HEADER TRANSFERASE/TRANSFERASE INHIBITOR 28-JAN-14 4ONJ TITLE CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF NTDRM COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA METHYLTRANSFERASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: CATALYTIC DOMAIN (UNP RESIDUES 255-608); COMPND 5 SYNONYM: NTDRM; COMPND 6 EC: 2.1.1.-; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NICOTIANA TABACUM; SOURCE 3 ORGANISM_COMMON: TOBACCO; SOURCE 4 ORGANISM_TAXID: 4097; SOURCE 5 GENE: DRM, NTDRM1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) RIL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-SUMO KEYWDS DNA METHYLTRANSFERASE, TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.DU,D.J.PATEL REVDAT 2 28-FEB-24 4ONJ 1 REMARK SEQADV REVDAT 1 04-JUN-14 4ONJ 0 JRNL AUTH X.ZHONG,J.DU,C.J.HALE,J.GALLEGO-BARTOLOME,S.FENG, JRNL AUTH 2 A.A.VASHISHT,J.CHORY,J.A.WOHLSCHLEGEL,D.J.PATEL,S.E.JACOBSEN JRNL TITL MOLECULAR MECHANISM OF ACTION OF PLANT DRM DE NOVO DNA JRNL TITL 2 METHYLTRANSFERASES. JRNL REF CELL(CAMBRIDGE,MASS.) V. 157 1050 2014 JRNL REFN ISSN 0092-8674 JRNL PMID 24855943 JRNL DOI 10.1016/J.CELL.2014.03.056 REMARK 2 REMARK 2 RESOLUTION. 2.81 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.3_928) 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) : 2.81 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.51 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 49507 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.202 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 2508 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 46.5163 - 7.3475 0.99 2771 127 0.1881 0.1776 REMARK 3 2 7.3475 - 5.8356 1.00 2683 146 0.2308 0.2259 REMARK 3 3 5.8356 - 5.0990 1.00 2616 160 0.2122 0.2081 REMARK 3 4 5.0990 - 4.6332 1.00 2659 126 0.1663 0.1950 REMARK 3 5 4.6332 - 4.3014 1.00 2639 139 0.1559 0.1800 REMARK 3 6 4.3014 - 4.0479 1.00 2592 168 0.1534 0.1603 REMARK 3 7 4.0479 - 3.8453 1.00 2620 148 0.1776 0.2107 REMARK 3 8 3.8453 - 3.6780 1.00 2617 139 0.2031 0.2312 REMARK 3 9 3.6780 - 3.5365 1.00 2605 136 0.2023 0.2390 REMARK 3 10 3.5365 - 3.4145 1.00 2645 118 0.2145 0.2845 REMARK 3 11 3.4145 - 3.3077 1.00 2629 105 0.2205 0.2536 REMARK 3 12 3.3077 - 3.2132 1.00 2600 154 0.2228 0.2589 REMARK 3 13 3.2132 - 3.1286 1.00 2534 160 0.2295 0.2890 REMARK 3 14 3.1286 - 3.0523 1.00 2637 127 0.2454 0.2918 REMARK 3 15 3.0523 - 2.9829 1.00 2616 122 0.2412 0.2711 REMARK 3 16 2.9829 - 2.9195 1.00 2591 146 0.2545 0.3021 REMARK 3 17 2.9195 - 2.8611 1.00 2568 144 0.2804 0.2993 REMARK 3 18 2.8611 - 2.8070 0.92 2377 143 0.3074 0.3623 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.20 REMARK 3 SHRINKAGE RADIUS : 0.98 REMARK 3 K_SOL : 0.33 REMARK 3 B_SOL : 50.17 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.340 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.040 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 60.66 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -10.32080 REMARK 3 B22 (A**2) : -10.32080 REMARK 3 B33 (A**2) : 20.64170 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 : 0.007 5535 REMARK 3 ANGLE : 1.288 7523 REMARK 3 CHIRALITY : 0.191 809 REMARK 3 PLANARITY : 0.005 972 REMARK 3 DIHEDRAL : 14.857 2069 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 13 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 258:302) REMARK 3 ORIGIN FOR THE GROUP (A): -68.2343 -70.0337 -40.7168 REMARK 3 T TENSOR REMARK 3 T11: 0.2679 T22: 1.1605 REMARK 3 T33: 0.6011 T12: 0.0394 REMARK 3 T13: -0.0120 T23: -0.0902 REMARK 3 L TENSOR REMARK 3 L11: 5.2300 L22: 3.9789 REMARK 3 L33: 1.7741 L12: 1.7812 REMARK 3 L13: 2.0313 L23: 0.4038 REMARK 3 S TENSOR REMARK 3 S11: -0.0914 S12: 1.1443 S13: -0.1721 REMARK 3 S21: -0.5521 S22: 0.0568 S23: 0.1259 REMARK 3 S31: 0.0663 S32: 0.5522 S33: -0.1153 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 303:382) REMARK 3 ORIGIN FOR THE GROUP (A): -79.3904 -61.4754 -40.1137 REMARK 3 T TENSOR REMARK 3 T11: 0.1330 T22: 0.9767 REMARK 3 T33: 0.4811 T12: -0.1403 REMARK 3 T13: -0.0628 T23: -0.1430 REMARK 3 L TENSOR REMARK 3 L11: 1.8725 L22: 0.1613 REMARK 3 L33: 0.6809 L12: -0.3593 REMARK 3 L13: 0.8939 L23: -0.1734 REMARK 3 S TENSOR REMARK 3 S11: -0.1336 S12: 0.3084 S13: 0.1442 REMARK 3 S21: -0.0790 S22: 0.0216 S23: -0.0336 REMARK 3 S31: -0.1080 S32: 0.4269 S33: 0.0963 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 383:401) REMARK 3 ORIGIN FOR THE GROUP (A): -92.8449 -35.5088 -46.7342 REMARK 3 T TENSOR REMARK 3 T11: 0.9065 T22: 0.6832 REMARK 3 T33: 1.0758 T12: -0.2954 REMARK 3 T13: -0.3415 T23: 0.1143 REMARK 3 L TENSOR REMARK 3 L11: 6.0718 L22: 5.5143 REMARK 3 L33: 2.8806 L12: -0.9014 REMARK 3 L13: 0.4751 L23: 3.2489 REMARK 3 S TENSOR REMARK 3 S11: -0.4802 S12: 0.1190 S13: 1.1571 REMARK 3 S21: -0.7129 S22: 0.2614 S23: -0.1028 REMARK 3 S31: -1.3618 S32: 0.2481 S33: 0.0664 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 402:527) REMARK 3 ORIGIN FOR THE GROUP (A): -82.8046 -59.0228 -29.0190 REMARK 3 T TENSOR REMARK 3 T11: -0.0022 T22: 0.9275 REMARK 3 T33: 0.4477 T12: -0.0824 REMARK 3 T13: -0.0893 T23: -0.1072 REMARK 3 L TENSOR REMARK 3 L11: 2.7617 L22: 1.3108 REMARK 3 L33: 1.3143 L12: -0.9778 REMARK 3 L13: 1.7082 L23: -0.3157 REMARK 3 S TENSOR REMARK 3 S11: -0.2788 S12: -0.0140 S13: 0.2119 REMARK 3 S21: 0.0490 S22: 0.2046 S23: -0.1884 REMARK 3 S31: -0.1951 S32: 0.1377 S33: 0.2281 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 528:606) REMARK 3 ORIGIN FOR THE GROUP (A): -65.7939 -69.3004 -17.9339 REMARK 3 T TENSOR REMARK 3 T11: 0.1677 T22: 0.8753 REMARK 3 T33: 0.3900 T12: 0.0842 REMARK 3 T13: -0.0626 T23: -0.0897 REMARK 3 L TENSOR REMARK 3 L11: 8.6075 L22: 2.4035 REMARK 3 L33: 2.6988 L12: 1.0154 REMARK 3 L13: 0.0650 L23: -0.0485 REMARK 3 S TENSOR REMARK 3 S11: -0.0790 S12: -0.4665 S13: -0.1087 REMARK 3 S21: 0.2038 S22: 0.2432 S23: -0.1689 REMARK 3 S31: 0.1779 S32: 0.0674 S33: -0.1649 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'B' AND (RESSEQ 257:276) REMARK 3 ORIGIN FOR THE GROUP (A): -35.7643 -60.5797 -3.2924 REMARK 3 T TENSOR REMARK 3 T11: 0.1871 T22: 0.4553 REMARK 3 T33: 0.3622 T12: 0.0965 REMARK 3 T13: -0.0498 T23: -0.0019 REMARK 3 L TENSOR REMARK 3 L11: 5.7923 L22: 2.1188 REMARK 3 L33: 3.9045 L12: 0.9514 REMARK 3 L13: -0.9664 L23: 1.6976 REMARK 3 S TENSOR REMARK 3 S11: -0.0607 S12: -0.1616 S13: 0.5994 REMARK 3 S21: -0.1696 S22: 0.4947 S23: 0.0922 REMARK 3 S31: -0.2501 S32: -0.2300 S33: -0.1030 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'B' AND (RESSEQ 277:302) REMARK 3 ORIGIN FOR THE GROUP (A): -44.6778 -66.2621 -14.2523 REMARK 3 T TENSOR REMARK 3 T11: 0.2098 T22: 0.5903 REMARK 3 T33: 0.4900 T12: 0.0566 REMARK 3 T13: -0.0429 T23: -0.0484 REMARK 3 L TENSOR REMARK 3 L11: 3.7586 L22: 1.1681 REMARK 3 L33: 2.8432 L12: -0.1540 REMARK 3 L13: 1.5310 L23: -0.9501 REMARK 3 S TENSOR REMARK 3 S11: -0.0423 S12: 0.3495 S13: 0.0611 REMARK 3 S21: 0.1133 S22: 0.3054 S23: 0.5075 REMARK 3 S31: 0.1696 S32: -0.2498 S33: -0.1726 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'B' AND (RESSEQ 303:356) REMARK 3 ORIGIN FOR THE GROUP (A): -34.4576 -61.1605 -12.1779 REMARK 3 T TENSOR REMARK 3 T11: 0.2236 T22: 0.6110 REMARK 3 T33: 0.4870 T12: 0.1327 REMARK 3 T13: 0.0064 T23: -0.0162 REMARK 3 L TENSOR REMARK 3 L11: 2.9010 L22: 0.9796 REMARK 3 L33: 1.5170 L12: 0.1837 REMARK 3 L13: 0.3040 L23: 0.3420 REMARK 3 S TENSOR REMARK 3 S11: -0.1612 S12: 0.5246 S13: -0.0523 REMARK 3 S21: 0.0050 S22: 0.1319 S23: -0.0076 REMARK 3 S31: -0.1525 S32: -0.0307 S33: 0.0176 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'B' AND (RESSEQ 357:382) REMARK 3 ORIGIN FOR THE GROUP (A): -18.3838 -43.4285 -14.2780 REMARK 3 T TENSOR REMARK 3 T11: 0.3048 T22: 0.5584 REMARK 3 T33: 0.5950 T12: 0.1239 REMARK 3 T13: 0.1465 T23: -0.0146 REMARK 3 L TENSOR REMARK 3 L11: 1.5069 L22: 6.7482 REMARK 3 L33: 6.6392 L12: -0.0658 REMARK 3 L13: -0.4299 L23: 0.3308 REMARK 3 S TENSOR REMARK 3 S11: 0.3212 S12: 0.1641 S13: 0.5452 REMARK 3 S21: -0.0918 S22: 0.1953 S23: -0.4823 REMARK 3 S31: -0.5903 S32: 0.2063 S33: -0.4654 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'B' AND (RESSEQ 383:429) REMARK 3 ORIGIN FOR THE GROUP (A): -18.2845 -33.5972 -16.1802 REMARK 3 T TENSOR REMARK 3 T11: 0.7226 T22: 0.6516 REMARK 3 T33: 1.1179 T12: -0.0322 REMARK 3 T13: 0.2445 T23: -0.0107 REMARK 3 L TENSOR REMARK 3 L11: 4.0240 L22: 8.6347 REMARK 3 L33: 7.4827 L12: 0.3067 REMARK 3 L13: 0.3611 L23: 0.4720 REMARK 3 S TENSOR REMARK 3 S11: 0.0795 S12: -0.1944 S13: 1.1975 REMARK 3 S21: -0.0578 S22: 0.7302 S23: -0.3896 REMARK 3 S31: -1.8831 S32: 0.0404 S33: -0.4466 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'B' AND (RESSEQ 430:514) REMARK 3 ORIGIN FOR THE GROUP (A): -27.8941 -63.7510 -24.9081 REMARK 3 T TENSOR REMARK 3 T11: 0.1520 T22: 0.7551 REMARK 3 T33: 0.4095 T12: 0.0310 REMARK 3 T13: -0.0022 T23: -0.0982 REMARK 3 L TENSOR REMARK 3 L11: 3.1975 L22: 1.9895 REMARK 3 L33: 1.0992 L12: 1.2057 REMARK 3 L13: -0.1971 L23: 0.0811 REMARK 3 S TENSOR REMARK 3 S11: -0.0393 S12: 0.6223 S13: 0.2694 REMARK 3 S21: -0.2808 S22: 0.1104 S23: 0.0807 REMARK 3 S31: -0.0153 S32: 0.1659 S33: -0.1076 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: CHAIN 'B' AND (RESSEQ 515:544) REMARK 3 ORIGIN FOR THE GROUP (A): -31.0412 -67.6720 -35.4226 REMARK 3 T TENSOR REMARK 3 T11: 0.2108 T22: 1.1584 REMARK 3 T33: 0.3834 T12: 0.0011 REMARK 3 T13: 0.0605 T23: -0.0867 REMARK 3 L TENSOR REMARK 3 L11: 3.6155 L22: 2.9446 REMARK 3 L33: 0.3070 L12: 0.9264 REMARK 3 L13: -0.8389 L23: -0.7660 REMARK 3 S TENSOR REMARK 3 S11: -0.1464 S12: 1.2558 S13: -0.2238 REMARK 3 S21: -0.3308 S22: 0.3942 S23: 0.1371 REMARK 3 S31: 0.1181 S32: -0.1263 S33: 0.3538 REMARK 3 TLS GROUP : 13 REMARK 3 SELECTION: CHAIN 'B' AND (RESSEQ 545:605) REMARK 3 ORIGIN FOR THE GROUP (A): -45.5901 -70.7168 -28.4877 REMARK 3 T TENSOR REMARK 3 T11: 0.1400 T22: 0.9510 REMARK 3 T33: 0.2939 T12: -0.0515 REMARK 3 T13: -0.0047 T23: -0.1422 REMARK 3 L TENSOR REMARK 3 L11: 7.3621 L22: 3.5166 REMARK 3 L33: 1.9780 L12: -1.4722 REMARK 3 L13: 0.3036 L23: 0.1901 REMARK 3 S TENSOR REMARK 3 S11: -0.0105 S12: 0.5769 S13: -0.3181 REMARK 3 S21: -0.2716 S22: 0.1921 S23: -0.0583 REMARK 3 S31: 0.0752 S32: -0.2847 S33: -0.1076 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 4ONJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-JAN-14. REMARK 100 THE DEPOSITION ID IS D_1000084716. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-JUN-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 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-E 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 : CRYOGENICALLY-COOLED SINGLE REMARK 200 CRYSTAL SI(220) SIDE BOUNCE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 52015 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : 0.12200 REMARK 200 R SYM (I) : 0.12200 REMARK 200 FOR THE DATA SET : 24.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.30 REMARK 200 R MERGE FOR SHELL (I) : 0.72300 REMARK 200 R SYM FOR SHELL (I) : 0.72300 REMARK 200 FOR SHELL : 2.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 80.29 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 6.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.19 M CALCIUM CHLORIDE, 5% GLYCEROL, REMARK 280 26.6% PEG400, 0.095 M HEPES, PH 7.5, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 49.65567 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 99.31133 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 99.31133 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 49.65567 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 SER A 252 REMARK 465 GLU A 253 REMARK 465 PHE A 254 REMARK 465 GLU A 255 REMARK 465 THR A 256 REMARK 465 ILE A 257 REMARK 465 CYS A 567 REMARK 465 ASN A 568 REMARK 465 ASN A 569 REMARK 465 LEU A 570 REMARK 465 ALA A 571 REMARK 465 GLY A 572 REMARK 465 SER A 573 REMARK 465 ASN A 574 REMARK 465 ARG A 575 REMARK 465 VAL A 576 REMARK 465 SER A 577 REMARK 465 ARG A 578 REMARK 465 ASP A 579 REMARK 465 GLY A 580 REMARK 465 LEU A 581 REMARK 465 GLU A 582 REMARK 465 GLY A 583 REMARK 465 LYS A 584 REMARK 465 LYS A 607 REMARK 465 HIS A 608 REMARK 465 SER B 252 REMARK 465 GLU B 253 REMARK 465 PHE B 254 REMARK 465 GLU B 255 REMARK 465 THR B 256 REMARK 465 ASN B 569 REMARK 465 LEU B 570 REMARK 465 ALA B 571 REMARK 465 GLY B 572 REMARK 465 SER B 573 REMARK 465 ASN B 574 REMARK 465 ARG B 575 REMARK 465 VAL B 576 REMARK 465 SER B 577 REMARK 465 ARG B 578 REMARK 465 ASP B 579 REMARK 465 GLY B 580 REMARK 465 LEU B 581 REMARK 465 GLU B 582 REMARK 465 GLY B 583 REMARK 465 LYS B 584 REMARK 465 HIS B 606 REMARK 465 LYS B 607 REMARK 465 HIS B 608 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 PRO A 260 C - N - CD ANGL. DEV. = -17.5 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 LYS A 261 -94.10 -35.32 REMARK 500 LEU A 311 54.39 -101.58 REMARK 500 ARG A 329 107.78 -168.66 REMARK 500 GLU A 399 31.67 106.55 REMARK 500 PRO A 400 159.87 -47.34 REMARK 500 ARG B 258 49.32 -61.75 REMARK 500 ALA B 275 -12.56 69.18 REMARK 500 LEU B 311 57.03 -114.46 REMARK 500 ARG B 329 107.10 -160.29 REMARK 500 GLU B 394 52.92 -67.44 REMARK 500 PRO B 401 140.99 -34.29 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLY A 398 GLU A 399 -149.13 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 SFG A 700 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SFG B 700 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4ONQ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF NTDRM E283S/R309S/F310S/Y590S/D591S MUTANT DBREF 4ONJ A 255 608 UNP Q76KU6 Q76KU6_TOBAC 255 608 DBREF 4ONJ B 255 608 UNP Q76KU6 Q76KU6_TOBAC 255 608 SEQADV 4ONJ SER A 252 UNP Q76KU6 EXPRESSION TAG SEQADV 4ONJ GLU A 253 UNP Q76KU6 EXPRESSION TAG SEQADV 4ONJ PHE A 254 UNP Q76KU6 EXPRESSION TAG SEQADV 4ONJ SER B 252 UNP Q76KU6 EXPRESSION TAG SEQADV 4ONJ GLU B 253 UNP Q76KU6 EXPRESSION TAG SEQADV 4ONJ PHE B 254 UNP Q76KU6 EXPRESSION TAG SEQRES 1 A 357 SER GLU PHE GLU THR ILE ARG LEU PRO LYS PRO MET ILE SEQRES 2 A 357 GLY PHE GLY VAL PRO THR GLU PRO LEU PRO ALA MET VAL SEQRES 3 A 357 ARG ARG THR LEU PRO GLU GLN ALA VAL GLY PRO PRO PHE SEQRES 4 A 357 PHE TYR TYR GLU ASN VAL ALA LEU ALA PRO LYS GLY VAL SEQRES 5 A 357 TRP ASP THR ILE SER ARG PHE LEU TYR ASP ILE GLU PRO SEQRES 6 A 357 GLU PHE VAL ASP SER LYS TYR PHE CYS ALA ALA ALA ARG SEQRES 7 A 357 LYS ARG GLY TYR ILE HIS ASN LEU PRO VAL GLU ASN ARG SEQRES 8 A 357 PHE PRO LEU PHE PRO LEU ALA PRO ARG THR ILE HIS GLU SEQRES 9 A 357 ALA LEU PRO LEU SER LYS LYS TRP TRP PRO SER TRP ASP SEQRES 10 A 357 PRO ARG THR LYS LEU ASN CYS LEU GLN THR ALA ILE GLY SEQRES 11 A 357 SER ALA GLN LEU THR ASN ARG ILE ARG LYS ALA VAL GLU SEQRES 12 A 357 ASP PHE ASP GLY GLU PRO PRO MET ARG VAL GLN LYS PHE SEQRES 13 A 357 VAL LEU ASP GLN CYS ARG LYS TRP ASN LEU VAL TRP VAL SEQRES 14 A 357 GLY ARG ASN LYS VAL ALA PRO LEU GLU PRO ASP GLU VAL SEQRES 15 A 357 GLU MET LEU LEU GLY PHE PRO LYS ASN HIS THR ARG GLY SEQRES 16 A 357 GLY GLY ILE SER ARG THR ASP ARG TYR LYS SER LEU GLY SEQRES 17 A 357 ASN SER PHE GLN VAL ASP THR VAL ALA TYR HIS LEU SER SEQRES 18 A 357 VAL LEU LYS ASP LEU PHE PRO GLY GLY ILE ASN VAL LEU SEQRES 19 A 357 SER LEU PHE SER GLY ILE GLY GLY GLY GLU VAL ALA LEU SEQRES 20 A 357 TYR ARG LEU GLY ILE PRO LEU ASN THR VAL VAL SER VAL SEQRES 21 A 357 GLU LYS SER GLU VAL ASN ARG ASP ILE VAL ARG SER TRP SEQRES 22 A 357 TRP GLU GLN THR ASN GLN ARG GLY ASN LEU ILE HIS PHE SEQRES 23 A 357 ASN ASP VAL GLN GLN LEU ASN GLY ASP ARG LEU GLU GLN SEQRES 24 A 357 LEU ILE GLU SER PHE GLY GLY PHE ASP LEU VAL ILE GLY SEQRES 25 A 357 GLY SER PRO CYS ASN ASN LEU ALA GLY SER ASN ARG VAL SEQRES 26 A 357 SER ARG ASP GLY LEU GLU GLY LYS GLU SER SER LEU PHE SEQRES 27 A 357 TYR ASP TYR VAL ARG ILE LEU ASP LEU VAL LYS SER ILE SEQRES 28 A 357 MET SER ARG HIS LYS HIS SEQRES 1 B 357 SER GLU PHE GLU THR ILE ARG LEU PRO LYS PRO MET ILE SEQRES 2 B 357 GLY PHE GLY VAL PRO THR GLU PRO LEU PRO ALA MET VAL SEQRES 3 B 357 ARG ARG THR LEU PRO GLU GLN ALA VAL GLY PRO PRO PHE SEQRES 4 B 357 PHE TYR TYR GLU ASN VAL ALA LEU ALA PRO LYS GLY VAL SEQRES 5 B 357 TRP ASP THR ILE SER ARG PHE LEU TYR ASP ILE GLU PRO SEQRES 6 B 357 GLU PHE VAL ASP SER LYS TYR PHE CYS ALA ALA ALA ARG SEQRES 7 B 357 LYS ARG GLY TYR ILE HIS ASN LEU PRO VAL GLU ASN ARG SEQRES 8 B 357 PHE PRO LEU PHE PRO LEU ALA PRO ARG THR ILE HIS GLU SEQRES 9 B 357 ALA LEU PRO LEU SER LYS LYS TRP TRP PRO SER TRP ASP SEQRES 10 B 357 PRO ARG THR LYS LEU ASN CYS LEU GLN THR ALA ILE GLY SEQRES 11 B 357 SER ALA GLN LEU THR ASN ARG ILE ARG LYS ALA VAL GLU SEQRES 12 B 357 ASP PHE ASP GLY GLU PRO PRO MET ARG VAL GLN LYS PHE SEQRES 13 B 357 VAL LEU ASP GLN CYS ARG LYS TRP ASN LEU VAL TRP VAL SEQRES 14 B 357 GLY ARG ASN LYS VAL ALA PRO LEU GLU PRO ASP GLU VAL SEQRES 15 B 357 GLU MET LEU LEU GLY PHE PRO LYS ASN HIS THR ARG GLY SEQRES 16 B 357 GLY GLY ILE SER ARG THR ASP ARG TYR LYS SER LEU GLY SEQRES 17 B 357 ASN SER PHE GLN VAL ASP THR VAL ALA TYR HIS LEU SER SEQRES 18 B 357 VAL LEU LYS ASP LEU PHE PRO GLY GLY ILE ASN VAL LEU SEQRES 19 B 357 SER LEU PHE SER GLY ILE GLY GLY GLY GLU VAL ALA LEU SEQRES 20 B 357 TYR ARG LEU GLY ILE PRO LEU ASN THR VAL VAL SER VAL SEQRES 21 B 357 GLU LYS SER GLU VAL ASN ARG ASP ILE VAL ARG SER TRP SEQRES 22 B 357 TRP GLU GLN THR ASN GLN ARG GLY ASN LEU ILE HIS PHE SEQRES 23 B 357 ASN ASP VAL GLN GLN LEU ASN GLY ASP ARG LEU GLU GLN SEQRES 24 B 357 LEU ILE GLU SER PHE GLY GLY PHE ASP LEU VAL ILE GLY SEQRES 25 B 357 GLY SER PRO CYS ASN ASN LEU ALA GLY SER ASN ARG VAL SEQRES 26 B 357 SER ARG ASP GLY LEU GLU GLY LYS GLU SER SER LEU PHE SEQRES 27 B 357 TYR ASP TYR VAL ARG ILE LEU ASP LEU VAL LYS SER ILE SEQRES 28 B 357 MET SER ARG HIS LYS HIS HET SFG A 700 27 HET SFG B 700 27 HETNAM SFG SINEFUNGIN HETSYN SFG ADENOSYL-ORNITHINE FORMUL 3 SFG 2(C15 H23 N7 O5) HELIX 1 1 GLY A 302 LEU A 311 1 10 HELIX 2 2 LYS A 322 PHE A 324 5 3 HELIX 3 3 THR A 352 LEU A 357 1 6 HELIX 4 4 PRO A 358 LYS A 362 5 5 HELIX 5 5 SER A 382 GLU A 394 1 13 HELIX 6 6 PRO A 401 ASN A 416 1 16 HELIX 7 7 GLU A 429 LEU A 437 1 9 HELIX 8 8 SER A 450 ASN A 460 1 11 HELIX 9 9 GLN A 463 SER A 472 1 10 HELIX 10 10 VAL A 473 PHE A 478 1 6 HELIX 11 11 GLY A 492 LEU A 501 1 10 HELIX 12 12 SER A 514 THR A 528 1 15 HELIX 13 13 ASP A 539 LEU A 543 5 5 HELIX 14 14 ASN A 544 GLY A 556 1 13 HELIX 15 15 SER A 587 MET A 603 1 17 HELIX 16 16 GLY B 302 LEU B 311 1 10 HELIX 17 17 LYS B 322 PHE B 324 5 3 HELIX 18 18 THR B 352 LEU B 357 1 6 HELIX 19 19 SER B 360 TRP B 364 5 5 HELIX 20 20 SER B 382 VAL B 393 1 12 HELIX 21 21 PRO B 401 ASN B 416 1 16 HELIX 22 22 GLU B 429 LEU B 437 1 9 HELIX 23 23 SER B 450 ASN B 460 1 11 HELIX 24 24 GLN B 463 SER B 472 1 10 HELIX 25 25 VAL B 473 LYS B 475 5 3 HELIX 26 26 GLY B 492 LEU B 501 1 10 HELIX 27 27 SER B 514 THR B 528 1 15 HELIX 28 28 ASP B 539 LEU B 543 5 5 HELIX 29 29 ASN B 544 GLY B 556 1 13 HELIX 30 30 SER B 587 SER B 604 1 18 SHEET 1 A 7 GLU A 317 ASP A 320 0 SHEET 2 A 7 LYS A 330 HIS A 335 -1 O TYR A 333 N GLU A 317 SHEET 3 A 7 PHE A 290 VAL A 296 -1 N ASN A 295 O GLY A 332 SHEET 4 A 7 LEU A 560 GLY A 564 1 O GLY A 563 N TYR A 292 SHEET 5 A 7 ILE A 482 LEU A 487 1 N LEU A 487 O ILE A 562 SHEET 6 A 7 LEU A 505 VAL A 511 1 O VAL A 509 N VAL A 484 SHEET 7 A 7 ASN A 533 PHE A 537 1 O ILE A 535 N SER A 510 SHEET 1 B 2 LEU A 417 GLY A 421 0 SHEET 2 B 2 LYS A 424 PRO A 427 -1 O ALA A 426 N VAL A 418 SHEET 1 C 7 GLU B 317 ASP B 320 0 SHEET 2 C 7 LYS B 330 HIS B 335 -1 O TYR B 333 N GLU B 317 SHEET 3 C 7 PHE B 290 VAL B 296 -1 N ASN B 295 O GLY B 332 SHEET 4 C 7 LEU B 560 GLY B 564 1 O VAL B 561 N PHE B 290 SHEET 5 C 7 ILE B 482 LEU B 487 1 N LEU B 485 O LEU B 560 SHEET 6 C 7 LEU B 505 VAL B 511 1 O VAL B 511 N SER B 486 SHEET 7 C 7 ASN B 533 PHE B 537 1 O ILE B 535 N VAL B 508 SHEET 1 D 2 LEU B 417 GLY B 421 0 SHEET 2 D 2 LYS B 424 PRO B 427 -1 O ALA B 426 N VAL B 418 CISPEP 1 PRO A 288 PRO A 289 0 -6.28 CISPEP 2 PHE A 346 PRO A 347 0 1.85 CISPEP 3 LYS B 261 PRO B 262 0 1.31 CISPEP 4 GLY B 287 PRO B 288 0 -2.92 CISPEP 5 PRO B 288 PRO B 289 0 0.52 CISPEP 6 PHE B 346 PRO B 347 0 -0.45 SITE 1 AC1 15 ASN A 460 SER A 461 PHE A 462 PHE A 488 SITE 2 AC1 15 SER A 489 GLY A 490 ILE A 491 GLY A 493 SITE 3 AC1 15 GLU A 512 LYS A 513 ASN A 517 ASN A 538 SITE 4 AC1 15 ASP A 539 SER A 565 LEU A 588 SITE 1 AC2 12 ASN B 460 SER B 461 PHE B 462 PHE B 488 SITE 2 AC2 12 GLU B 512 LYS B 513 SER B 514 ASN B 517 SITE 3 AC2 12 ASN B 538 SER B 565 PRO B 566 LEU B 588 CRYST1 153.324 153.324 148.967 90.00 90.00 120.00 P 31 2 1 12 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 0.006522 0.003766 0.000000 0.00000 SCALE2 0.000000 0.007531 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006713 0.00000