HEADER DNA BINDING PROTEIN/DNA 19-DEC-20 7L4H TITLE CRYSTAL STRUCTURE OF THE DRM2-CTG 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*CP*AP*GP*AP*TP*TP*AP*GP*GP*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*CP*CP*TP*AP*AP*TP*(C49) COMPND 14 P*TP*GP*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 7L4H 1 REMARK REVDAT 1 04-AUG-21 7L4H 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. 2.56 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) : 2.56 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 115.19 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 23629 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.212 REMARK 3 R VALUE (WORKING SET) : 0.209 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.450 REMARK 3 FREE R VALUE TEST SET COUNT : 1996 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1115.1900 - 6.1800 0.97 1660 154 0.1625 0.2080 REMARK 3 2 6.1700 - 4.9000 0.98 1594 147 0.1627 0.1995 REMARK 3 3 4.9000 - 4.2800 0.99 1587 146 0.1509 0.1758 REMARK 3 4 4.2800 - 3.8900 0.97 1523 140 0.1620 0.2138 REMARK 3 5 3.8900 - 3.6100 0.99 1570 145 0.1970 0.2302 REMARK 3 6 3.6100 - 3.4000 0.99 1554 143 0.2232 0.2470 REMARK 3 7 3.4000 - 3.2300 0.99 1563 145 0.2196 0.2557 REMARK 3 8 3.2300 - 3.0900 0.98 1544 143 0.2553 0.2821 REMARK 3 9 3.0900 - 2.9700 0.99 1523 140 0.2890 0.3724 REMARK 3 10 2.9700 - 2.8700 0.99 1530 143 0.3116 0.3426 REMARK 3 11 2.8700 - 2.7800 1.00 1568 143 0.3170 0.4121 REMARK 3 12 2.7800 - 2.7000 0.99 1528 141 0.3282 0.4045 REMARK 3 13 2.7000 - 2.6300 0.99 1523 142 0.3523 0.3541 REMARK 3 14 2.6300 - 2.5600 0.88 1366 124 0.3679 0.4006 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) : 0.400 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.510 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 50.78 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 : 0.009 3773 REMARK 3 ANGLE : 0.702 5269 REMARK 3 CHIRALITY : 0.169 567 REMARK 3 PLANARITY : 0.005 554 REMARK 3 DIHEDRAL : 22.795 753 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 17 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 275 THROUGH 294 ) REMARK 3 ORIGIN FOR THE GROUP (A): 13.2996 20.3191 -5.5354 REMARK 3 T TENSOR REMARK 3 T11: 0.8270 T22: 0.2834 REMARK 3 T33: 0.5038 T12: 0.0668 REMARK 3 T13: -0.0007 T23: 0.0153 REMARK 3 L TENSOR REMARK 3 L11: 8.2628 L22: 1.4480 REMARK 3 L33: 7.5784 L12: 3.2791 REMARK 3 L13: 4.0855 L23: 1.1173 REMARK 3 S TENSOR REMARK 3 S11: 0.9612 S12: 0.0485 S13: -0.6719 REMARK 3 S21: 0.7089 S22: -0.1967 S23: 0.2021 REMARK 3 S31: 0.7514 S32: 0.3547 S33: -0.8702 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 295 THROUGH 320 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.7825 29.5449 6.1485 REMARK 3 T TENSOR REMARK 3 T11: 0.5049 T22: 0.3402 REMARK 3 T33: 0.3241 T12: -0.0064 REMARK 3 T13: 0.0081 T23: 0.0429 REMARK 3 L TENSOR REMARK 3 L11: 1.5659 L22: 2.8221 REMARK 3 L33: 4.0318 L12: -1.3622 REMARK 3 L13: 0.1137 L23: 0.1611 REMARK 3 S TENSOR REMARK 3 S11: -0.1337 S12: 0.0893 S13: -0.2049 REMARK 3 S21: 0.3690 S22: -0.0441 S23: 0.1715 REMARK 3 S31: 0.5638 S32: -0.2652 S33: 0.1963 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 321 THROUGH 353 ) REMARK 3 ORIGIN FOR THE GROUP (A): 17.9475 28.1088 0.2003 REMARK 3 T TENSOR REMARK 3 T11: 0.5170 T22: 0.3684 REMARK 3 T33: 0.3540 T12: 0.0147 REMARK 3 T13: -0.0293 T23: 0.0346 REMARK 3 L TENSOR REMARK 3 L11: 3.1878 L22: 2.2425 REMARK 3 L33: 2.3074 L12: 0.2617 REMARK 3 L13: -0.1879 L23: 0.3251 REMARK 3 S TENSOR REMARK 3 S11: 0.1414 S12: -0.3990 S13: -0.2881 REMARK 3 S21: 0.2597 S22: -0.1301 S23: -0.1078 REMARK 3 S31: 0.1131 S32: -0.1606 S33: 0.0342 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 354 THROUGH 400 ) REMARK 3 ORIGIN FOR THE GROUP (A): 19.1991 30.5717 -19.7685 REMARK 3 T TENSOR REMARK 3 T11: 0.5461 T22: 0.3873 REMARK 3 T33: 0.3639 T12: 0.0586 REMARK 3 T13: 0.0261 T23: -0.0049 REMARK 3 L TENSOR REMARK 3 L11: 1.8034 L22: 0.5054 REMARK 3 L33: 2.7328 L12: -0.5301 REMARK 3 L13: -0.7916 L23: 0.0714 REMARK 3 S TENSOR REMARK 3 S11: -0.0431 S12: 0.3036 S13: -0.1558 REMARK 3 S21: -0.0590 S22: -0.0874 S23: 0.0358 REMARK 3 S31: 0.3485 S32: 0.0766 S33: 0.1613 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 401 THROUGH 435 ) REMARK 3 ORIGIN FOR THE GROUP (A): 39.5700 26.8019 -27.6557 REMARK 3 T TENSOR REMARK 3 T11: 0.6361 T22: 0.8521 REMARK 3 T33: 0.5630 T12: 0.2785 REMARK 3 T13: 0.0011 T23: 0.1372 REMARK 3 L TENSOR REMARK 3 L11: 6.1268 L22: 3.5658 REMARK 3 L33: 4.3812 L12: 1.5967 REMARK 3 L13: -1.1352 L23: 2.1093 REMARK 3 S TENSOR REMARK 3 S11: -0.0361 S12: -0.2528 S13: -0.8689 REMARK 3 S21: -0.2366 S22: -0.0864 S23: -0.4986 REMARK 3 S31: 0.6417 S32: 0.9432 S33: 0.2273 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 436 THROUGH 470 ) REMARK 3 ORIGIN FOR THE GROUP (A): 25.0010 41.2943 -20.1599 REMARK 3 T TENSOR REMARK 3 T11: 0.6173 T22: 0.5357 REMARK 3 T33: 0.4109 T12: 0.0348 REMARK 3 T13: -0.0087 T23: 0.0677 REMARK 3 L TENSOR REMARK 3 L11: 3.5328 L22: 0.0822 REMARK 3 L33: 2.0184 L12: 0.4042 REMARK 3 L13: -1.8163 L23: -0.3690 REMARK 3 S TENSOR REMARK 3 S11: 0.1599 S12: 0.6280 S13: 0.3464 REMARK 3 S21: -0.1562 S22: -0.1569 S23: -0.0308 REMARK 3 S31: -0.1687 S32: -0.3009 S33: -0.0414 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 471 THROUGH 494 ) REMARK 3 ORIGIN FOR THE GROUP (A): 18.4413 39.8453 -8.7610 REMARK 3 T TENSOR REMARK 3 T11: 0.4581 T22: 0.3765 REMARK 3 T33: 0.3895 T12: 0.0885 REMARK 3 T13: 0.0127 T23: 0.0001 REMARK 3 L TENSOR REMARK 3 L11: 7.6801 L22: 1.7493 REMARK 3 L33: 2.4765 L12: 3.1207 REMARK 3 L13: -3.4107 L23: -1.1660 REMARK 3 S TENSOR REMARK 3 S11: 0.1838 S12: 0.2665 S13: -0.1051 REMARK 3 S21: -0.0715 S22: -0.0762 S23: -0.0255 REMARK 3 S31: -0.1875 S32: 0.0004 S33: -0.1753 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 495 THROUGH 547 ) REMARK 3 ORIGIN FOR THE GROUP (A): 10.7110 47.7816 -3.1329 REMARK 3 T TENSOR REMARK 3 T11: 0.4962 T22: 0.3057 REMARK 3 T33: 0.2750 T12: 0.0511 REMARK 3 T13: -0.0136 T23: 0.0436 REMARK 3 L TENSOR REMARK 3 L11: 8.7321 L22: 1.9773 REMARK 3 L33: 1.6417 L12: 2.1914 REMARK 3 L13: 0.9586 L23: 1.0797 REMARK 3 S TENSOR REMARK 3 S11: -0.0288 S12: 0.1185 S13: 0.3388 REMARK 3 S21: -0.2749 S22: 0.1167 S23: -0.0358 REMARK 3 S31: -0.0743 S32: -0.1751 S33: -0.0935 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 548 THROUGH 575 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.7240 52.4649 7.6333 REMARK 3 T TENSOR REMARK 3 T11: 0.6040 T22: 0.3369 REMARK 3 T33: 0.3620 T12: -0.0678 REMARK 3 T13: -0.0028 T23: -0.0158 REMARK 3 L TENSOR REMARK 3 L11: 8.7536 L22: 3.7006 REMARK 3 L33: 6.0665 L12: -2.3412 REMARK 3 L13: 3.5715 L23: 0.4816 REMARK 3 S TENSOR REMARK 3 S11: -0.2242 S12: -0.6213 S13: 0.4618 REMARK 3 S21: 0.5350 S22: 0.0206 S23: 0.0720 REMARK 3 S31: -0.6787 S32: -0.1648 S33: 0.2968 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 576 THROUGH 605 ) REMARK 3 ORIGIN FOR THE GROUP (A): 26.2918 37.1572 3.5896 REMARK 3 T TENSOR REMARK 3 T11: 0.5217 T22: 0.4192 REMARK 3 T33: 0.3614 T12: -0.0030 REMARK 3 T13: -0.0447 T23: 0.0562 REMARK 3 L TENSOR REMARK 3 L11: 7.0815 L22: 2.1826 REMARK 3 L33: 0.7998 L12: -3.1167 REMARK 3 L13: -0.8944 L23: 0.7151 REMARK 3 S TENSOR REMARK 3 S11: 0.2171 S12: -0.2905 S13: 0.0563 REMARK 3 S21: -0.0121 S22: -0.1406 S23: -0.1661 REMARK 3 S31: -0.0946 S32: 0.1954 S33: -0.0876 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 606 THROUGH 626 ) REMARK 3 ORIGIN FOR THE GROUP (A): 14.8604 40.0343 13.8458 REMARK 3 T TENSOR REMARK 3 T11: 0.6135 T22: 0.5591 REMARK 3 T33: 0.3290 T12: 0.0236 REMARK 3 T13: -0.0000 T23: 0.0551 REMARK 3 L TENSOR REMARK 3 L11: 2.9790 L22: 5.6723 REMARK 3 L33: 3.7476 L12: -3.9457 REMARK 3 L13: -2.6007 L23: 2.2895 REMARK 3 S TENSOR REMARK 3 S11: -0.4172 S12: -1.1867 S13: -0.2778 REMARK 3 S21: 1.0035 S22: 0.3857 S23: 0.3547 REMARK 3 S31: 0.2220 S32: 0.4497 S33: 0.2042 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 5 ) REMARK 3 ORIGIN FOR THE GROUP (A): 38.7554 52.6059 -12.7489 REMARK 3 T TENSOR REMARK 3 T11: 0.7383 T22: 0.4876 REMARK 3 T33: 0.5900 T12: -0.0416 REMARK 3 T13: 0.0976 T23: 0.0797 REMARK 3 L TENSOR REMARK 3 L11: 5.5259 L22: 3.8742 REMARK 3 L33: 8.3938 L12: -0.6010 REMARK 3 L13: 0.9282 L23: 5.5158 REMARK 3 S TENSOR REMARK 3 S11: 0.3541 S12: -0.2287 S13: 0.1200 REMARK 3 S21: 0.0602 S22: -0.0430 S23: -0.4635 REMARK 3 S31: 0.2107 S32: -0.0580 S33: -0.3306 REMARK 3 TLS GROUP : 13 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 6 THROUGH 10 ) REMARK 3 ORIGIN FOR THE GROUP (A): 42.9654 33.3239 -9.8561 REMARK 3 T TENSOR REMARK 3 T11: 0.8502 T22: 0.6052 REMARK 3 T33: 0.8626 T12: 0.2570 REMARK 3 T13: 0.0933 T23: 0.1466 REMARK 3 L TENSOR REMARK 3 L11: 5.2543 L22: 2.0205 REMARK 3 L33: 9.6961 L12: -3.3657 REMARK 3 L13: 4.5670 L23: -7.7455 REMARK 3 S TENSOR REMARK 3 S11: 1.2721 S12: 0.3894 S13: 0.0497 REMARK 3 S21: -2.4604 S22: -1.5854 S23: 0.0808 REMARK 3 S31: 0.6103 S32: 1.3383 S33: 0.3463 REMARK 3 TLS GROUP : 14 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 11 THROUGH 15 ) REMARK 3 ORIGIN FOR THE GROUP (A): 31.9883 16.9177 -3.3669 REMARK 3 T TENSOR REMARK 3 T11: 1.0665 T22: 0.5163 REMARK 3 T33: 0.9809 T12: 0.0795 REMARK 3 T13: -0.0379 T23: 0.0228 REMARK 3 L TENSOR REMARK 3 L11: 2.7307 L22: 3.3081 REMARK 3 L33: 4.0825 L12: -0.5305 REMARK 3 L13: -2.1081 L23: 3.2441 REMARK 3 S TENSOR REMARK 3 S11: 0.2493 S12: -0.1572 S13: -2.0722 REMARK 3 S21: -0.6349 S22: -1.0915 S23: -0.0000 REMARK 3 S31: 2.1323 S32: -0.4738 S33: 0.5584 REMARK 3 TLS GROUP : 15 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 16 THROUGH 18 ) REMARK 3 ORIGIN FOR THE GROUP (A): 34.7868 2.5121 -8.1923 REMARK 3 T TENSOR REMARK 3 T11: 1.6006 T22: 0.6350 REMARK 3 T33: 2.1078 T12: 0.1427 REMARK 3 T13: -0.2974 T23: -0.0883 REMARK 3 L TENSOR REMARK 3 L11: 9.5574 L22: 2.8491 REMARK 3 L33: 2.0034 L12: -3.9990 REMARK 3 L13: -5.8222 L23: 3.3608 REMARK 3 S TENSOR REMARK 3 S11: -0.3229 S12: 0.8346 S13: -2.2320 REMARK 3 S21: -1.1539 S22: -0.7692 S23: 3.8123 REMARK 3 S31: -0.2284 S32: 0.2953 S33: 1.0753 REMARK 3 TLS GROUP : 16 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 1 THROUGH 5 ) REMARK 3 ORIGIN FOR THE GROUP (A): 39.3737 7.7641 -2.9509 REMARK 3 T TENSOR REMARK 3 T11: 1.5363 T22: 0.7531 REMARK 3 T33: 1.7448 T12: 0.1525 REMARK 3 T13: -0.0172 T23: 0.3959 REMARK 3 L TENSOR REMARK 3 L11: 5.2761 L22: 3.8093 REMARK 3 L33: 5.3629 L12: -2.9030 REMARK 3 L13: 2.1735 L23: 1.3370 REMARK 3 S TENSOR REMARK 3 S11: 0.4445 S12: -0.6304 S13: -0.1466 REMARK 3 S21: -0.6592 S22: -0.3068 S23: 0.8313 REMARK 3 S31: 3.0989 S32: 0.9442 S33: -0.1182 REMARK 3 TLS GROUP : 17 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 6 THROUGH 18 ) REMARK 3 ORIGIN FOR THE GROUP (A): 38.4935 37.5748 -9.9449 REMARK 3 T TENSOR REMARK 3 T11: 0.4006 T22: 0.3629 REMARK 3 T33: 0.4498 T12: 0.1492 REMARK 3 T13: 0.1288 T23: 0.0143 REMARK 3 L TENSOR REMARK 3 L11: 3.7810 L22: 8.1286 REMARK 3 L33: 5.4441 L12: 4.2922 REMARK 3 L13: -1.1019 L23: -5.3844 REMARK 3 S TENSOR REMARK 3 S11: 0.2390 S12: -0.1944 S13: -0.2842 REMARK 3 S21: -0.0919 S22: -0.4873 S23: -0.5999 REMARK 3 S31: -0.1446 S32: 0.4489 S33: 0.2766 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 7L4H 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_1000253692. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-JUL-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5-7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C 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 0.5.32 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23715 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.560 REMARK 200 RESOLUTION RANGE LOW (A) : 115.190 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : 0.16400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.56 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.68 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.3 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : 1.37300 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: 4ONJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.53 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M POTASSIUM IODIDE,20% W/V REMARK 280 POLYETHYLENE GLYCOL 3,350, PH 7.0., VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 277K 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 27.12200 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 27.12200 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 58.44400 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 115.18950 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 58.44400 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 115.18950 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 27.12200 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 58.44400 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 115.18950 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 27.12200 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 58.44400 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 115.18950 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: 6980 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19880 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -38.0 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 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 277 NE CZ NH1 NH2 REMARK 470 LYS A 422 CG CD CE NZ REMARK 470 LYS A 442 CE NZ REMARK 470 DA C 1 O5' REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES 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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) 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 ATM2 ATM3 REMARK 500 DA B 16 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DA B 17 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES 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 347 97.01 -163.80 REMARK 500 SER A 558 -77.15 -100.48 REMARK 500 REMARK 500 REMARK: NULL DBREF 7L4H A 275 626 UNP Q9M548 DRM2_ARATH 275 626 DBREF 7L4H B 1 18 PDB 7L4H 7L4H 1 18 DBREF 7L4H C 1 18 PDB 7L4H 7L4H 1 18 SEQRES 1 A 352 PRO ILE ARG LEU PRO ASN PRO MET ILE GLY PHE GLY VAL SEQRES 2 A 352 PRO ASN GLU PRO GLY LEU ILE THR HIS ARG SER LEU PRO SEQRES 3 A 352 GLU LEU ALA ARG GLY PRO PRO PHE PHE TYR TYR GLU ASN SEQRES 4 A 352 VAL ALA LEU THR PRO LYS GLY VAL TRP GLU THR ILE SER SEQRES 5 A 352 ARG HIS LEU PHE GLU ILE PRO PRO GLU PHE VAL ASP SER SEQRES 6 A 352 LYS TYR PHE CYS VAL ALA ALA ARG LYS ARG GLY TYR ILE SEQRES 7 A 352 HIS ASN LEU PRO ILE ASN ASN ARG PHE GLN ILE GLN PRO SEQRES 8 A 352 PRO PRO LYS TYR THR ILE HIS ASP ALA PHE PRO LEU SER SEQRES 9 A 352 LYS ARG TRP TRP PRO GLU TRP ASP LYS ARG THR LYS LEU SEQRES 10 A 352 ASN CYS ILE LEU THR CYS THR GLY SER ALA GLN LEU THR SEQRES 11 A 352 ASN ARG ILE ARG VAL ALA LEU GLU PRO TYR ASN GLU GLU SEQRES 12 A 352 PRO GLU PRO PRO LYS HIS VAL GLN ARG TYR VAL ILE ASP SEQRES 13 A 352 GLN CYS LYS LYS TRP ASN LEU VAL TRP VAL GLY LYS ASN SEQRES 14 A 352 LYS ALA ALA PRO LEU GLU PRO ASP GLU MET GLU SER ILE SEQRES 15 A 352 LEU GLY PHE PRO LYS ASN HIS THR ARG GLY GLY GLY MET SEQRES 16 A 352 SER ARG THR GLU ARG PHE LYS SER LEU GLY ASN SER PHE SEQRES 17 A 352 GLN VAL ASP THR VAL ALA TYR HIS LEU SER VAL LEU LYS SEQRES 18 A 352 PRO ILE PHE PRO HIS GLY ILE ASN VAL LEU SER LEU PHE SEQRES 19 A 352 THR GLY ILE GLY GLY GLY GLU VAL ALA LEU HIS ARG LEU SEQRES 20 A 352 GLN ILE LYS MET LYS LEU VAL VAL SER VAL GLU ILE SER SEQRES 21 A 352 LYS VAL ASN ARG ASN ILE LEU LYS ASP PHE TRP GLU GLN SEQRES 22 A 352 THR ASN GLN THR GLY GLU LEU ILE GLU PHE SER ASP ILE SEQRES 23 A 352 GLN HIS LEU THR ASN ASP THR ILE GLU GLY LEU MET GLU SEQRES 24 A 352 LYS TYR GLY GLY PHE ASP LEU VAL ILE GLY GLY SER PRO SEQRES 25 A 352 CYS ASN ASN LEU ALA GLY GLY ASN ARG VAL SER ARG VAL SEQRES 26 A 352 GLY LEU GLU GLY ASP GLN SER SER LEU PHE PHE GLU TYR SEQRES 27 A 352 CYS ARG ILE LEU GLU VAL VAL ARG ALA ARG MET ARG GLY SEQRES 28 A 352 SER SEQRES 1 B 18 DT DA DA DA DT DT DC DA DG DA DT DT DA SEQRES 2 B 18 DG DG DA DA DT SEQRES 1 C 18 DA DT DT DC DC DT DA DA DT C49 DT DG DA SEQRES 2 C 18 DA DT DT DT DA HET C49 C 10 21 HET SAH A1001 26 HET GOL A1002 6 HET GOL A1003 6 HET GOL A1004 6 HET GOL A1005 6 HET IOD A1006 1 HET IOD A1007 1 HET IOD A1008 1 HET IOD A1009 1 HET IOD A1010 1 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 HETNAM IOD IODIDE ION 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 4(C3 H8 O3) FORMUL 9 IOD 5(I 1-) FORMUL 14 HOH *98(H2 O) HELIX 1 AA1 PRO A 300 ARG A 304 5 5 HELIX 2 AA2 GLY A 320 HIS A 328 1 9 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 ASN A 436 1 16 HELIX 9 AA9 GLU A 449 LEU A 457 1 9 HELIX 10 AB1 SER A 470 ASN A 480 1 11 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 LEU A 527 N VAL A 504 SHEET 7 AA1 7 GLU A 553 PHE A 557 1 O PHE A 557 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 1.92 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 2.07 CISPEP 2 GLY A 305 PRO A 306 0 1.82 CISPEP 3 PRO A 306 PRO A 307 0 2.69 CISPEP 4 GLN A 364 PRO A 365 0 -3.61 CRYST1 116.888 230.379 54.244 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 0.008555 0.000000 0.000000 0.00000 SCALE2 0.000000 0.004341 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018435 0.00000