HEADER DNA BINDING PROTEIN/DNA 18-DEC-20 7L4C TITLE CRYSTAL STRUCTURE OF THE DRM2-CTT DNA COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (CYTOSINE-5)-METHYLTRANSFERASE DRM2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PROTEIN DOMAINS REARRANGED METHYLASE 2; COMPND 5 EC: 2.1.1.37; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'- COMPND 9 D(*TP*AP*AP*AP*TP*TP*AP*AP*GP*AP*TP*TP*AP*AP*TP*AP*AP*T)-3'); COMPND 10 CHAIN: B; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: DNA (5'-D(*AP*TP*TP*AP*TP*TP*AP*AP*TP*(C49) COMPND 14 P*TP*TP*AP*AP*TP*TP*TP*A)-3'); COMPND 15 CHAIN: C; COMPND 16 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 3 ORGANISM_COMMON: MOUSE-EAR CRESS; SOURCE 4 ORGANISM_TAXID: 3702; SOURCE 5 GENE: DRM2, AT5G14620/AT5G14630, T15N1.110/T15N1.120; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 11 ORGANISM_COMMON: MOUSE-EAR CRESS; SOURCE 12 ORGANISM_TAXID: 3702; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES; SOURCE 15 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 16 ORGANISM_COMMON: MOUSE-EAR CRESS; SOURCE 17 ORGANISM_TAXID: 3702 KEYWDS DNA METHYLTRANSFERASE, COMPLEX, DNA BINDING PROTEIN, DNA BINDING KEYWDS 2 PROTEIN-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.FANG,J.SONG REVDAT 2 18-OCT-23 7L4C 1 REMARK REVDAT 1 04-AUG-21 7L4C 0 JRNL AUTH J.FANG,S.M.LEICHTER,J.JIANG,M.BISWAL,J.LU,Z.M.ZHANG,W.REN, JRNL AUTH 2 J.ZHAI,Q.CUI,X.ZHONG,J.SONG JRNL TITL SUBSTRATE DEFORMATION REGULATES DRM2-MEDIATED DNA JRNL TITL 2 METHYLATION IN PLANTS. JRNL REF SCI ADV V. 7 2021 JRNL REFN ESSN 2375-2548 JRNL PMID 34078593 JRNL DOI 10.1126/SCIADV.ABD9224 REMARK 2 REMARK 2 RESOLUTION. 2.11 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19_4092 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) : 2.11 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.29 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 43158 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.630 REMARK 3 FREE R VALUE TEST SET COUNT : 1999 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 48.2900 - 5.0800 0.99 3146 153 0.1559 0.1804 REMARK 3 2 5.0800 - 4.0400 1.00 3018 147 0.1315 0.1350 REMARK 3 3 4.0400 - 3.5300 1.00 2976 144 0.1500 0.1972 REMARK 3 4 3.5300 - 3.2000 1.00 2966 144 0.1684 0.2158 REMARK 3 5 3.2000 - 2.9700 0.99 2940 143 0.1950 0.2244 REMARK 3 6 2.9700 - 2.8000 0.99 2936 143 0.2031 0.2778 REMARK 3 7 2.8000 - 2.6600 0.99 2933 142 0.2120 0.2680 REMARK 3 8 2.6600 - 2.5400 0.99 2901 141 0.2255 0.2247 REMARK 3 9 2.5400 - 2.4400 0.99 2900 141 0.2479 0.2750 REMARK 3 10 2.4400 - 2.3600 1.00 2911 142 0.2535 0.2850 REMARK 3 11 2.3600 - 2.2900 0.99 2915 140 0.2597 0.2785 REMARK 3 12 2.2900 - 2.2200 0.98 2856 139 0.2885 0.3235 REMARK 3 13 2.2200 - 2.1600 0.99 2865 140 0.2975 0.2832 REMARK 3 14 2.1600 - 2.1100 0.98 2896 140 0.3368 0.3438 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) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.110 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 38.44 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.57 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 : 14 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 275 THROUGH 294 ) REMARK 3 ORIGIN FOR THE GROUP (A): -19.1135 -21.1143 -16.3775 REMARK 3 T TENSOR REMARK 3 T11: 0.3646 T22: 0.2914 REMARK 3 T33: 0.5007 T12: 0.0050 REMARK 3 T13: 0.0038 T23: 0.0571 REMARK 3 L TENSOR REMARK 3 L11: 7.2936 L22: 6.5816 REMARK 3 L33: 2.2761 L12: 0.7066 REMARK 3 L13: 0.9373 L23: 1.3093 REMARK 3 S TENSOR REMARK 3 S11: -0.0950 S12: 0.1263 S13: 0.6640 REMARK 3 S21: -0.2889 S22: -0.1033 S23: -0.3979 REMARK 3 S31: -0.5937 S32: -0.1711 S33: 0.3307 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 295 THROUGH 353 ) REMARK 3 ORIGIN FOR THE GROUP (A): -10.8805 -29.4961 -13.8200 REMARK 3 T TENSOR REMARK 3 T11: 0.2261 T22: 0.2047 REMARK 3 T33: 0.2659 T12: -0.0226 REMARK 3 T13: -0.0126 T23: 0.0142 REMARK 3 L TENSOR REMARK 3 L11: 6.4631 L22: 2.1897 REMARK 3 L33: 2.0393 L12: -0.2930 REMARK 3 L13: -0.6491 L23: 0.5021 REMARK 3 S TENSOR REMARK 3 S11: 0.1498 S12: 0.1771 S13: 0.4474 REMARK 3 S21: -0.0520 S22: -0.0201 S23: -0.2664 REMARK 3 S31: -0.2451 S32: 0.2127 S33: -0.0976 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 354 THROUGH 400 ) REMARK 3 ORIGIN FOR THE GROUP (A): -33.3647 -31.3231 -10.3371 REMARK 3 T TENSOR REMARK 3 T11: 0.2977 T22: 0.2912 REMARK 3 T33: 0.3201 T12: 0.0157 REMARK 3 T13: -0.0217 T23: -0.0026 REMARK 3 L TENSOR REMARK 3 L11: 5.4687 L22: 0.6712 REMARK 3 L33: 2.7655 L12: 0.3770 REMARK 3 L13: -2.5781 L23: 0.1349 REMARK 3 S TENSOR REMARK 3 S11: 0.1254 S12: 0.3064 S13: 0.3330 REMARK 3 S21: -0.0853 S22: -0.0356 S23: 0.1853 REMARK 3 S31: -0.1643 S32: -0.5092 S33: -0.0779 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 401 THROUGH 435 ) REMARK 3 ORIGIN FOR THE GROUP (A): -41.1609 -27.6516 9.9886 REMARK 3 T TENSOR REMARK 3 T11: 0.5358 T22: 0.6033 REMARK 3 T33: 0.3859 T12: -0.0882 REMARK 3 T13: 0.0025 T23: -0.1191 REMARK 3 L TENSOR REMARK 3 L11: 9.3015 L22: 8.5392 REMARK 3 L33: 8.2071 L12: -2.8963 REMARK 3 L13: -1.8113 L23: -1.2139 REMARK 3 S TENSOR REMARK 3 S11: -0.0139 S12: -1.1524 S13: 0.3930 REMARK 3 S21: 1.0667 S22: -0.1530 S23: 0.2819 REMARK 3 S31: -0.8867 S32: -0.2203 S33: 0.2046 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 436 THROUGH 494 ) REMARK 3 ORIGIN FOR THE GROUP (A): -28.9880 -41.2058 -7.3814 REMARK 3 T TENSOR REMARK 3 T11: 0.2456 T22: 0.3006 REMARK 3 T33: 0.2999 T12: -0.0285 REMARK 3 T13: -0.0133 T23: -0.0041 REMARK 3 L TENSOR REMARK 3 L11: 2.4283 L22: 0.5368 REMARK 3 L33: 2.3846 L12: -0.6409 REMARK 3 L13: -1.3277 L23: 0.2736 REMARK 3 S TENSOR REMARK 3 S11: -0.0992 S12: 0.0370 S13: -0.2683 REMARK 3 S21: 0.0412 S22: 0.0485 S23: 0.2340 REMARK 3 S31: 0.1844 S32: -0.4827 S33: 0.0591 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 495 THROUGH 547 ) REMARK 3 ORIGIN FOR THE GROUP (A): -16.6858 -48.4774 -18.5785 REMARK 3 T TENSOR REMARK 3 T11: 0.2061 T22: 0.2093 REMARK 3 T33: 0.3165 T12: -0.0158 REMARK 3 T13: 0.0048 T23: -0.0422 REMARK 3 L TENSOR REMARK 3 L11: 2.2124 L22: 2.6519 REMARK 3 L33: 8.0713 L12: 0.0512 REMARK 3 L13: -0.3598 L23: -2.9068 REMARK 3 S TENSOR REMARK 3 S11: -0.1164 S12: 0.1400 S13: -0.3366 REMARK 3 S21: -0.2629 S22: 0.1353 S23: 0.2202 REMARK 3 S31: 0.5515 S32: -0.3521 S33: 0.0062 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 548 THROUGH 575 ) REMARK 3 ORIGIN FOR THE GROUP (A): -5.9188 -53.0832 -16.5820 REMARK 3 T TENSOR REMARK 3 T11: 0.2669 T22: 0.1899 REMARK 3 T33: 0.3344 T12: 0.0402 REMARK 3 T13: 0.0334 T23: 0.0226 REMARK 3 L TENSOR REMARK 3 L11: 5.7450 L22: 3.3223 REMARK 3 L33: 4.9849 L12: 0.7787 REMARK 3 L13: 0.8617 L23: 1.2053 REMARK 3 S TENSOR REMARK 3 S11: -0.0575 S12: 0.0141 S13: -0.4248 REMARK 3 S21: -0.2012 S22: 0.0305 S23: -0.3718 REMARK 3 S31: 0.2653 S32: 0.3187 S33: -0.0023 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 576 THROUGH 605 ) REMARK 3 ORIGIN FOR THE GROUP (A): -9.9956 -37.7189 -3.2001 REMARK 3 T TENSOR REMARK 3 T11: 0.2717 T22: 0.3128 REMARK 3 T33: 0.3003 T12: -0.0211 REMARK 3 T13: -0.0231 T23: 0.0452 REMARK 3 L TENSOR REMARK 3 L11: 0.3561 L22: 0.9971 REMARK 3 L33: 3.8797 L12: -0.1546 REMARK 3 L13: -0.6052 L23: 1.2926 REMARK 3 S TENSOR REMARK 3 S11: 0.0158 S12: -0.1369 S13: -0.0151 REMARK 3 S21: 0.1200 S22: 0.0458 S23: -0.0607 REMARK 3 S31: 0.1960 S32: 0.3452 S33: -0.0377 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 606 THROUGH 626 ) REMARK 3 ORIGIN FOR THE GROUP (A): 0.2537 -40.6651 -14.6072 REMARK 3 T TENSOR REMARK 3 T11: 0.2190 T22: 0.2820 REMARK 3 T33: 0.3857 T12: -0.0221 REMARK 3 T13: -0.0081 T23: 0.0079 REMARK 3 L TENSOR REMARK 3 L11: 8.3275 L22: 5.4174 REMARK 3 L33: 9.5370 L12: -2.7711 REMARK 3 L13: -8.5576 L23: 4.7812 REMARK 3 S TENSOR REMARK 3 S11: 0.2491 S12: -0.3911 S13: 0.2422 REMARK 3 S21: -0.2937 S22: 0.1380 S23: -0.6085 REMARK 3 S31: -0.3503 S32: 0.7867 S33: -0.3931 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 10 ) REMARK 3 ORIGIN FOR THE GROUP (A): -24.8067 -43.2078 11.4513 REMARK 3 T TENSOR REMARK 3 T11: 0.4589 T22: 0.3473 REMARK 3 T33: 0.4160 T12: -0.0378 REMARK 3 T13: 0.0124 T23: 0.0291 REMARK 3 L TENSOR REMARK 3 L11: 7.7827 L22: 2.0905 REMARK 3 L33: 1.9316 L12: 8.7372 REMARK 3 L13: -0.7315 L23: -1.4520 REMARK 3 S TENSOR REMARK 3 S11: 0.2787 S12: -0.6536 S13: 0.4565 REMARK 3 S21: 0.8730 S22: -0.5542 S23: 1.0233 REMARK 3 S31: 0.0707 S32: -0.0066 S33: 0.2692 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 11 THROUGH 15 ) REMARK 3 ORIGIN FOR THE GROUP (A): -17.9129 -18.8679 1.3725 REMARK 3 T TENSOR REMARK 3 T11: 0.5415 T22: 0.3098 REMARK 3 T33: 0.4640 T12: -0.0123 REMARK 3 T13: -0.0033 T23: -0.0673 REMARK 3 L TENSOR REMARK 3 L11: 5.3457 L22: 2.7157 REMARK 3 L33: 2.0331 L12: -1.5782 REMARK 3 L13: -0.2878 L23: -4.3763 REMARK 3 S TENSOR REMARK 3 S11: 0.1616 S12: 0.3934 S13: 0.5851 REMARK 3 S21: 0.6228 S22: -0.2299 S23: 0.3003 REMARK 3 S31: -1.1815 S32: 0.1460 S33: -0.1113 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 16 THROUGH 18 ) REMARK 3 ORIGIN FOR THE GROUP (A): -25.0948 -5.4041 2.6337 REMARK 3 T TENSOR REMARK 3 T11: 1.3921 T22: 0.4236 REMARK 3 T33: 1.2777 T12: 0.1363 REMARK 3 T13: 0.3806 T23: -0.0946 REMARK 3 L TENSOR REMARK 3 L11: 7.3034 L22: 4.5549 REMARK 3 L33: 1.9800 L12: -0.6226 REMARK 3 L13: 0.0638 L23: -5.8175 REMARK 3 S TENSOR REMARK 3 S11: 0.5206 S12: -0.4451 S13: 1.8446 REMARK 3 S21: 0.8066 S22: -1.4482 S23: 0.2607 REMARK 3 S31: -1.9632 S32: -0.6919 S33: 0.8667 REMARK 3 TLS GROUP : 13 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 1 THROUGH 5 ) REMARK 3 ORIGIN FOR THE GROUP (A): -17.8360 -6.6204 4.0979 REMARK 3 T TENSOR REMARK 3 T11: 1.7730 T22: 0.4331 REMARK 3 T33: 1.5886 T12: -0.1089 REMARK 3 T13: 0.1360 T23: -0.0790 REMARK 3 L TENSOR REMARK 3 L11: 7.1560 L22: 6.8467 REMARK 3 L33: 7.8289 L12: 2.5555 REMARK 3 L13: -0.1487 L23: -6.8145 REMARK 3 S TENSOR REMARK 3 S11: 0.4281 S12: 0.1399 S13: 2.2635 REMARK 3 S21: 0.7971 S22: 0.0228 S23: -2.5229 REMARK 3 S31: -0.9328 S32: 1.1402 S33: -0.2612 REMARK 3 TLS GROUP : 14 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 6 THROUGH 18 ) REMARK 3 ORIGIN FOR THE GROUP (A): -23.4914 -37.9962 9.0234 REMARK 3 T TENSOR REMARK 3 T11: 0.4671 T22: 0.3405 REMARK 3 T33: 0.2742 T12: -0.0260 REMARK 3 T13: 0.0888 T23: -0.0291 REMARK 3 L TENSOR REMARK 3 L11: 4.5505 L22: 7.3294 REMARK 3 L33: 2.7675 L12: 5.2526 REMARK 3 L13: -0.8084 L23: -3.0733 REMARK 3 S TENSOR REMARK 3 S11: 0.4592 S12: -0.4644 S13: -0.2687 REMARK 3 S21: 1.2835 S22: -0.7064 S23: 0.0744 REMARK 3 S31: -0.4794 S32: 0.2518 S33: 0.2573 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 7L4C COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-DEC-20. REMARK 100 THE DEPOSITION ID IS D_1000253678. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-NOV-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.2 - 7.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : NONIUS KAPPA CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 43203 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.110 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : 0.13200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.11 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.17 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.1 REMARK 200 DATA REDUNDANCY IN SHELL : 5.30 REMARK 200 R MERGE FOR SHELL (I) : 2.00400 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: PHENIX REMARK 200 STARTING MODEL: 4ONJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.83 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2% V/V TACSIMATE TM (PH 6.0), 0.1 M REMARK 280 BIS-TRIS (PH 6.5) AND 20% W/V POLYETHYLENE GLYCOL 3,350., VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 58.89450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 58.89450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 27.18800 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 116.25600 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 27.18800 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 116.25600 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 58.89450 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 27.18800 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 116.25600 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 58.89450 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 27.18800 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 116.25600 REMARK 290 SMTRY3 8 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5580 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19800 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -33.0 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 A1092 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 GLU A 274 CG CD OE1 OE2 REMARK 470 ARG A 277 NE CZ NH1 NH2 REMARK 470 ARG A 304 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 416 CG CD OE1 OE2 REMARK 470 LYS A 422 CG CD CE NZ REMARK 470 ARG A 426 NE CZ NH1 NH2 REMARK 470 DA C 1 O5' 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 347 96.83 -162.12 REMARK 500 PRO A 413 3.81 -64.98 REMARK 500 SER A 558 -77.36 -94.84 REMARK 500 REMARK 500 REMARK: NULL DBREF 7L4C A 274 626 UNP Q9M548 DRM2_ARATH 274 626 DBREF 7L4C B 1 18 PDB 7L4C 7L4C 1 18 DBREF 7L4C C 1 18 PDB 7L4C 7L4C 1 18 SEQRES 1 A 353 GLU PRO ILE ARG LEU PRO ASN PRO MET ILE GLY PHE GLY SEQRES 2 A 353 VAL PRO ASN GLU PRO GLY LEU ILE THR HIS ARG SER LEU SEQRES 3 A 353 PRO GLU LEU ALA ARG GLY PRO PRO PHE PHE TYR TYR GLU SEQRES 4 A 353 ASN VAL ALA LEU THR PRO LYS GLY VAL TRP GLU THR ILE SEQRES 5 A 353 SER ARG HIS LEU PHE GLU ILE PRO PRO GLU PHE VAL ASP SEQRES 6 A 353 SER LYS TYR PHE CYS VAL ALA ALA ARG LYS ARG GLY TYR SEQRES 7 A 353 ILE HIS ASN LEU PRO ILE ASN ASN ARG PHE GLN ILE GLN SEQRES 8 A 353 PRO PRO PRO LYS TYR THR ILE HIS ASP ALA PHE PRO LEU SEQRES 9 A 353 SER LYS ARG TRP TRP PRO GLU TRP ASP LYS ARG THR LYS SEQRES 10 A 353 LEU ASN CYS ILE LEU THR CYS THR GLY SER ALA GLN LEU SEQRES 11 A 353 THR ASN ARG ILE ARG VAL ALA LEU GLU PRO TYR ASN GLU SEQRES 12 A 353 GLU PRO GLU PRO PRO LYS HIS VAL GLN ARG TYR VAL ILE SEQRES 13 A 353 ASP GLN CYS LYS LYS TRP ASN LEU VAL TRP VAL GLY LYS SEQRES 14 A 353 ASN LYS ALA ALA PRO LEU GLU PRO ASP GLU MET GLU SER SEQRES 15 A 353 ILE LEU GLY PHE PRO LYS ASN HIS THR ARG GLY GLY GLY SEQRES 16 A 353 MET SER ARG THR GLU ARG PHE LYS SER LEU GLY ASN SER SEQRES 17 A 353 PHE GLN VAL ASP THR VAL ALA TYR HIS LEU SER VAL LEU SEQRES 18 A 353 LYS PRO ILE PHE PRO HIS GLY ILE ASN VAL LEU SER LEU SEQRES 19 A 353 PHE THR GLY ILE GLY GLY GLY GLU VAL ALA LEU HIS ARG SEQRES 20 A 353 LEU GLN ILE LYS MET LYS LEU VAL VAL SER VAL GLU ILE SEQRES 21 A 353 SER LYS VAL ASN ARG ASN ILE LEU LYS ASP PHE TRP GLU SEQRES 22 A 353 GLN THR ASN GLN THR GLY GLU LEU ILE GLU PHE SER ASP SEQRES 23 A 353 ILE GLN HIS LEU THR ASN ASP THR ILE GLU GLY LEU MET SEQRES 24 A 353 GLU LYS TYR GLY GLY PHE ASP LEU VAL ILE GLY GLY SER SEQRES 25 A 353 PRO CYS ASN ASN LEU ALA GLY GLY ASN ARG VAL SER ARG SEQRES 26 A 353 VAL GLY LEU GLU GLY ASP GLN SER SER LEU PHE PHE GLU SEQRES 27 A 353 TYR CYS ARG ILE LEU GLU VAL VAL ARG ALA ARG MET ARG SEQRES 28 A 353 GLY SER SEQRES 1 B 18 DT DA DA DA DT DT DA DA DG DA DT DT DA SEQRES 2 B 18 DA DT DA DA DT SEQRES 1 C 18 DA DT DT DA DT DT DA DA DT C49 DT DT DA SEQRES 2 C 18 DA DT DT DT DA HET C49 C 10 21 HET SAH A 701 26 HET GOL A 702 6 HETNAM C49 4-THIO,5-FLUORO,5-METHYL-2'-DEOXY-CYTIDINE-5'- HETNAM 2 C49 MONOPHOSPHATE HETNAM SAH S-ADENOSYL-L-HOMOCYSTEINE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 C49 C10 H15 F N3 O7 P S FORMUL 4 SAH C14 H20 N6 O5 S FORMUL 5 GOL C3 H8 O3 FORMUL 6 HOH *379(H2 O) HELIX 1 AA1 PRO A 300 ARG A 304 5 5 HELIX 2 AA2 GLY A 320 LEU A 329 1 10 HELIX 3 AA3 LYS A 340 PHE A 342 5 3 HELIX 4 AA4 THR A 370 PHE A 375 1 6 HELIX 5 AA5 PRO A 376 TRP A 381 5 6 HELIX 6 AA6 SER A 400 GLU A 412 1 13 HELIX 7 AA7 PRO A 413 ASN A 415 5 3 HELIX 8 AA8 PRO A 421 TRP A 435 1 15 HELIX 9 AA9 GLU A 449 LEU A 457 1 9 HELIX 10 AB1 SER A 470 SER A 481 1 12 HELIX 11 AB2 GLN A 483 SER A 492 1 10 HELIX 12 AB3 VAL A 493 PHE A 498 1 6 HELIX 13 AB4 GLY A 512 LEU A 521 1 10 HELIX 14 AB5 SER A 534 THR A 548 1 15 HELIX 15 AB6 ASP A 559 LEU A 563 5 5 HELIX 16 AB7 THR A 564 GLY A 576 1 13 HELIX 17 AB8 GLN A 605 SER A 607 5 3 HELIX 18 AB9 LEU A 608 ARG A 624 1 17 SHEET 1 AA1 7 GLU A 335 ASP A 338 0 SHEET 2 AA1 7 LYS A 348 HIS A 353 -1 O TYR A 351 N GLU A 335 SHEET 3 AA1 7 PHE A 308 VAL A 314 -1 N TYR A 311 O ILE A 352 SHEET 4 AA1 7 LEU A 580 GLY A 584 1 O VAL A 581 N TYR A 310 SHEET 5 AA1 7 ILE A 502 LEU A 507 1 N LEU A 505 O LEU A 580 SHEET 6 AA1 7 MET A 525 VAL A 531 1 O VAL A 529 N SER A 506 SHEET 7 AA1 7 GLU A 553 PHE A 557 1 O ILE A 555 N SER A 530 SHEET 1 AA2 2 VAL A 438 GLY A 441 0 SHEET 2 AA2 2 LYS A 444 ALA A 446 -1 O ALA A 446 N VAL A 438 LINK SG CYS A 587 C6 C49 C 10 1555 1555 1.80 LINK O3' DT C 9 P C49 C 10 1555 1555 1.60 LINK O3' C49 C 10 P DT C 11 1555 1555 1.59 CISPEP 1 ASN A 280 PRO A 281 0 5.36 CISPEP 2 GLY A 305 PRO A 306 0 -0.85 CISPEP 3 PRO A 306 PRO A 307 0 -1.07 CISPEP 4 GLN A 364 PRO A 365 0 -5.80 CRYST1 54.376 232.512 117.789 90.00 90.00 90.00 C 2 2 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 0.018390 0.000000 0.000000 0.00000 SCALE2 0.000000 0.004301 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008490 0.00000