OD2 REMARK 470 LYS A 115 CD CE NZ REMARK 470 LYS B 13 CG CD CE NZ REMARK 470 ARG B 19 CD NE CZ NH1 NH2 REMARK 470 GLN B 93 CD OE1 NE2 REMARK 470 ARG B 136 CD NE CZ NH1 NH2 REMARK 470 DG C 2 P OP1 OP2 REMARK 470 DG D 2 P OP1 OP2 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 ASP A 25 36.54 -80.23 REMARK 500 ASN A 61 87.77 -163.07 REMARK 500 TYR A 64 146.37 -171.61 REMARK 500 SER A 96 -138.89 -92.29 REMARK 500 ASP B 25 41.64 -77.34 REMARK 500 ASN B 61 98.18 -161.67 REMARK 500 TYR B 64 149.55 -170.11 REMARK 500 ALA B 123 -60.04 -108.85 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 294 DISTANCE = 7.89 ANGSTROMS DBREF 8IKD A 1 161 UNP P15005 MCRB_ECOLI 1 161 DBREF 8IKD B 1 161 UNP P15005 MCRB_ECOLI 1 161 DBREF 8IKD C 1 13 PDB 8IKD 8IKD 1 13 DBREF 8IKD D 1 13 PDB 8IKD 8IKD 1 13 SEQADV 8IKD PHE A 41 UNP P15005 TYR 41 ENGINEERED MUTATION SEQADV 8IKD TYR A 68 UNP P15005 LEU 68 ENGINEERED MUTATION SEQADV 8IKD LEU A 162 UNP P15005 EXPRESSION TAG SEQADV 8IKD GLU A 163 UNP P15005 EXPRESSION TAG SEQADV 8IKD GLY A 164 UNP P15005 EXPRESSION TAG SEQADV 8IKD HIS A 165 UNP P15005 EXPRESSION TAG SEQADV 8IKD HIS A 166 UNP P15005 EXPRESSION TAG SEQADV 8IKD HIS A 167 UNP P15005 EXPRESSION TAG SEQADV 8IKD HIS A 168 UNP P15005 EXPRESSION TAG SEQADV 8IKD HIS A 169 UNP P15005 EXPRESSION TAG SEQADV 8IKD HIS A 170 UNP P15005 EXPRESSION TAG SEQADV 8IKD PHE B 41 UNP P15005 TYR 41 ENGINEERED MUTATION SEQADV 8IKD TYR B 68 UNP P15005 LEU 68 ENGINEERED MUTATION SEQADV 8IKD LEU B 162 UNP P15005 EXPRESSION TAG SEQADV 8IKD GLU B 163 UNP P15005 EXPRESSION TAG SEQADV 8IKD GLY B 164 UNP P15005 EXPRESSION TAG SEQADV 8IKD HIS B 165 UNP P15005 EXPRESSION TAG SEQADV 8IKD HIS B 166 UNP P15005 EXPRESSION TAG SEQADV 8IKD HIS B 167 UNP P15005 EXPRESSION TAG SEQADV 8IKD HIS B 168 UNP P15005 EXPRESSION TAG SEQADV 8IKD HIS B 169 UNP P15005 EXPRESSION TAG SEQADV 8IKD HIS B 170 UNP P15005 EXPRESSION TAG SEQRES 1 A 170 MET GLU SER ILE GLN PRO TRP ILE GLU LYS PHE ILE LYS SEQRES 2 A 170 GLN ALA GLN GLN GLN ARG SER GLN SER THR LYS ASP TYR SEQRES 3 A 170 PRO THR SER TYR ARG ASN LEU ARG VAL LYS LEU SER PHE SEQRES 4 A 170 GLY PHE GLY ASN PHE THR SER ILE PRO TRP PHE ALA PHE SEQRES 5 A 170 LEU GLY GLU GLY GLN GLU ALA SER ASN GLY ILE TYR PRO SEQRES 6 A 170 VAL ILE TYR TYR TYR LYS ASP PHE ASP GLU LEU VAL LEU SEQRES 7 A 170 ALA TYR GLY ILE SER ASP THR ASN GLU PRO HIS ALA GLN SEQRES 8 A 170 TRP GLN PHE SER SER ASP ILE PRO LYS THR ILE ALA GLU SEQRES 9 A 170 TYR PHE GLN ALA THR SER GLY VAL TYR PRO LYS LYS TYR SEQRES 10 A 170 GLY GLN SER TYR TYR ALA CYS SER GLN LYS VAL SER GLN SEQRES 11 A 170 GLY ILE ASP TYR THR ARG PHE ALA SER MET LEU ASP ASN SEQRES 12 A 170 ILE ILE ASN ASP TYR LYS LEU ILE PHE ASN SER GLY LYS SEQRES 13 A 170 SER VAL ILE PRO PRO LEU GLU GLY HIS HIS HIS HIS HIS SEQRES 14 A 170 HIS SEQRES 1 B 170 MET GLU SER ILE GLN PRO TRP ILE GLU LYS PHE ILE LYS SEQRES 2 B 170 GLN ALA GLN GLN GLN ARG SER GLN SER THR LYS ASP TYR SEQRES 3 B 170 PRO THR SER TYR ARG ASN LEU ARG VAL LYS LEU SER PHE SEQRES 4 B 170 GLY PHE GLY ASN PHE THR SER ILE PRO TRP PHE ALA PHE SEQRES 5 B 170 LEU GLY GLU GLY GLN GLU ALA SER ASN GLY ILE TYR PRO SEQRES 6 B 170 VAL ILE TYR TYR TYR LYS ASP PHE ASP GLU LEU VAL LEU SEQRES 7 B 170 ALA TYR GLY ILE SER ASP THR ASN GLU PRO HIS ALA GLN SEQRES 8 B 170 TRP GLN PHE SER SER ASP ILE PRO LYS THR ILE ALA GLU SEQRES 9 B 170 TYR PHE GLN ALA THR SER GLY VAL TYR PRO LYS LYS TYR SEQRES 10 B 170 GLY GLN SER TYR TYR ALA CYS SER GLN LYS VAL SER GLN SEQRES 11 B 170 GLY ILE ASP TYR THR ARG PHE ALA SER MET LEU ASP ASN SEQRES 12 B 170 ILE ILE ASN ASP TYR LYS LEU ILE PHE ASN SER GLY LYS SEQRES 13 B 170 SER VAL ILE PRO PRO LEU GLU GLY HIS HIS HIS HIS HIS SEQRES 14 B 170 HIS SEQRES 1 C 13 DT DG DA DG DA DC DC DG DG DT DA DG DC SEQRES 1 D 13 DA DG DC DT DA DC DC DG DG DT DC DT DC HET BTB C 101 14 HET BTB D 101 14 HETNAM BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL- HETNAM 2 BTB PROPANE-1,3-DIOL HETSYN BTB BIS-TRIS BUFFER FORMUL 5 BTB 2(C8 H19 N O5) FORMUL 7 HOH *202(H2 O) HELIX 1 AA1 ILE A 4 GLN A 18 1 15 HELIX 2 AA2 LYS A 71 PHE A 73 5 3 HELIX 3 AA3 THR A 101 GLY A 111 1 11 HELIX 4 AA4 SER A 129 GLY A 131 5 3 HELIX 5 AA5 ASP A 133 SER A 154 1 22 HELIX 6 AA6 ILE B 4 GLN B 18 1 15 HELIX 7 AA7 THR B 101 SER B 110 1 10 HELIX 8 AA8 SER B 129 GLY B 131 5 3 HELIX 9 AA9 ASP B 133 LYS B 149 1 17 SHEET 1 AA1 6 SER A 29 TYR A 30 0 SHEET 2 AA1 6 LEU A 33 SER A 38 -1 O LEU A 33 N TYR A 30 SHEET 3 AA1 6 TRP A 49 LEU A 53 -1 O ALA A 51 N LYS A 36 SHEET 4 AA1 6 ILE A 63 TYR A 70 -1 O PRO A 65 N PHE A 52 SHEET 5 AA1 6 GLU A 75 ILE A 82 -1 O VAL A 77 N TYR A 68 SHEET 6 AA1 6 TYR A 121 LYS A 127 -1 O CYS A 124 N LEU A 78 SHEET 1 AA2 6 SER B 29 TYR B 30 0 SHEET 2 AA2 6 LEU B 33 SER B 38 -1 O LEU B 33 N TYR B 30 SHEET 3 AA2 6 TRP B 49 LEU B 53 -1 O LEU B 53 N ARG B 34 SHEET 4 AA2 6 ILE B 63 TYR B 70 -1 O PRO B 65 N PHE B 52 SHEET 5 AA2 6 GLU B 75 ILE B 82 -1 O VAL B 77 N TYR B 68 SHEET 6 AA2 6 TYR B 121 LYS B 127 -1 O GLN B 126 N LEU B 76 CRYST1 35.909 68.410 144.849 90.00 90.00 90.00 P 21 21 21 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 0.027848 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014618 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006904 0.00000